From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:12:53 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:12:53 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHF5Evgf6PzjwPf91PL=Or8MzQoVJgrc7KT1nQNf5hbVuw@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 07:11
Subject: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


Hello Renaud,

I just tried unsuccessfully to upgrade my Apple desktop to
Mac OS X 10.9 (Mavericks), but due to a few technical
problems I had to backtrack to the previous version
10.8 for now.

After restoring from backups and checking
that everything works, I discovered that RcppOctave
does not install. I get the same invalid malloc error that
I was getting before. But this time I have not used
MacPorts at all, only Homebrew, and the version of
Octave is 3.6.4 as it should be.

(I am downloading source, not using install.packages(), because
the latter tends to download old archives.)

Indeed, with my fresh install of Mac OS X, with the
command line tools and Xcode installed, R does not
issue the correct command: R CMD config CXX
returns: llvm-g++-4.2 -arch x86_64.

But there is no llvm-g++-4.2, only /usr/bin/g++ (version
4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
this problem by defining symbolic links llvm-g++-4.2 and
llvm-gcc-4.2 pointing to these files, but this does not work.

There are a couple of open issues:
1. Apple no longer ships binaries named llvm-g++-4.2 and
   llvm-gcc-4.2 (only g++ and gcc).
2. Apple no longer supports Fortran at all (the R core team
    provides gfortran-4.2?see R Mac OS FAQ).
3. 'brew install octave' does not show you what it is doing,
   and I think it may be using clang instead of gcc, clang++
   instead of g++.
4. The segfault error when I try to install RcppOctave is
    probably due to compiler version incompatibilities, either
    gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.

Thus under Mac OS X the correct long-term solution is to
stop using gcc/g++ and follow Apple in using clang/clang++.
In the mean time, Apple will make life difficult for people who
continue to use gcc/g++/gfortran! (There is an open source
project to write an LLVM Fortran front-end, but I don't know
what the status of that project is.)

Dominick
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:13:26 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:13:26 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHH47EKyMRrwOhJ0sg-_ohPzxPK4f90mjTvv9ixr5w_pxQ@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 07:32
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


A little more searching revealed that llvm-g++
and llvm-gcc are part of LLVM releases 2.9 and
earlier, see...
http://llvm.org/releases/download.html#3.3

It seems like Mac OS X users of R will have to
use a specific toolchain for all apps that need to
link against each other, and this is especially true
for RcppOctave?

And the easiest toolchain to use under Mac OS X is
the one specified by Apple! (Unfortunately this does
not solve the Fortran problem.)



On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:

> Hello Renaud,
>
> I just tried unsuccessfully to upgrade my Apple desktop to
> Mac OS X 10.9 (Mavericks), but due to a few technical
> problems I had to backtrack to the previous version
> 10.8 for now.
>
> After restoring from backups and checking
> that everything works, I discovered that RcppOctave
> does not install. I get the same invalid malloc error that
> I was getting before. But this time I have not used
> MacPorts at all, only Homebrew, and the version of
> Octave is 3.6.4 as it should be.
>
> (I am downloading source, not using install.packages(), because
> the latter tends to download old archives.)
>
> Indeed, with my fresh install of Mac OS X, with the
> command line tools and Xcode installed, R does not
> issue the correct command: R CMD config CXX
> returns: llvm-g++-4.2 -arch x86_64.
>
> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
> this problem by defining symbolic links llvm-g++-4.2 and
> llvm-gcc-4.2 pointing to these files, but this does not work.
>
> There are a couple of open issues:
> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>    llvm-gcc-4.2 (only g++ and gcc).
> 2. Apple no longer supports Fortran at all (the R core team
>     provides gfortran-4.2?see R Mac OS FAQ).
> 3. 'brew install octave' does not show you what it is doing,
>    and I think it may be using clang instead of gcc, clang++
>    instead of g++.
> 4. The segfault error when I try to install RcppOctave is
>     probably due to compiler version incompatibilities, either
>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>
> Thus under Mac OS X the correct long-term solution is to
> stop using gcc/g++ and follow Apple in using clang/clang++.
> In the mean time, Apple will make life difficult for people who
> continue to use gcc/g++/gfortran! (There is an open source
> project to write an LLVM Fortran front-end, but I don't know
> what the status of that project is.)
>
> Dominick
>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:13:48 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:13:48 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHGr0uKoytf2+gpbnnaoyFiX=tbbnRBFf3jDX3U6wrTdmg@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 18:04
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


I built R using clang/clang++/gfortran-4.2(from Simon of R core) and
installed Rcpp using the same tools, and
there were no obvious problems.

There was a problem with RcppOctave/src/modules/Makefile.in.
I've attached my work-around.

When I try to install RcppOctave with Octave 3.6.4
I get the familiar issue:

clang++ -arch x86_64 -std=c++11
-I/Users/dsamperi/bin/R-clang/R.framework/Resources/include -DNDEBUG
`"/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/Rscript" -e
"Rcpp:::CxxFlags()"` -DOCT_POST_3_4_0=1
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave"
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/../"
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/octave"
-I/usr/local/include
-I"/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/include"
  -fPIC  -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
clang++ -arch x86_64 -std=c++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o RcppOctave.so conversion.o
rcpp_octave.o
/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
-L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
-L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
-F/Users/dsamperi/bin/R-clang/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
R(45582) malloc: *** error for object 0x1058257c0: pointer being freed was
not allocated
*** set a breakpoint in malloc_error_break to debug
/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/INSTALL: line 34:
45581 Done                    echo 'tools:::.install_packages()'
     45582 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}


On Wed, Oct 30, 2013 at 1:32 AM, Dominick Samperi <djsamperi at gmail.com>wrote:

> A little more searching revealed that llvm-g++
> and llvm-gcc are part of LLVM releases 2.9 and
> earlier, see...
> http://llvm.org/releases/download.html#3.3
>
> It seems like Mac OS X users of R will have to
> use a specific toolchain for all apps that need to
> link against each other, and this is especially true
> for RcppOctave?
>
> And the easiest toolchain to use under Mac OS X is
> the one specified by Apple! (Unfortunately this does
> not solve the Fortran problem.)
>
>
>
> On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> Hello Renaud,
>>
>> I just tried unsuccessfully to upgrade my Apple desktop to
>> Mac OS X 10.9 (Mavericks), but due to a few technical
>> problems I had to backtrack to the previous version
>> 10.8 for now.
>>
>> After restoring from backups and checking
>> that everything works, I discovered that RcppOctave
>> does not install. I get the same invalid malloc error that
>> I was getting before. But this time I have not used
>> MacPorts at all, only Homebrew, and the version of
>> Octave is 3.6.4 as it should be.
>>
>> (I am downloading source, not using install.packages(), because
>> the latter tends to download old archives.)
>>
>> Indeed, with my fresh install of Mac OS X, with the
>> command line tools and Xcode installed, R does not
>> issue the correct command: R CMD config CXX
>> returns: llvm-g++-4.2 -arch x86_64.
>>
>> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
>> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
>> this problem by defining symbolic links llvm-g++-4.2 and
>> llvm-gcc-4.2 pointing to these files, but this does not work.
>>
>> There are a couple of open issues:
>> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>>    llvm-gcc-4.2 (only g++ and gcc).
>> 2. Apple no longer supports Fortran at all (the R core team
>>     provides gfortran-4.2?see R Mac OS FAQ).
>> 3. 'brew install octave' does not show you what it is doing,
>>    and I think it may be using clang instead of gcc, clang++
>>    instead of g++.
>> 4. The segfault error when I try to install RcppOctave is
>>     probably due to compiler version incompatibilities, either
>>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>>
>> Thus under Mac OS X the correct long-term solution is to
>> stop using gcc/g++ and follow Apple in using clang/clang++.
>> In the mean time, Apple will make life difficult for people who
>> continue to use gcc/g++/gfortran! (There is an open source
>> project to write an LLVM Fortran front-end, but I don't know
>> what the status of that project is.)
>>
>> Dominick
>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:15:05 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:15:05 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHGL5ayZKRpxkXYeTkV72-6b+nuFQk1JPsR+QePwbwti3A@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 18:07
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


I am not familiar with what mkoctfile does, and I suspect it may
be the source of the problem. Can you provide some background
on what this does?


On Wed, Oct 30, 2013 at 12:04 PM, Dominick Samperi <djsamperi at gmail.com>wrote:

> I built R using clang/clang++/gfortran-4.2(from Simon of R core) and
> installed Rcpp using the same tools, and
> there were no obvious problems.
>
> There was a problem with RcppOctave/src/modules/Makefile.in.
> I've attached my work-around.
>
> When I try to install RcppOctave with Octave 3.6.4
> I get the familiar issue:
>
> clang++ -arch x86_64 -std=c++11
> -I/Users/dsamperi/bin/R-clang/R.framework/Resources/include -DNDEBUG
> `"/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -DOCT_POST_3_4_0=1
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave"
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/../"
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/octave"
> -I/usr/local/include
> -I"/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
> clang++ -arch x86_64 -std=c++11 -dynamiclib
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/lib -o RcppOctave.so conversion.o
> rcpp_octave.o
> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
> -F/Users/dsamperi/bin/R-clang/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> R(45582) malloc: *** error for object 0x1058257c0: pointer being freed was
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> /Users/dsamperi/bin/R-clang/R.framework/Resources/bin/INSTALL: line 34:
> 45581 Done                    echo 'tools:::.install_packages()'
>      45582 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>
>
> On Wed, Oct 30, 2013 at 1:32 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> A little more searching revealed that llvm-g++
>> and llvm-gcc are part of LLVM releases 2.9 and
>> earlier, see...
>> http://llvm.org/releases/download.html#3.3
>>
>> It seems like Mac OS X users of R will have to
>> use a specific toolchain for all apps that need to
>> link against each other, and this is especially true
>> for RcppOctave?
>>
>> And the easiest toolchain to use under Mac OS X is
>> the one specified by Apple! (Unfortunately this does
>> not solve the Fortran problem.)
>>
>>
>>
>> On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>>
>>> Hello Renaud,
>>>
>>> I just tried unsuccessfully to upgrade my Apple desktop to
>>> Mac OS X 10.9 (Mavericks), but due to a few technical
>>> problems I had to backtrack to the previous version
>>> 10.8 for now.
>>>
>>> After restoring from backups and checking
>>> that everything works, I discovered that RcppOctave
>>> does not install. I get the same invalid malloc error that
>>> I was getting before. But this time I have not used
>>> MacPorts at all, only Homebrew, and the version of
>>> Octave is 3.6.4 as it should be.
>>>
>>> (I am downloading source, not using install.packages(), because
>>> the latter tends to download old archives.)
>>>
>>> Indeed, with my fresh install of Mac OS X, with the
>>> command line tools and Xcode installed, R does not
>>> issue the correct command: R CMD config CXX
>>> returns: llvm-g++-4.2 -arch x86_64.
>>>
>>> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
>>> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
>>> this problem by defining symbolic links llvm-g++-4.2 and
>>> llvm-gcc-4.2 pointing to these files, but this does not work.
>>>
>>> There are a couple of open issues:
>>> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>>>    llvm-gcc-4.2 (only g++ and gcc).
>>> 2. Apple no longer supports Fortran at all (the R core team
>>>     provides gfortran-4.2?see R Mac OS FAQ).
>>> 3. 'brew install octave' does not show you what it is doing,
>>>    and I think it may be using clang instead of gcc, clang++
>>>    instead of g++.
>>> 4. The segfault error when I try to install RcppOctave is
>>>     probably due to compiler version incompatibilities, either
>>>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>>>
>>> Thus under Mac OS X the correct long-term solution is to
>>> stop using gcc/g++ and follow Apple in using clang/clang++.
>>> In the mean time, Apple will make life difficult for people who
>>> continue to use gcc/g++/gfortran! (There is an open source
>>> project to write an LLVM Fortran front-end, but I don't know
>>> what the status of that project is.)
>>>
>>> Dominick
>>>
>>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:17:00 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:17:00 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHH6XWZYGP6OtPnN2SmpSCSwpht9KAtO0FG-r7NbbJzU5A@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 20:10
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


We are pretty much back to where we were some weeks ago. Remember
the trivial change that I made to Rcpp that caused it to fail with the
pointer error, by adding a function that was not even called?

Well, I just did the same with Octave 3.6.4 (the latest Homebrew
version, not the ancient MacPorts version), and now I get that pointer
error! Just drop the attached files into the Rcpp/src directory and the
build will fail due to memory corruption.

So the previous theory (old Octave version) is wrong, and once again
I suspect that there is an issue with static initializers?




On Wed, Oct 30, 2013 at 12:07 PM, Dominick Samperi <djsamperi at gmail.com>wrote:

> I am not familiar with what mkoctfile does, and I suspect it may
> be the source of the problem. Can you provide some background
> on what this does?
>
>
> On Wed, Oct 30, 2013 at 12:04 PM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> I built R using clang/clang++/gfortran-4.2(from Simon of R core) and
>> installed Rcpp using the same tools, and
>> there were no obvious problems.
>>
>> There was a problem with RcppOctave/src/modules/Makefile.in.
>> I've attached my work-around.
>>
>> When I try to install RcppOctave with Octave 3.6.4
>> I get the familiar issue:
>>
>> clang++ -arch x86_64 -std=c++11
>> -I/Users/dsamperi/bin/R-clang/R.framework/Resources/include -DNDEBUG
>> `"/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/Rscript" -e
>> "Rcpp:::CxxFlags()"` -DOCT_POST_3_4_0=1
>> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave"
>> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/../"
>> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/octave"
>> -I/usr/local/include
>> -I"/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>   -fPIC  -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
>> clang++ -arch x86_64 -std=c++11 -dynamiclib
>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
>> -multiply_defined suppress -L/usr/local/lib -o RcppOctave.so conversion.o
>> rcpp_octave.o
>> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
>> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
>> -F/Users/dsamperi/bin/R-clang/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>> installing to
>> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> R(45582) malloc: *** error for object 0x1058257c0: pointer being freed
>> was not allocated
>> *** set a breakpoint in malloc_error_break to debug
>> /Users/dsamperi/bin/R-clang/R.framework/Resources/bin/INSTALL: line 34:
>> 45581 Done                    echo 'tools:::.install_packages()'
>>      45582 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
>> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>>
>>
>> On Wed, Oct 30, 2013 at 1:32 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>>
>>> A little more searching revealed that llvm-g++
>>> and llvm-gcc are part of LLVM releases 2.9 and
>>> earlier, see...
>>> http://llvm.org/releases/download.html#3.3
>>>
>>> It seems like Mac OS X users of R will have to
>>> use a specific toolchain for all apps that need to
>>> link against each other, and this is especially true
>>> for RcppOctave?
>>>
>>> And the easiest toolchain to use under Mac OS X is
>>> the one specified by Apple! (Unfortunately this does
>>> not solve the Fortran problem.)
>>>
>>>
>>>
>>> On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>>>
>>>> Hello Renaud,
>>>>
>>>> I just tried unsuccessfully to upgrade my Apple desktop to
>>>> Mac OS X 10.9 (Mavericks), but due to a few technical
>>>> problems I had to backtrack to the previous version
>>>> 10.8 for now.
>>>>
>>>> After restoring from backups and checking
>>>> that everything works, I discovered that RcppOctave
>>>> does not install. I get the same invalid malloc error that
>>>> I was getting before. But this time I have not used
>>>> MacPorts at all, only Homebrew, and the version of
>>>> Octave is 3.6.4 as it should be.
>>>>
>>>> (I am downloading source, not using install.packages(), because
>>>> the latter tends to download old archives.)
>>>>
>>>> Indeed, with my fresh install of Mac OS X, with the
>>>> command line tools and Xcode installed, R does not
>>>> issue the correct command: R CMD config CXX
>>>> returns: llvm-g++-4.2 -arch x86_64.
>>>>
>>>> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
>>>> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
>>>> this problem by defining symbolic links llvm-g++-4.2 and
>>>> llvm-gcc-4.2 pointing to these files, but this does not work.
>>>>
>>>> There are a couple of open issues:
>>>> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>>>>    llvm-gcc-4.2 (only g++ and gcc).
>>>> 2. Apple no longer supports Fortran at all (the R core team
>>>>     provides gfortran-4.2?see R Mac OS FAQ).
>>>> 3. 'brew install octave' does not show you what it is doing,
>>>>    and I think it may be using clang instead of gcc, clang++
>>>>    instead of g++.
>>>> 4. The segfault error when I try to install RcppOctave is
>>>>     probably due to compiler version incompatibilities, either
>>>>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>>>>
>>>> Thus under Mac OS X the correct long-term solution is to
>>>> stop using gcc/g++ and follow Apple in using clang/clang++.
>>>> In the mean time, Apple will make life difficult for people who
>>>> continue to use gcc/g++/gfortran! (There is an open source
>>>> project to write an LLVM Fortran front-end, but I don't know
>>>> what the status of that project is.)
>>>>
>>>> Dominick
>>>>
>>>>
>>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:17:30 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:17:30 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHFbtN8gBPDfEvckgLGiaWZL55CbA23bV81CT2D2cZge2A@mail.gmail.com>

---------- Forwarded message ----------
From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
Date: 31 October 2013 09:25
Subject: Re: Apple Blues
To: Dominick Samperi <djsamperi at gmail.com>



On 30 October 2013 18:07, Dominick Samperi <djsamperi at gmail.com> wrote:

> I am not familiar with what mkoctfile does, and I suspect it may
> be the source of the problem. Can you provide some background
> on what this does?
>
>
mkoctfile is the compiler tool from Octave, which is used to compile Octave
modules, and wraps calls to the compiler adding Octave include and lib
directory where needed.
It sort of is the equivalent of R CMD compile/SHLIB, for Octave.
This is all I know about it, I don't know the technical details, just the
user perspective.

Renaud
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:17:50 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:17:50 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHF=S_ktDK5KSNMBUnG+YaLtxqbsh-0AxdYxC3Ax3_EVUw@mail.gmail.com>

---------- Forwarded message ----------
From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
Date: 31 October 2013 09:27
Subject: Re: Apple Blues
To: Dominick Samperi <djsamperi at gmail.com>


I find it strange that you have to modify Makefile.in. It should get R
locations and flags associated with the R binary you are using to build the
package, in this case the clang-compiled one.
Can you please send the install log, which shows the resolved LDFLAGS and
CPPFLAGS?


On 30 October 2013 18:04, Dominick Samperi <djsamperi at gmail.com> wrote:

> I built R using clang/clang++/gfortran-4.2(from Simon of R core) and
> installed Rcpp using the same tools, and
> there were no obvious problems.
>
> There was a problem with RcppOctave/src/modules/Makefile.in.
> I've attached my work-around.
>
> When I try to install RcppOctave with Octave 3.6.4
> I get the familiar issue:
>
> clang++ -arch x86_64 -std=c++11
> -I/Users/dsamperi/bin/R-clang/R.framework/Resources/include -DNDEBUG
> `"/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -DOCT_POST_3_4_0=1
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave"
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/../"
> -I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/octave"
> -I/usr/local/include
> -I"/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
> clang++ -arch x86_64 -std=c++11 -dynamiclib
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/usr/local/lib -o RcppOctave.so conversion.o
> rcpp_octave.o
> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
> -F/Users/dsamperi/bin/R-clang/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> R(45582) malloc: *** error for object 0x1058257c0: pointer being freed was
> not allocated
> *** set a breakpoint in malloc_error_break to debug
> /Users/dsamperi/bin/R-clang/R.framework/Resources/bin/INSTALL: line 34:
> 45581 Done                    echo 'tools:::.install_packages()'
>      45582 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>
>
> On Wed, Oct 30, 2013 at 1:32 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> A little more searching revealed that llvm-g++
>> and llvm-gcc are part of LLVM releases 2.9 and
>> earlier, see...
>> http://llvm.org/releases/download.html#3.3
>>
>> It seems like Mac OS X users of R will have to
>> use a specific toolchain for all apps that need to
>> link against each other, and this is especially true
>> for RcppOctave?
>>
>> And the easiest toolchain to use under Mac OS X is
>> the one specified by Apple! (Unfortunately this does
>> not solve the Fortran problem.)
>>
>>
>>
>> On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>>
>>> Hello Renaud,
>>>
>>> I just tried unsuccessfully to upgrade my Apple desktop to
>>> Mac OS X 10.9 (Mavericks), but due to a few technical
>>> problems I had to backtrack to the previous version
>>> 10.8 for now.
>>>
>>> After restoring from backups and checking
>>> that everything works, I discovered that RcppOctave
>>> does not install. I get the same invalid malloc error that
>>> I was getting before. But this time I have not used
>>> MacPorts at all, only Homebrew, and the version of
>>> Octave is 3.6.4 as it should be.
>>>
>>> (I am downloading source, not using install.packages(), because
>>> the latter tends to download old archives.)
>>>
>>> Indeed, with my fresh install of Mac OS X, with the
>>> command line tools and Xcode installed, R does not
>>> issue the correct command: R CMD config CXX
>>> returns: llvm-g++-4.2 -arch x86_64.
>>>
>>> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
>>> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
>>> this problem by defining symbolic links llvm-g++-4.2 and
>>> llvm-gcc-4.2 pointing to these files, but this does not work.
>>>
>>> There are a couple of open issues:
>>> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>>>    llvm-gcc-4.2 (only g++ and gcc).
>>> 2. Apple no longer supports Fortran at all (the R core team
>>>     provides gfortran-4.2?see R Mac OS FAQ).
>>> 3. 'brew install octave' does not show you what it is doing,
>>>    and I think it may be using clang instead of gcc, clang++
>>>    instead of g++.
>>> 4. The segfault error when I try to install RcppOctave is
>>>     probably due to compiler version incompatibilities, either
>>>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>>>
>>> Thus under Mac OS X the correct long-term solution is to
>>> stop using gcc/g++ and follow Apple in using clang/clang++.
>>> In the mean time, Apple will make life difficult for people who
>>> continue to use gcc/g++/gfortran! (There is an open source
>>> project to write an LLVM Fortran front-end, but I don't know
>>> what the status of that project is.)
>>>
>>> Dominick
>>>
>>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:18:04 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:18:04 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHF6g4wfJULJjE4mR3mZ+D5Jyd1BykfQ4cX7P22ZkDiM8g@mail.gmail.com>

---------- Forwarded message ----------
From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
Date: 31 October 2013 09:36
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


Thanks again for going into debug-mode on RcppOctave!

Did you look at these sections of the R Mac-FAQ and R installation and
administration manual:
http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Installation-of-source-packages
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages

You might need to change paths to compilers etc.. in ~/.R/Makevars
Please let me know if you think this helps?

Renaud
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:18:23 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:18:23 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHFMwz_y4ZZScus+8BaSvymTbMtTaC=EoFwD=vCkcpxhPw@mail.gmail.com>

---------- Forwarded message ----------
From: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
Date: 31 October 2013 09:37
Subject: Re: Apple Blues
To: Dominick Samperi <djsamperi at gmail.com>



On 30 October 2013 20:10, Dominick Samperi <djsamperi at gmail.com> wrote:

> We are pretty much back to where we were some weeks ago. Remember
> the trivial change that I made to Rcpp that caused it to fail with the
> pointer error, by adding a function that was not even called?
>
>
>
Did you try this in a plain package, without any Rcpp stuff?
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:18:38 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:18:38 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHHROORDcWbr0XEnTJ_wFv-zfrWiWUMcLHSRZvNeqZpf+g@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 1 November 2013 03:44
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


It turns out that the Octave problem has nothing to do with R or Rcpp.
This is a clash between Octave and MacOS, and there is also a problem
under Fedora Linux (or the Octave documentation is not up-to-date).

Process the attached file like so (under MacOS):
mkoctfile --link-stand-alone embedded.cc -o embedded

Note that most of the code in this file has been commented out,
leaving only the string_vector declaration at the top.

This is what happens when I run embedded:
/Users/dsamperi/c++bug $ ./embedded
embedded(64345) malloc: *** error for object 0x7fff7e114570: pointer being
freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

If I uncomment the code and create embedded under Fedora Linux
I get an error saying gcd is not invoked properly. But this example
is copied directly from the documentation, so I guess it has not
been checked/updated for some time?

Dominick


On Thu, Oct 31, 2013 at 3:37 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

>
> On 30 October 2013 20:10, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> We are pretty much back to where we were some weeks ago. Remember
>> the trivial change that I made to Rcpp that caused it to fail with the
>> pointer error, by adding a function that was not even called?
>>
>>
>>
> Did you try this in a plain package, without any Rcpp stuff?
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 08:19:17 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 09:19:17 +0200
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CAHavPHFOP0JjDU1m-uVTBT9U1jP_bcK6eZdxH3Bk_+YS3eF+6A@mail.gmail.com>

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 1 November 2013 07:14
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


I can finally close this issue, after:

1. Updating to Mac OS X 10.9 (Mavericks)
2. Installing Xcode and command line tools (again).
3. Deleting ALL old brew builds: rm -rf /usr/local/Cellar
4. Install octave using brew (includes recent patches for Mavericks)
5. Downloading the latest development Octave source using hg
    to fetch a correct octave/examples/embedded.cc

As you probably know, the last line of embedded.cc (attached)
is very important. Without it there is still a memory error!



On Thu, Oct 31, 2013 at 9:44 PM, Dominick Samperi <djsamperi at gmail.com>wrote:

> It turns out that the Octave problem has nothing to do with R or Rcpp.
> This is a clash between Octave and MacOS, and there is also a problem
> under Fedora Linux (or the Octave documentation is not up-to-date).
>
> Process the attached file like so (under MacOS):
> mkoctfile --link-stand-alone embedded.cc -o embedded
>
> Note that most of the code in this file has been commented out,
> leaving only the string_vector declaration at the top.
>
> This is what happens when I run embedded:
> /Users/dsamperi/c++bug $ ./embedded
> embedded(64345) malloc: *** error for object 0x7fff7e114570: pointer being
> freed was not allocated
>  *** set a breakpoint in malloc_error_break to debug
> Abort trap: 6
>
> If I uncomment the code and create embedded under Fedora Linux
> I get an error saying gcd is not invoked properly. But this example
> is copied directly from the documentation, so I guess it has not
> been checked/updated for some time?
>
> Dominick
>
>
> On Thu, Oct 31, 2013 at 3:37 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>>
>> On 30 October 2013 20:10, Dominick Samperi <djsamperi at gmail.com> wrote:
>>
>>> We are pretty much back to where we were some weeks ago. Remember
>>> the trivial change that I made to Rcpp that caused it to fail with the
>>> pointer error, by adding a function that was not even called?
>>>
>>>
>>>
>> Did you try this in a plain package, without any Rcpp stuff?
>>
>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 09:11:27 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 10:11:27 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
Message-ID: <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>

What type of R installation did you test this procedure with?
Ideally this would work with the plain CRAN binary, modulo adapting
~/.R/Makevars.


As you probably know, the last line of embedded.cc (attached)
> is very important. Without it there is still a memory error!
>
>
>
I checked Octave source and clean_up_and_exit is a simple wrapper to
do_octave_atexit, which I call directly to skip the call to exit, which
would otherwise terminate the R session as well:

[from
http://hg.savannah.gnu.org/hgweb/octave/file/eff3d78367f0/src/toplev.cc#l667
]

void clean_up_and_exit (int retval)
{
  do_octave_atexit ();
  if (octave_exit)
    (*octave_exit) (retval == EOF ? 0 : retval);
}

Note that I actually don't know how to effectively terminate the Octave
session. Don't know if this even possible since it currently runs in the
same thread as R (that's at least my understanding). So even after cleaning
up with do_octave_atexit(), we can still send commands to Octave which
responds fine, except if errors occurs and then a segfault sometimes come
up suggesting some thing is in a bad state. Anyway, this is not really a
big issue.

library(RcppOctave)
o_runif(1)
octave_end()
o_runif(1)
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From djsamperi at gmail.com  Fri Nov  1 15:07:12 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 1 Nov 2013 10:07:12 -0400
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
Message-ID: <CADUbQ5jU-ao9YM3C33=6+xGH7FemYsReMCJRf5PDBaqqp3m=KA@mail.gmail.com>

Well, I convinced myself (I could be wrong) that the problem is not related
to R or Rcpp,
and I did not test RcppOctave. As you suggest, termination protocol may
need to be
tested...


On Fri, Nov 1, 2013 at 4:11 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> What type of R installation did you test this procedure with?
> Ideally this would work with the plain CRAN binary, modulo adapting
> ~/.R/Makevars.
>
>
> As you probably know, the last line of embedded.cc (attached)
>> is very important. Without it there is still a memory error!
>>
>>
>>
> I checked Octave source and clean_up_and_exit is a simple wrapper to
> do_octave_atexit, which I call directly to skip the call to exit, which
> would otherwise terminate the R session as well:
>
> [from
> http://hg.savannah.gnu.org/hgweb/octave/file/eff3d78367f0/src/toplev.cc#l667
> ]
>
> void clean_up_and_exit (int retval)
> {
>   do_octave_atexit ();
>   if (octave_exit)
>     (*octave_exit) (retval == EOF ? 0 : retval);
> }
>
> Note that I actually don't know how to effectively terminate the Octave
> session. Don't know if this even possible since it currently runs in the
> same thread as R (that's at least my understanding). So even after cleaning
> up with do_octave_atexit(), we can still send commands to Octave which
> responds fine, except if errors occurs and then a segfault sometimes come
> up suggesting some thing is in a bad state. Anyway, this is not really a
> big issue.
>
> library(RcppOctave)
> o_runif(1)
> octave_end()
> o_runif(1)
>
>
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  1 15:17:58 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 1 Nov 2013 16:17:58 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5jU-ao9YM3C33=6+xGH7FemYsReMCJRf5PDBaqqp3m=KA@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jU-ao9YM3C33=6+xGH7FemYsReMCJRf5PDBaqqp3m=KA@mail.gmail.com>
Message-ID: <CAHavPHG=0sxTt=xiM69i+XJ5TDMXVRTx=Emed2V0rZum0jfS9w@mail.gmail.com>

You were initially suggesting that if R is compiled using a compiler
different than Octave then one might end up having troubles.
Would this still be an issue if one follows the procedure you described?

Generally speaking (and this is for my curiosity), does this mean that
libraries generated by one compiler cannot necessarily be linked with
another program using another compiler. I had hoped the interface would be
platform-dependent only, but not compiler dependent, with compilers needing
to follow some standard specs of a given platform.



On 1 November 2013 16:07, Dominick Samperi <djsamperi at gmail.com> wrote:

> Well, I convinced myself (I could be wrong) that the problem is not
> related to R or Rcpp,
> and I did not test RcppOctave. As you suggest, termination protocol may
> need to be
> tested...
>
>
> On Fri, Nov 1, 2013 at 4:11 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>> What type of R installation did you test this procedure with?
>> Ideally this would work with the plain CRAN binary, modulo adapting
>> ~/.R/Makevars.
>>
>>
>> As you probably know, the last line of embedded.cc (attached)
>>> is very important. Without it there is still a memory error!
>>>
>>>
>>>
>> I checked Octave source and clean_up_and_exit is a simple wrapper to
>> do_octave_atexit, which I call directly to skip the call to exit, which
>> would otherwise terminate the R session as well:
>>
>> [from
>> http://hg.savannah.gnu.org/hgweb/octave/file/eff3d78367f0/src/toplev.cc#l667
>> ]
>>
>> void clean_up_and_exit (int retval)
>> {
>>   do_octave_atexit ();
>>   if (octave_exit)
>>     (*octave_exit) (retval == EOF ? 0 : retval);
>> }
>>
>> Note that I actually don't know how to effectively terminate the Octave
>> session. Don't know if this even possible since it currently runs in the
>> same thread as R (that's at least my understanding). So even after cleaning
>> up with do_octave_atexit(), we can still send commands to Octave which
>> responds fine, except if errors occurs and then a segfault sometimes come
>> up suggesting some thing is in a bad state. Anyway, this is not really a
>> big issue.
>>
>> library(RcppOctave)
>> o_runif(1)
>> octave_end()
>> o_runif(1)
>>
>>
>>
>
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From djsamperi at gmail.com  Fri Nov  1 15:31:16 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 1 Nov 2013 10:31:16 -0400
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHG=0sxTt=xiM69i+XJ5TDMXVRTx=Emed2V0rZum0jfS9w@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jU-ao9YM3C33=6+xGH7FemYsReMCJRf5PDBaqqp3m=KA@mail.gmail.com>
 <CAHavPHG=0sxTt=xiM69i+XJ5TDMXVRTx=Emed2V0rZum0jfS9w@mail.gmail.com>
Message-ID: <CADUbQ5jRSAhSP7JNekpoSOu+BEZuLWOQEpXpwaWzqY8iqqS55g@mail.gmail.com>

Apple is changing the plumbing (moving to LLVM/clang from gcc/g++), and
while these compilers are
largely compatible, there can be binary inconsistencies. In general,
different compiler versions (even
of the same compiler) may create binaries that will not work together, esp.
when you consider
exception processing or foreign function interfaces. There is no standard
for how FFI's should work.


On Fri, Nov 1, 2013 at 10:17 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> You were initially suggesting that if R is compiled using a compiler
> different than Octave then one might end up having troubles.
> Would this still be an issue if one follows the procedure you described?
>
> Generally speaking (and this is for my curiosity), does this mean that
> libraries generated by one compiler cannot necessarily be linked with
> another program using another compiler. I had hoped the interface would be
> platform-dependent only, but not compiler dependent, with compilers needing
> to follow some standard specs of a given platform.
>
>
>
> On 1 November 2013 16:07, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> Well, I convinced myself (I could be wrong) that the problem is not
>> related to R or Rcpp,
>> and I did not test RcppOctave. As you suggest, termination protocol may
>> need to be
>> tested...
>>
>>
>> On Fri, Nov 1, 2013 at 4:11 AM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>>> What type of R installation did you test this procedure with?
>>> Ideally this would work with the plain CRAN binary, modulo adapting
>>> ~/.R/Makevars.
>>>
>>>
>>> As you probably know, the last line of embedded.cc (attached)
>>>> is very important. Without it there is still a memory error!
>>>>
>>>>
>>>>
>>> I checked Octave source and clean_up_and_exit is a simple wrapper to
>>> do_octave_atexit, which I call directly to skip the call to exit, which
>>> would otherwise terminate the R session as well:
>>>
>>> [from
>>> http://hg.savannah.gnu.org/hgweb/octave/file/eff3d78367f0/src/toplev.cc#l667
>>> ]
>>>
>>> void clean_up_and_exit (int retval)
>>> {
>>>   do_octave_atexit ();
>>>   if (octave_exit)
>>>     (*octave_exit) (retval == EOF ? 0 : retval);
>>> }
>>>
>>> Note that I actually don't know how to effectively terminate the Octave
>>> session. Don't know if this even possible since it currently runs in the
>>> same thread as R (that's at least my understanding). So even after cleaning
>>> up with do_octave_atexit(), we can still send commands to Octave which
>>> responds fine, except if errors occurs and then a segfault sometimes come
>>> up suggesting some thing is in a bad state. Anyway, this is not really a
>>> big issue.
>>>
>>> library(RcppOctave)
>>> o_runif(1)
>>> octave_end()
>>> o_runif(1)
>>>
>>>
>>>
>>
>
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From djsamperi at gmail.com  Fri Nov  1 22:49:58 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 1 Nov 2013 17:49:58 -0400
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
Message-ID: <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>

Ranaud,

RcppOctave can now be installed and used under Mac OS X Mavericks
like this:

$ R CMD INSTALL RcppOctave --no-test-load
$ R
> library(RcppOctave)
> .O$version()
...
> .Call('octave_end')
> q("no")

The --no-test-load option is used because the embedded Octave session
is not terminated properly at test time (during installation), and the
embedded Octave session needs to be explicitly terminated before
leaving the R session using the 'octave_end' entry point.

Some cosmetic changes will need to be made so that everything
happens automatically before a CRAN submission.

Dominick


On Fri, Nov 1, 2013 at 4:11 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> What type of R installation did you test this procedure with?
> Ideally this would work with the plain CRAN binary, modulo adapting
> ~/.R/Makevars.
>
>
> As you probably know, the last line of embedded.cc (attached)
>> is very important. Without it there is still a memory error!
>>
>>
>>
> I checked Octave source and clean_up_and_exit is a simple wrapper to
> do_octave_atexit, which I call directly to skip the call to exit, which
> would otherwise terminate the R session as well:
>
> [from
> http://hg.savannah.gnu.org/hgweb/octave/file/eff3d78367f0/src/toplev.cc#l667
> ]
>
> void clean_up_and_exit (int retval)
> {
>   do_octave_atexit ();
>   if (octave_exit)
>     (*octave_exit) (retval == EOF ? 0 : retval);
> }
>
> Note that I actually don't know how to effectively terminate the Octave
> session. Don't know if this even possible since it currently runs in the
> same thread as R (that's at least my understanding). So even after cleaning
> up with do_octave_atexit(), we can still send commands to Octave which
> responds fine, except if errors occurs and then a segfault sometimes come
> up suggesting some thing is in a bad state. Anyway, this is not really a
> big issue.
>
> library(RcppOctave)
> o_runif(1)
> octave_end()
> o_runif(1)
>
>
>
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From renaud at mancala.cbio.uct.ac.za  Sat Nov  2 05:19:00 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sat, 2 Nov 2013 06:19:00 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
Message-ID: <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>

> The --no-test-load option is used because the embedded Octave session
> is not terminated properly at test time (during installation), and the
> embedded Octave session needs to be explicitly terminated before
> leaving the R session using the 'octave_end' entry point.
>

octave_end is normally called when the package is unloaded in .onUnload as
well as when the library is unloaded by in R_init_unload (or something like
that).
There is no errors on Linux at load test.
Can you please post the install logs showing the error?

Thanks
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From djsamperi at gmail.com  Sat Nov  2 06:00:34 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Sat, 2 Nov 2013 01:00:34 -0400
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
Message-ID: <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>

It appears that octave_end is not called at all under Mac OS X. But it
is also not called under Linux! I inserted Rprintf statements to check.

Perhaps the explanation is that failing to call octave_end under Linux
(or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
is so the Mac OS X behavior is less dangerous...

If I do not use --no-test-load, I get the result in RcppOctave.log
(attached).

Also, I'm attaching RcppOctave/src/modules/Makefile.in
with a small edit (the sed script generates a path with an extra '..').



On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

>
> The --no-test-load option is used because the embedded Octave session
>> is not terminated properly at test time (during installation), and the
>> embedded Octave session needs to be explicitly terminated before
>> leaving the R session using the 'octave_end' entry point.
>>
>
> octave_end is normally called when the package is unloaded in .onUnload as
> well as when the library is unloaded by in R_init_unload (or something like
> that).
> There is no errors on Linux at load test.
> Can you please post the install logs showing the error?
>
> Thanks
>
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From djsamperi at gmail.com  Sat Nov  2 06:18:36 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Sat, 2 Nov 2013 01:18:36 -0400
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
Message-ID: <CADUbQ5h+La1y0DbE7biucGFpx7UwemzpPk-cc3r3hqKyYC33VA@mail.gmail.com>

The log that I sent here shows C++ compilers clang++
and c++ (same as clang++ under Mac OS X), but there
is no change if g++ is used instead.


On Sat, Nov 2, 2013 at 1:00 AM, Dominick Samperi <djsamperi at gmail.com>wrote:

> It appears that octave_end is not called at all under Mac OS X. But it
> is also not called under Linux! I inserted Rprintf statements to check.
>
> Perhaps the explanation is that failing to call octave_end under Linux
> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
> is so the Mac OS X behavior is less dangerous...
>
> If I do not use --no-test-load, I get the result in RcppOctave.log
> (attached).
>
> Also, I'm attaching RcppOctave/src/modules/Makefile.in
> with a small edit (the sed script generates a path with an extra '..').
>
>
>
> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>>
>> The --no-test-load option is used because the embedded Octave session
>>> is not terminated properly at test time (during installation), and the
>>> embedded Octave session needs to be explicitly terminated before
>>> leaving the R session using the 'octave_end' entry point.
>>>
>>
>> octave_end is normally called when the package is unloaded in
>> .onUnload as well as when the library is unloaded by in R_init_unload (or
>> something like that).
>> There is no errors on Linux at load test.
>> Can you please post the install logs showing the error?
>>
>> Thanks
>>
>
>
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From neox86 at gmail.com  Mon Nov  4 16:18:54 2013
From: neox86 at gmail.com (Giuseppe)
Date: Mon, 4 Nov 2013 16:18:54 +0100
Subject: [Rcppoctave-user] Apple Blues
Message-ID: <CADerNuThoN=jmvTPV1r2ZbhfZGmVEDaqok+ygpAuKxQ8+C5R_g@mail.gmail.com>

I have been reading the thread about woes with osx and RcppOctave.

If I am correct, it seems that the issue is declared closed if
"--no-test-load" is added to "R CMD INSTALL". Unfortunately, this does not
work for me. This is what I get :

[omitted]

llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
rcpp_octave.o /Users/osxuser/Library/R/Rcpp/lib/libRcpp.a
-L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
-L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation

installing to /Users/osxuser/Library/R/RcppOctave/libs


R(24620) malloc: *** error for object 0x7fff71042570: pointer being freed
was not allocated
*** set a breakpoint in malloc_error_break to debug
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24619 Done
                   echo 'tools:::.install_packages()'
     24620 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}



However, i think the Makevars does not picks up the correct location of the
R library. I saw in the list that a patch was sent. Can I have it too to
test and see weather this is my case?

----

This is my setup:

[~/scratch]$ gfortran --version
GNU Fortran (GCC) 4.8.2

[~/scratch]$ octave --version
GNU Octave, version 3.6.4

[~/scratch]$ R --version
R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Platform: x86_64-apple-darwin10.8.0 (64-bit)


Octave and gfortran are from homebrew. Osx version is Maverick. Xcode tools
5.0.1.

[ ~/scratch]$ clang --version
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

[ ~/scratch]$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
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From djsamperi at gmail.com  Mon Nov  4 17:17:45 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Mon, 4 Nov 2013 11:17:45 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADerNuThoN=jmvTPV1r2ZbhfZGmVEDaqok+ygpAuKxQ8+C5R_g@mail.gmail.com>
References: <CADerNuThoN=jmvTPV1r2ZbhfZGmVEDaqok+ygpAuKxQ8+C5R_g@mail.gmail.com>
Message-ID: <CADUbQ5gP8vKgp5-az6KmkjRMaRtgteb+Vmd5yqoiyktOWqbrkA@mail.gmail.com>

By default R package builds will use the C/C++ compiler that was used
to build R, but llvm-g++-4.2 does not work under Mavericks. Try
creating .R/Makevars containing
CXX=g++
CC=gcc
or
CXX=clang++
CC=clang



On Mon, Nov 4, 2013 at 10:18 AM, Giuseppe <neox86 at gmail.com> wrote:

> I have been reading the thread about woes with osx and RcppOctave.
>
> If I am correct, it seems that the issue is declared closed if
> "--no-test-load" is added to "R CMD INSTALL". Unfortunately, this does not
> work for me. This is what I get :
>
> [omitted]
>
> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
> rcpp_octave.o /Users/osxuser/Library/R/Rcpp/lib/libRcpp.a
> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>
> installing to /Users/osxuser/Library/R/RcppOctave/libs
>
>
> R(24620) malloc: *** error for object 0x7fff71042570: pointer being freed
> was not allocated
> *** set a breakpoint in malloc_error_break to debug
> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24619 Done
>                    echo 'tools:::.install_packages()'
>      24620 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>
>
>
> However, i think the Makevars does not picks up the correct location of
> the R library. I saw in the list that a patch was sent. Can I have it too
> to test and see weather this is my case?
>
> ----
>
> This is my setup:
>
> [~/scratch]$ gfortran --version
> GNU Fortran (GCC) 4.8.2
>
> [~/scratch]$ octave --version
> GNU Octave, version 3.6.4
>
> [~/scratch]$ R --version
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>
> Octave and gfortran are from homebrew. Osx version is Maverick. Xcode
> tools 5.0.1.
>
> [ ~/scratch]$ clang --version
> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>
> [ ~/scratch]$ g++ --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/usr/include/c++/4.2.1
> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>
>
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From neox86 at gmail.com  Tue Nov  5 00:16:34 2013
From: neox86 at gmail.com (Giuseppe)
Date: Tue, 5 Nov 2013 00:16:34 +0100
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5gP8vKgp5-az6KmkjRMaRtgteb+Vmd5yqoiyktOWqbrkA@mail.gmail.com>
References: <CADerNuThoN=jmvTPV1r2ZbhfZGmVEDaqok+ygpAuKxQ8+C5R_g@mail.gmail.com>
 <CADUbQ5gP8vKgp5-az6KmkjRMaRtgteb+Vmd5yqoiyktOWqbrkA@mail.gmail.com>
Message-ID: <CADerNuTt6dJV6WtKgxdbM448m5r6C_dfFf+tZQmBAb=xVPGT1w@mail.gmail.com>

I tried with the .R/Makevars trick. The malloc error is gone, but now I get
the following error:

Error : /Users/osxuser/scratch/RcppOctave/man/o_addpath.Rd:41: .onLoad
failed in loadNamespace() for 'RcppOctave', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object
'/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so':
  dlopen(/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so, 6): Symbol
not found:
__ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
  Referenced from: /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
  Expected in: flat namespace
 in /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
ERROR: installing Rd objects failed for package ?RcppOctave?


Any pointer on what this may be due?



On Mon, Nov 4, 2013 at 5:17 PM, Dominick Samperi <djsamperi at gmail.com>wrote:

> By default R package builds will use the C/C++ compiler that was used
> to build R, but llvm-g++-4.2 does not work under Mavericks. Try
> creating .R/Makevars containing
> CXX=g++
> CC=gcc
> or
> CXX=clang++
> CC=clang
>
>
>
> On Mon, Nov 4, 2013 at 10:18 AM, Giuseppe <neox86 at gmail.com> wrote:
>
>> I have been reading the thread about woes with osx and RcppOctave.
>>
>> If I am correct, it seems that the issue is declared closed if
>> "--no-test-load" is added to "R CMD INSTALL". Unfortunately, this does not
>> work for me. This is what I get :
>>
>> [omitted]
>>
>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>> rcpp_octave.o /Users/osxuser/Library/R/Rcpp/lib/libRcpp.a
>> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
>> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>>
>> installing to /Users/osxuser/Library/R/RcppOctave/libs
>>
>>
>> R(24620) malloc: *** error for object 0x7fff71042570: pointer being freed
>> was not allocated
>>  *** set a breakpoint in malloc_error_break to debug
>> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24619
>> Done                    echo 'tools:::.install_packages()'
>>      24620 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
>> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>>
>>
>>
>> However, i think the Makevars does not picks up the correct location of
>> the R library. I saw in the list that a patch was sent. Can I have it too
>> to test and see weather this is my case?
>>
>> ----
>>
>> This is my setup:
>>
>> [~/scratch]$ gfortran --version
>> GNU Fortran (GCC) 4.8.2
>>
>> [~/scratch]$ octave --version
>> GNU Octave, version 3.6.4
>>
>> [~/scratch]$ R --version
>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>>
>> Octave and gfortran are from homebrew. Osx version is Maverick. Xcode
>> tools 5.0.1.
>>
>> [ ~/scratch]$ clang --version
>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>
>> [ ~/scratch]$ g++ --version
>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>>
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>
>>
>
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From djsamperi at gmail.com  Tue Nov  5 02:11:30 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Mon, 4 Nov 2013 20:11:30 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADerNuTt6dJV6WtKgxdbM448m5r6C_dfFf+tZQmBAb=xVPGT1w@mail.gmail.com>
References: <CADerNuThoN=jmvTPV1r2ZbhfZGmVEDaqok+ygpAuKxQ8+C5R_g@mail.gmail.com>
 <CADUbQ5gP8vKgp5-az6KmkjRMaRtgteb+Vmd5yqoiyktOWqbrkA@mail.gmail.com>
 <CADerNuTt6dJV6WtKgxdbM448m5r6C_dfFf+tZQmBAb=xVPGT1w@mail.gmail.com>
Message-ID: <CADUbQ5gBMwfnhQHvhZvdbtBRNHS0xR9exC+Wzf_PRgi7cuqJLg@mail.gmail.com>

Make sure to install Rcpp and RcppOctave from
source using the same tool chain (g++/gcc or
clang++/clang). Remove any old .o, .so, and .oct
files.
On Nov 4, 2013 6:16 PM, "Giuseppe" <neox86 at gmail.com> wrote:

> I tried with the .R/Makevars trick. The malloc error is gone, but now I
> get the following error:
>
> Error : /Users/osxuser/scratch/RcppOctave/man/o_addpath.Rd:41: .onLoad
> failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so':
>   dlopen(/Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so, 6):
> Symbol not found:
> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>   Referenced from: /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in /Users/osxuser/Library/R/RcppOctave/libs/RcppOctave.so
> ERROR: installing Rd objects failed for package ?RcppOctave?
>
>
> Any pointer on what this may be due?
>
>
>
> On Mon, Nov 4, 2013 at 5:17 PM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> By default R package builds will use the C/C++ compiler that was used
>> to build R, but llvm-g++-4.2 does not work under Mavericks. Try
>> creating .R/Makevars containing
>> CXX=g++
>> CC=gcc
>> or
>> CXX=clang++
>> CC=clang
>>
>>
>>
>> On Mon, Nov 4, 2013 at 10:18 AM, Giuseppe <neox86 at gmail.com> wrote:
>>
>>> I have been reading the thread about woes with osx and RcppOctave.
>>>
>>> If I am correct, it seems that the issue is declared closed if
>>> "--no-test-load" is added to "R CMD INSTALL". Unfortunately, this does not
>>> work for me. This is what I get :
>>>
>>> [omitted]
>>>
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>> rcpp_octave.o /Users/osxuser/Library/R/Rcpp/lib/libRcpp.a
>>> -L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
>>> -L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>>
>>> installing to /Users/osxuser/Library/R/RcppOctave/libs
>>>
>>>
>>> R(24620) malloc: *** error for object 0x7fff71042570: pointer being
>>> freed was not allocated
>>>  *** set a breakpoint in malloc_error_break to debug
>>> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 24619
>>> Done                    echo 'tools:::.install_packages()'
>>>      24620 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
>>> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>>>
>>>
>>>
>>> However, i think the Makevars does not picks up the correct location of
>>> the R library. I saw in the list that a patch was sent. Can I have it too
>>> to test and see weather this is my case?
>>>
>>> ----
>>>
>>> This is my setup:
>>>
>>> [~/scratch]$ gfortran --version
>>> GNU Fortran (GCC) 4.8.2
>>>
>>> [~/scratch]$ octave --version
>>> GNU Octave, version 3.6.4
>>>
>>> [~/scratch]$ R --version
>>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>>
>>> Octave and gfortran are from homebrew. Osx version is Maverick. Xcode
>>> tools 5.0.1.
>>>
>>> [ ~/scratch]$ clang --version
>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>
>>> [ ~/scratch]$ g++ --version
>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>> Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Rcppoctave-user mailing list
>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>
>>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Tue Nov  5 15:04:08 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Tue, 5 Nov 2013 16:04:08 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
Message-ID: <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>

Not sure where the extra '..' would come from.
Are you installing the latest version from github?

devtools::install_github('RcppOctave', 'renozao')



On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com> wrote:

> It appears that octave_end is not called at all under Mac OS X. But it
> is also not called under Linux! I inserted Rprintf statements to check.
>
> Perhaps the explanation is that failing to call octave_end under Linux
> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
> is so the Mac OS X behavior is less dangerous...
>
> If I do not use --no-test-load, I get the result in RcppOctave.log
> (attached).
>
> Also, I'm attaching RcppOctave/src/modules/Makefile.in
> with a small edit (the sed script generates a path with an extra '..').
>
>
>
> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>>
>> The --no-test-load option is used because the embedded Octave session
>>> is not terminated properly at test time (during installation), and the
>>> embedded Octave session needs to be explicitly terminated before
>>> leaving the R session using the 'octave_end' entry point.
>>>
>>
>> octave_end is normally called when the package is unloaded in
>> .onUnload as well as when the library is unloaded by in R_init_unload (or
>> something like that).
>> There is no errors on Linux at load test.
>> Can you please post the install logs showing the error?
>>
>> Thanks
>>
>
>
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From djsamperi at gmail.com  Tue Nov  5 15:38:52 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Tue, 5 Nov 2013 09:38:52 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
Message-ID: <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>

R CMD config --ldflags
yields
-F/Library/Frameworks/R.framework/.. -framework R

This needs to be hacked for mkoctfile to:
-L/Library/Frameworks/R.framework/Libraries -lR
(no '..')

Applying this to the github source fixes it for
Mac OS X Mavericks provided the --no-test-load
and octave_end tricks are used.


On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> Not sure where the extra '..' would come from.
> Are you installing the latest version from github?
>
> devtools::install_github('RcppOctave', 'renozao')
>
>
>
> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> It appears that octave_end is not called at all under Mac OS X. But it
>> is also not called under Linux! I inserted Rprintf statements to check.
>>
>> Perhaps the explanation is that failing to call octave_end under Linux
>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
>> is so the Mac OS X behavior is less dangerous...
>>
>> If I do not use --no-test-load, I get the result in RcppOctave.log
>> (attached).
>>
>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
>> with a small edit (the sed script generates a path with an extra '..').
>>
>>
>>
>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>>>
>>> The --no-test-load option is used because the embedded Octave session
>>>> is not terminated properly at test time (during installation), and the
>>>> embedded Octave session needs to be explicitly terminated before
>>>> leaving the R session using the 'octave_end' entry point.
>>>>
>>>
>>> octave_end is normally called when the package is unloaded in
>>> .onUnload as well as when the library is unloaded by in R_init_unload (or
>>> something like that).
>>> There is no errors on Linux at load test.
>>> Can you please post the install logs showing the error?
>>>
>>> Thanks
>>>
>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Wed Nov  6 10:15:51 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 6 Nov 2013 11:15:51 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
Message-ID: <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>

Couple of questions to understand what is going on:

  * why does R CMD config --ldflags returns these extra '..' if they are
incorrect?
  * why does the compilation work if the path is incorrect to R library is
incorrect?
  * why removing the dots should solve the malloc error?



On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:

> R CMD config --ldflags
> yields
> -F/Library/Frameworks/R.framework/.. -framework R
>
> This needs to be hacked for mkoctfile to:
> -L/Library/Frameworks/R.framework/Libraries -lR
> (no '..')
>
> Applying this to the github source fixes it for
> Mac OS X Mavericks provided the --no-test-load
> and octave_end tricks are used.
>
>
> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>> Not sure where the extra '..' would come from.
>> Are you installing the latest version from github?
>>
>> devtools::install_github('RcppOctave', 'renozao')
>>
>>
>>
>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com> wrote:
>>
>>> It appears that octave_end is not called at all under Mac OS X. But it
>>> is also not called under Linux! I inserted Rprintf statements to check.
>>>
>>> Perhaps the explanation is that failing to call octave_end under Linux
>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
>>> is so the Mac OS X behavior is less dangerous...
>>>
>>> If I do not use --no-test-load, I get the result in RcppOctave.log
>>> (attached).
>>>
>>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
>>> with a small edit (the sed script generates a path with an extra '..').
>>>
>>>
>>>
>>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux <
>>> renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>>>
>>>> The --no-test-load option is used because the embedded Octave session
>>>>> is not terminated properly at test time (during installation), and the
>>>>> embedded Octave session needs to be explicitly terminated before
>>>>> leaving the R session using the 'octave_end' entry point.
>>>>>
>>>>
>>>> octave_end is normally called when the package is unloaded in
>>>> .onUnload as well as when the library is unloaded by in R_init_unload (or
>>>> something like that).
>>>> There is no errors on Linux at load test.
>>>> Can you please post the install logs showing the error?
>>>>
>>>> Thanks
>>>>
>>>
>>>
>>
>
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From renaud at mancala.cbio.uct.ac.za  Wed Nov  6 14:19:24 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 6 Nov 2013 15:19:24 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
Message-ID: <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>

Hi,

I made some changes available in the develop version, which should
hopefully solve both issues:
  * octave_end is now called on exit (via reg.finalizer: see my post
on r-devel https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
  * the extra dots are removed by the sed in configure.ac, but I think
we still need to figure out why these dots are there...

To test:

devtools::install_github('RcppOctave', 'renozao', ref = 'develop')

Thanks.

Bests,
Renaud

On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> Couple of questions to understand what is going on:
>
>   * why does R CMD config --ldflags returns these extra '..' if they are
> incorrect?
>   * why does the compilation work if the path is incorrect to R library is
> incorrect?
>   * why removing the dots should solve the malloc error?
>
>
>
> On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:
>>
>> R CMD config --ldflags
>> yields
>> -F/Library/Frameworks/R.framework/.. -framework R
>>
>> This needs to be hacked for mkoctfile to:
>> -L/Library/Frameworks/R.framework/Libraries -lR
>> (no '..')
>>
>> Applying this to the github source fixes it for
>> Mac OS X Mavericks provided the --no-test-load
>> and octave_end tricks are used.
>>
>>
>> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>> Not sure where the extra '..' would come from.
>>> Are you installing the latest version from github?
>>>
>>> devtools::install_github('RcppOctave', 'renozao')
>>>
>>>
>>>
>>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com> wrote:
>>>>
>>>> It appears that octave_end is not called at all under Mac OS X. But it
>>>> is also not called under Linux! I inserted Rprintf statements to check.
>>>>
>>>> Perhaps the explanation is that failing to call octave_end under Linux
>>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
>>>> is so the Mac OS X behavior is less dangerous...
>>>>
>>>> If I do not use --no-test-load, I get the result in RcppOctave.log
>>>> (attached).
>>>>
>>>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
>>>> with a small edit (the sed script generates a path with an extra '..').
>>>>
>>>>
>>>>
>>>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux
>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>>
>>>>>
>>>>>> The --no-test-load option is used because the embedded Octave session
>>>>>> is not terminated properly at test time (during installation), and the
>>>>>> embedded Octave session needs to be explicitly terminated before
>>>>>> leaving the R session using the 'octave_end' entry point.
>>>>>
>>>>>
>>>>> octave_end is normally called when the package is unloaded in .onUnload
>>>>> as well as when the library is unloaded by in R_init_unload (or something
>>>>> like that).
>>>>> There is no errors on Linux at load test.
>>>>> Can you please post the install logs showing the error?
>>>>>
>>>>> Thanks
>>>>
>>>>
>>>
>>
>

From djsamperi at gmail.com  Wed Nov  6 16:25:40 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Wed, 6 Nov 2013 10:25:40 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
Message-ID: <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>

Hello Renaud,

So, this R technical issue (reg.finalizer) was the crux of the problem all
along. Good work!

The '..' is still there and the build still fails without my hacked
Makefile.in, but
with this change everything works (no more install memory errors).

The '..' in the output of R CMD config --ldflags is there for a purpose,
because
the R framework is under /Library/Frameworks, and not under
/Library/Frameworks/R.framework. This is analogous to
-L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
of libraries (instead of frameworks), not just libfoo.so.
(A Mac OS framework is analogous to an R package.)

Make sure '..' is not in the path supplied to '-L' and everything should
work.

Cheers,
Dominick


On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> Hi,
>
> I made some changes available in the develop version, which should
> hopefully solve both issues:
>   * octave_end is now called on exit (via reg.finalizer: see my post
> on r-devel
> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>   * the extra dots are removed by the sed in configure.ac, but I think
> we still need to figure out why these dots are there...
>
> To test:
>
> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>
> Thanks.
>
> Bests,
> Renaud
>
> On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
> > Couple of questions to understand what is going on:
> >
> >   * why does R CMD config --ldflags returns these extra '..' if they are
> > incorrect?
> >   * why does the compilation work if the path is incorrect to R library
> is
> > incorrect?
> >   * why removing the dots should solve the malloc error?
> >
> >
> >
> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:
> >>
> >> R CMD config --ldflags
> >> yields
> >> -F/Library/Frameworks/R.framework/.. -framework R
> >>
> >> This needs to be hacked for mkoctfile to:
> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >> (no '..')
> >>
> >> Applying this to the github source fixes it for
> >> Mac OS X Mavericks provided the --no-test-load
> >> and octave_end tricks are used.
> >>
> >>
> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>>
> >>> Not sure where the extra '..' would come from.
> >>> Are you installing the latest version from github?
> >>>
> >>> devtools::install_github('RcppOctave', 'renozao')
> >>>
> >>>
> >>>
> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
> wrote:
> >>>>
> >>>> It appears that octave_end is not called at all under Mac OS X. But it
> >>>> is also not called under Linux! I inserted Rprintf statements to
> check.
> >>>>
> >>>> Perhaps the explanation is that failing to call octave_end under Linux
> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
> >>>> is so the Mac OS X behavior is less dangerous...
> >>>>
> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
> >>>> (attached).
> >>>>
> >>>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
> >>>> with a small edit (the sed script generates a path with an extra
> '..').
> >>>>
> >>>>
> >>>>
> >>>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux
> >>>> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>>>>
> >>>>>
> >>>>>> The --no-test-load option is used because the embedded Octave
> session
> >>>>>> is not terminated properly at test time (during installation), and
> the
> >>>>>> embedded Octave session needs to be explicitly terminated before
> >>>>>> leaving the R session using the 'octave_end' entry point.
> >>>>>
> >>>>>
> >>>>> octave_end is normally called when the package is unloaded in
> .onUnload
> >>>>> as well as when the library is unloaded by in R_init_unload (or
> something
> >>>>> like that).
> >>>>> There is no errors on Linux at load test.
> >>>>> Can you please post the install logs showing the error?
> >>>>>
> >>>>> Thanks
> >>>>
> >>>>
> >>>
> >>
> >
>
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From djsamperi at gmail.com  Wed Nov  6 18:26:47 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Wed, 6 Nov 2013 12:26:47 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
Message-ID: <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>

The reason we have been hacking away at '-F' vs '-L' instead of
letting 'R CMD config' figure things out is that mkoctfile does not
know about R frameworks ('-F' is invalid). But mkoctfile does have
the -Wl,whatever option, which simply passes whatever down to
the linker.

I have attached a modified configure.ac that uses this option
instead of using sed to hack the output of R CMD config --ldflags.



On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <djsamperi at gmail.com>wrote:

> Hello Renaud,
>
> So, this R technical issue (reg.finalizer) was the crux of the problem all
> along. Good work!
>
> The '..' is still there and the build still fails without my hacked
> Makefile.in, but
> with this change everything works (no more install memory errors).
>
> The '..' in the output of R CMD config --ldflags is there for a purpose,
> because
> the R framework is under /Library/Frameworks, and not under
> /Library/Frameworks/R.framework. This is analogous to
> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
> of libraries (instead of frameworks), not just libfoo.so.
> (A Mac OS framework is analogous to an R package.)
>
> Make sure '..' is not in the path supplied to '-L' and everything should
> work.
>
> Cheers,
> Dominick
>
>
> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
>> Hi,
>>
>> I made some changes available in the develop version, which should
>> hopefully solve both issues:
>>   * octave_end is now called on exit (via reg.finalizer: see my post
>> on r-devel
>> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>>   * the extra dots are removed by the sed in configure.ac, but I think
>> we still need to figure out why these dots are there...
>>
>> To test:
>>
>> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>>
>> Thanks.
>>
>> Bests,
>> Renaud
>>
>> On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>> > Couple of questions to understand what is going on:
>> >
>> >   * why does R CMD config --ldflags returns these extra '..' if they are
>> > incorrect?
>> >   * why does the compilation work if the path is incorrect to R library
>> is
>> > incorrect?
>> >   * why removing the dots should solve the malloc error?
>> >
>> >
>> >
>> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:
>> >>
>> >> R CMD config --ldflags
>> >> yields
>> >> -F/Library/Frameworks/R.framework/.. -framework R
>> >>
>> >> This needs to be hacked for mkoctfile to:
>> >> -L/Library/Frameworks/R.framework/Libraries -lR
>> >> (no '..')
>> >>
>> >> Applying this to the github source fixes it for
>> >> Mac OS X Mavericks provided the --no-test-load
>> >> and octave_end tricks are used.
>> >>
>> >>
>> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>>
>> >>> Not sure where the extra '..' would come from.
>> >>> Are you installing the latest version from github?
>> >>>
>> >>> devtools::install_github('RcppOctave', 'renozao')
>> >>>
>> >>>
>> >>>
>> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
>> wrote:
>> >>>>
>> >>>> It appears that octave_end is not called at all under Mac OS X. But
>> it
>> >>>> is also not called under Linux! I inserted Rprintf statements to
>> check.
>> >>>>
>> >>>> Perhaps the explanation is that failing to call octave_end under
>> Linux
>> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
>> >>>> is so the Mac OS X behavior is less dangerous...
>> >>>>
>> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
>> >>>> (attached).
>> >>>>
>> >>>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
>> >>>> with a small edit (the sed script generates a path with an extra
>> '..').
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux
>> >>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>>>>
>> >>>>>
>> >>>>>> The --no-test-load option is used because the embedded Octave
>> session
>> >>>>>> is not terminated properly at test time (during installation), and
>> the
>> >>>>>> embedded Octave session needs to be explicitly terminated before
>> >>>>>> leaving the R session using the 'octave_end' entry point.
>> >>>>>
>> >>>>>
>> >>>>> octave_end is normally called when the package is unloaded in
>> .onUnload
>> >>>>> as well as when the library is unloaded by in R_init_unload (or
>> something
>> >>>>> like that).
>> >>>>> There is no errors on Linux at load test.
>> >>>>> Can you please post the install logs showing the error?
>> >>>>>
>> >>>>> Thanks
>> >>>>
>> >>>>
>> >>>
>> >>
>> >
>>
>
>
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From renaud at mancala.cbio.uct.ac.za  Wed Nov  6 21:37:05 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 6 Nov 2013 22:37:05 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
Message-ID: <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>

Nice. It is indeed a better solution than changing the flags and their
values. The sed command did not work probably because I forgot to double
the square brackets, which is necessary to correctly pass configure's first
string evaluation.
I will incorporate the change tomorrow.
Thanks!

Bests,
Renaud

On Wednesday, November 6, 2013, Dominick Samperi wrote:

> The reason we have been hacking away at '-F' vs '-L' instead of
> letting 'R CMD config' figure things out is that mkoctfile does not
> know about R frameworks ('-F' is invalid). But mkoctfile does have
> the -Wl,whatever option, which simply passes whatever down to
> the linker.
>
> I have attached a modified configure.ac that uses this option
> instead of using sed to hack the output of R CMD config --ldflags.
>
>
>
> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
> Hello Renaud,
>
> So, this R technical issue (reg.finalizer) was the crux of the problem all
> along. Good work!
>
> The '..' is still there and the build still fails without my hacked
> Makefile.in, but
> with this change everything works (no more install memory errors).
>
> The '..' in the output of R CMD config --ldflags is there for a purpose,
> because
> the R framework is under /Library/Frameworks, and not under
> /Library/Frameworks/R.framework. This is analogous to
> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
> of libraries (instead of frameworks), not just libfoo.so.
> (A Mac OS framework is analogous to an R package.)
>
> Make sure '..' is not in the path supplied to '-L' and everything should
> work.
>
> Cheers,
> Dominick
>
>
> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
> Hi,
>
> I made some changes available in the develop version, which should
> hopefully solve both issues:
>   * octave_end is now called on exit (via reg.finalizer: see my post
> on r-devel
> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>   * the extra dots are removed by the sed in configure.ac, but I think
> we still need to figure out why these dots are there...
>
> To test:
>
> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>
> Thanks.
>
> Bests,
> Renaud
>
> On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
> > Couple of questions to understand what is going on:
> >
> >   * why does R CMD config --ldflags returns these extra '..' if they are
> > incorrect?
> >   * why does the compilation work if the path is incorrect to R library
> is
> > incorrect?
> >   * why removing the dots should solve the malloc error?
> >
> >
> >
> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:
> >>
> >> R CMD config --ldflags
> >> yields
> >> -F/Library/Frameworks/R.framework/.. -framework R
> >>
> >> This needs to be hacked for mkoctfile to:
> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >> (no '..')
> >>
> >> Applying this to the github source fixes it for
> >> Mac OS X Mavericks provided the --no-test-load
> >> and octave_end tricks are used.
> >>
> >>
> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>>
> >>> Not sure where the extra '..' would come from.
> >>> Are you installing the latest version from github?
> >>>
> >>> devtools::install_github('RcppOctave', 'renozao')
> >>>
> >>>
> >>>
> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
> wrote:
> >>>>
> >>>> It appears that octave_end is not called at all under Mac OS X. But it
> >>>> is also not called under Linux! I inserted Rprintf statements to
> check.
> >>>>
> >>>> Perhaps the explanation is that failing to call octave_end under Linux
> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
> >>>> is so the Mac OS X behavior is less dangerous...
> >>>>
> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
> >>>> (attached)
>
>
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From renaud at mancala.cbio.uct.ac.za  Thu Nov  7 13:20:05 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 7 Nov 2013 14:20:05 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
Message-ID: <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>

I changed configure.ac into:
R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`

as I read/saw that multiple options must be comma separated.
This will break if the path to the R framework contains spaces though.
Can you please try again:

install_github('RcppOctave', 'renozao', ref = 'develop')

Thanks.

Bests,
Renaud

On 6 November 2013 22:37, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> Nice. It is indeed a better solution than changing the flags and their
> values. The sed command did not work probably because I forgot to double the
> square brackets, which is necessary to correctly pass configure's first
> string evaluation.
> I will incorporate the change tomorrow.
> Thanks!
>
> Bests,
> Renaud
>
> On Wednesday, November 6, 2013, Dominick Samperi wrote:
>>
>> The reason we have been hacking away at '-F' vs '-L' instead of
>> letting 'R CMD config' figure things out is that mkoctfile does not
>> know about R frameworks ('-F' is invalid). But mkoctfile does have
>> the -Wl,whatever option, which simply passes whatever down to
>> the linker.
>>
>> I have attached a modified configure.ac that uses this option
>> instead of using sed to hack the output of R CMD config --ldflags.
>>
>>
>>
>> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <djsamperi at gmail.com>
>> wrote:
>>
>> Hello Renaud,
>>
>> So, this R technical issue (reg.finalizer) was the crux of the problem all
>> along. Good work!
>>
>> The '..' is still there and the build still fails without my hacked
>> Makefile.in, but
>> with this change everything works (no more install memory errors).
>>
>> The '..' in the output of R CMD config --ldflags is there for a purpose,
>> because
>> the R framework is under /Library/Frameworks, and not under
>> /Library/Frameworks/R.framework. This is analogous to
>> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
>> of libraries (instead of frameworks), not just libfoo.so.
>> (A Mac OS framework is analogous to an R package.)
>>
>> Make sure '..' is not in the path supplied to '-L' and everything should
>> work.
>>
>> Cheers,
>> Dominick
>>
>>
>> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> Hi,
>>
>> I made some changes available in the develop version, which should
>> hopefully solve both issues:
>>   * octave_end is now called on exit (via reg.finalizer: see my post
>> on r-devel
>> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>>   * the extra dots are removed by the sed in configure.ac, but I think
>> we still need to figure out why these dots are there...
>>
>> To test:
>>
>> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>>
>> Thanks.
>>
>> Bests,
>> Renaud
>>
>> On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>> > Couple of questions to understand what is going on:
>> >
>> >   * why does R CMD config --ldflags returns these extra '..' if they are
>> > incorrect?
>> >   * why does the compilation work if the path is incorrect to R library
>> > is
>> > incorrect?
>> >   * why removing the dots should solve the malloc error?
>> >
>> >
>> >
>> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com> wrote:
>> >>
>> >> R CMD config --ldflags
>> >> yields
>> >> -F/Library/Frameworks/R.framework/.. -framework R
>> >>
>> >> This needs to be hacked for mkoctfile to:
>> >> -L/Library/Frameworks/R.framework/Libraries -lR
>> >> (no '..')
>> >>
>> >> Applying this to the github source fixes it for
>> >> Mac OS X Mavericks provided the --no-test-load
>> >> and octave_end tricks are used.
>> >>
>> >>
>> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>>
>> >>> Not sure where the extra '..' would come from.
>> >>> Are you installing the latest version from github?
>> >>>
>> >>> devtools::install_github('RcppOctave', 'renozao')
>> >>>
>> >>>
>> >>>
>> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
>> >>> wrote:
>> >>>>
>> >>>> It appears that octave_end is not called at all under Mac OS X. But
>> >>>> it
>> >>>> is also not called under Linux! I inserted Rprintf statements to
>> >>>> check.
>> >>>>
>> >>>> Perhaps the explanation is that failing to call octave_end under
>> >>>> Linux
>> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If this
>> >>>> is so the Mac OS X behavior is less dangerous...
>> >>>>
>> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
>> >>>> (attached)

From djsamperi at gmail.com  Thu Nov  7 16:13:34 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Thu, 7 Nov 2013 10:13:34 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
Message-ID: <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>

This solution yields:

-Wl,-F/Library/Frameworks/R.framework/..,-framework R ...

and the linker doesn't know that the last "R" belongs to the
-framework option.

To fix, simply add the 'g' qualifier to the sed command in
configure.ac:

R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`

My original solution works because the -Wl,"whatever"
option causes mkoctfile to insert the string "whatever"
into the linker command line without parsing. If instead
mkoctfile used a form of exec(3) that expects tokenized
options, the sed solution would be necessary.



On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> I changed configure.ac into:
> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
>
> as I read/saw that multiple options must be comma separated.
> This will break if the path to the R framework contains spaces though.
> Can you please try again:
>
> install_github('RcppOctave', 'renozao', ref = 'develop')
>
> Thanks.
>
> Bests,
> Renaud
>
> On 6 November 2013 22:37, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
> > Nice. It is indeed a better solution than changing the flags and their
> > values. The sed command did not work probably because I forgot to double
> the
> > square brackets, which is necessary to correctly pass configure's first
> > string evaluation.
> > I will incorporate the change tomorrow.
> > Thanks!
> >
> > Bests,
> > Renaud
> >
> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
> >>
> >> The reason we have been hacking away at '-F' vs '-L' instead of
> >> letting 'R CMD config' figure things out is that mkoctfile does not
> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
> >> the -Wl,whatever option, which simply passes whatever down to
> >> the linker.
> >>
> >> I have attached a modified configure.ac that uses this option
> >> instead of using sed to hack the output of R CMD config --ldflags.
> >>
> >>
> >>
> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <djsamperi at gmail.com>
> >> wrote:
> >>
> >> Hello Renaud,
> >>
> >> So, this R technical issue (reg.finalizer) was the crux of the problem
> all
> >> along. Good work!
> >>
> >> The '..' is still there and the build still fails without my hacked
> >> Makefile.in, but
> >> with this change everything works (no more install memory errors).
> >>
> >> The '..' in the output of R CMD config --ldflags is there for a purpose,
> >> because
> >> the R framework is under /Library/Frameworks, and not under
> >> /Library/Frameworks/R.framework. This is analogous to
> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
> >> of libraries (instead of frameworks), not just libfoo.so.
> >> (A Mac OS framework is analogous to an R package.)
> >>
> >> Make sure '..' is not in the path supplied to '-L' and everything should
> >> work.
> >>
> >> Cheers,
> >> Dominick
> >>
> >>
> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>
> >> Hi,
> >>
> >> I made some changes available in the develop version, which should
> >> hopefully solve both issues:
> >>   * octave_end is now called on exit (via reg.finalizer: see my post
> >> on r-devel
> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
> >>   * the extra dots are removed by the sed in configure.ac, but I think
> >> we still need to figure out why these dots are there...
> >>
> >> To test:
> >>
> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
> >>
> >> Thanks.
> >>
> >> Bests,
> >> Renaud
> >>
> >> On 6 November 2013 11:15, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za
> >
> >> wrote:
> >> > Couple of questions to understand what is going on:
> >> >
> >> >   * why does R CMD config --ldflags returns these extra '..' if they
> are
> >> > incorrect?
> >> >   * why does the compilation work if the path is incorrect to R
> library
> >> > is
> >> > incorrect?
> >> >   * why removing the dots should solve the malloc error?
> >> >
> >> >
> >> >
> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
> wrote:
> >> >>
> >> >> R CMD config --ldflags
> >> >> yields
> >> >> -F/Library/Frameworks/R.framework/.. -framework R
> >> >>
> >> >> This needs to be hacked for mkoctfile to:
> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >> >> (no '..')
> >> >>
> >> >> Applying this to the github source fixes it for
> >> >> Mac OS X Mavericks provided the --no-test-load
> >> >> and octave_end tricks are used.
> >> >>
> >> >>
> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >> >>>
> >> >>> Not sure where the extra '..' would come from.
> >> >>> Are you installing the latest version from github?
> >> >>>
> >> >>> devtools::install_github('RcppOctave', 'renozao')
> >> >>>
> >> >>>
> >> >>>
> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
> >> >>> wrote:
> >> >>>>
> >> >>>> It appears that octave_end is not called at all under Mac OS X. But
> >> >>>> it
> >> >>>> is also not called under Linux! I inserted Rprintf statements to
> >> >>>> check.
> >> >>>>
> >> >>>> Perhaps the explanation is that failing to call octave_end under
> >> >>>> Linux
> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If
> this
> >> >>>> is so the Mac OS X behavior is less dangerous...
> >> >>>>
> >> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
> >> >>>> (attached)
>
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  8 10:42:06 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 8 Nov 2013 11:42:06 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
Message-ID: <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>

True :D
I thought of trying to get a neat sequence of flags without quote but
clearly did not work.
I updated the gh and myCRAN versions: they now contain your solution
for -Wl and also use mkoctfile rather than octave-config to retrieve
the include and linker flags.

If possible, can anybody please try the windows binary from myCRAN:

source('http://www.bioconductor.org/biocLite.R')
biocLite('RcppOctave', siteRepos = 'http://web.cbio.uct.ac.za/~renaud/CRAN')

Thank you.

Bests,
Renaud

On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com> wrote:
> This solution yields:
>
> -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
>
> and the linker doesn't know that the last "R" belongs to the
> -framework option.
>
> To fix, simply add the 'g' qualifier to the sed command in
> configure.ac:
>
> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
>
>
> My original solution works because the -Wl,"whatever"
> option causes mkoctfile to insert the string "whatever"
> into the linker command line without parsing. If instead
> mkoctfile used a form of exec(3) that expects tokenized
> options, the sed solution would be necessary.
>
>
>
> On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
> <renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> I changed configure.ac into:
>> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
>>
>> as I read/saw that multiple options must be comma separated.
>> This will break if the path to the R framework contains spaces though.
>> Can you please try again:
>>
>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>
>> Thanks.
>>
>> Bests,
>> Renaud
>>
>> On 6 November 2013 22:37, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>> > Nice. It is indeed a better solution than changing the flags and their
>> > values. The sed command did not work probably because I forgot to double
>> > the
>> > square brackets, which is necessary to correctly pass configure's first
>> > string evaluation.
>> > I will incorporate the change tomorrow.
>> > Thanks!
>> >
>> > Bests,
>> > Renaud
>> >
>> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
>> >>
>> >> The reason we have been hacking away at '-F' vs '-L' instead of
>> >> letting 'R CMD config' figure things out is that mkoctfile does not
>> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
>> >> the -Wl,whatever option, which simply passes whatever down to
>> >> the linker.
>> >>
>> >> I have attached a modified configure.ac that uses this option
>> >> instead of using sed to hack the output of R CMD config --ldflags.
>> >>
>> >>
>> >>
>> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <djsamperi at gmail.com>
>> >> wrote:
>> >>
>> >> Hello Renaud,
>> >>
>> >> So, this R technical issue (reg.finalizer) was the crux of the problem
>> >> all
>> >> along. Good work!
>> >>
>> >> The '..' is still there and the build still fails without my hacked
>> >> Makefile.in, but
>> >> with this change everything works (no more install memory errors).
>> >>
>> >> The '..' in the output of R CMD config --ldflags is there for a
>> >> purpose,
>> >> because
>> >> the R framework is under /Library/Frameworks, and not under
>> >> /Library/Frameworks/R.framework. This is analogous to
>> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a collection
>> >> of libraries (instead of frameworks), not just libfoo.so.
>> >> (A Mac OS framework is analogous to an R package.)
>> >>
>> >> Make sure '..' is not in the path supplied to '-L' and everything
>> >> should
>> >> work.
>> >>
>> >> Cheers,
>> >> Dominick
>> >>
>> >>
>> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>
>> >> Hi,
>> >>
>> >> I made some changes available in the develop version, which should
>> >> hopefully solve both issues:
>> >>   * octave_end is now called on exit (via reg.finalizer: see my post
>> >> on r-devel
>> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>> >>   * the extra dots are removed by the sed in configure.ac, but I think
>> >> we still need to figure out why these dots are there...
>> >>
>> >> To test:
>> >>
>> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>> >>
>> >> Thanks.
>> >>
>> >> Bests,
>> >> Renaud
>> >>
>> >> On 6 November 2013 11:15, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za>
>> >> wrote:
>> >> > Couple of questions to understand what is going on:
>> >> >
>> >> >   * why does R CMD config --ldflags returns these extra '..' if they
>> >> > are
>> >> > incorrect?
>> >> >   * why does the compilation work if the path is incorrect to R
>> >> > library
>> >> > is
>> >> > incorrect?
>> >> >   * why removing the dots should solve the malloc error?
>> >> >
>> >> >
>> >> >
>> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> R CMD config --ldflags
>> >> >> yields
>> >> >> -F/Library/Frameworks/R.framework/.. -framework R
>> >> >>
>> >> >> This needs to be hacked for mkoctfile to:
>> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
>> >> >> (no '..')
>> >> >>
>> >> >> Applying this to the github source fixes it for
>> >> >> Mac OS X Mavericks provided the --no-test-load
>> >> >> and octave_end tricks are used.
>> >> >>
>> >> >>
>> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >> >>>
>> >> >>> Not sure where the extra '..' would come from.
>> >> >>> Are you installing the latest version from github?
>> >> >>>
>> >> >>> devtools::install_github('RcppOctave', 'renozao')
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
>> >> >>> wrote:
>> >> >>>>
>> >> >>>> It appears that octave_end is not called at all under Mac OS X.
>> >> >>>> But
>> >> >>>> it
>> >> >>>> is also not called under Linux! I inserted Rprintf statements to
>> >> >>>> check.
>> >> >>>>
>> >> >>>> Perhaps the explanation is that failing to call octave_end under
>> >> >>>> Linux
>> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If
>> >> >>>> this
>> >> >>>> is so the Mac OS X behavior is less dangerous...
>> >> >>>>
>> >> >>>> If I do not use --no-test-load, I get the result in RcppOctave.log
>> >> >>>> (attached)
>
>

From djsamperi at gmail.com  Fri Nov  8 15:23:16 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 8 Nov 2013 09:23:16 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
Message-ID: <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>

The biocLite windows binary install works (provided the user has Octave in
PATH).

The github (ref='develop') install works under Linux and Mac OS X
(Mavericks).

And by increasing the "biodiversity" (number of OS's supported) a hidden
bug was
uncovered and fixed (after 100 posts!).

Cheers,
Dominick


On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> True :D
> I thought of trying to get a neat sequence of flags without quote but
> clearly did not work.
> I updated the gh and myCRAN versions: they now contain your solution
> for -Wl and also use mkoctfile rather than octave-config to retrieve
> the include and linker flags.
>
> If possible, can anybody please try the windows binary from myCRAN:
>
> source('http://www.bioconductor.org/biocLite.R')
> biocLite('RcppOctave', siteRepos = 'http://web.cbio.uct.ac.za/~renaud/CRAN
> ')
>
> Thank you.
>
> Bests,
> Renaud
>
> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com> wrote:
> > This solution yields:
> >
> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
> >
> > and the linker doesn't know that the last "R" belongs to the
> > -framework option.
> >
> > To fix, simply add the 'g' qualifier to the sed command in
> > configure.ac:
> >
> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
> >
> >
> > My original solution works because the -Wl,"whatever"
> > option causes mkoctfile to insert the string "whatever"
> > into the linker command line without parsing. If instead
> > mkoctfile used a form of exec(3) that expects tokenized
> > options, the sed solution would be necessary.
> >
> >
> >
> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
> > <renaud at mancala.cbio.uct.ac.za> wrote:
> >>
> >> I changed configure.ac into:
> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
> >>
> >> as I read/saw that multiple options must be comma separated.
> >> This will break if the path to the R framework contains spaces though.
> >> Can you please try again:
> >>
> >> install_github('RcppOctave', 'renozao', ref = 'develop')
> >>
> >> Thanks.
> >>
> >> Bests,
> >> Renaud
> >>
> >> On 6 November 2013 22:37, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za
> >
> >> wrote:
> >> > Nice. It is indeed a better solution than changing the flags and their
> >> > values. The sed command did not work probably because I forgot to
> double
> >> > the
> >> > square brackets, which is necessary to correctly pass configure's
> first
> >> > string evaluation.
> >> > I will incorporate the change tomorrow.
> >> > Thanks!
> >> >
> >> > Bests,
> >> > Renaud
> >> >
> >> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
> >> >>
> >> >> The reason we have been hacking away at '-F' vs '-L' instead of
> >> >> letting 'R CMD config' figure things out is that mkoctfile does not
> >> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
> >> >> the -Wl,whatever option, which simply passes whatever down to
> >> >> the linker.
> >> >>
> >> >> I have attached a modified configure.ac that uses this option
> >> >> instead of using sed to hack the output of R CMD config --ldflags.
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <
> djsamperi at gmail.com>
> >> >> wrote:
> >> >>
> >> >> Hello Renaud,
> >> >>
> >> >> So, this R technical issue (reg.finalizer) was the crux of the
> problem
> >> >> all
> >> >> along. Good work!
> >> >>
> >> >> The '..' is still there and the build still fails without my hacked
> >> >> Makefile.in, but
> >> >> with this change everything works (no more install memory errors).
> >> >>
> >> >> The '..' in the output of R CMD config --ldflags is there for a
> >> >> purpose,
> >> >> because
> >> >> the R framework is under /Library/Frameworks, and not under
> >> >> /Library/Frameworks/R.framework. This is analogous to
> >> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a
> collection
> >> >> of libraries (instead of frameworks), not just libfoo.so.
> >> >> (A Mac OS framework is analogous to an R package.)
> >> >>
> >> >> Make sure '..' is not in the path supplied to '-L' and everything
> >> >> should
> >> >> work.
> >> >>
> >> >> Cheers,
> >> >> Dominick
> >> >>
> >> >>
> >> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> I made some changes available in the develop version, which should
> >> >> hopefully solve both issues:
> >> >>   * octave_end is now called on exit (via reg.finalizer: see my post
> >> >> on r-devel
> >> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
> >> >>   * the extra dots are removed by the sed in configure.ac, but I
> think
> >> >> we still need to figure out why these dots are there...
> >> >>
> >> >> To test:
> >> >>
> >> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
> >> >>
> >> >> Thanks.
> >> >>
> >> >> Bests,
> >> >> Renaud
> >> >>
> >> >> On 6 November 2013 11:15, Renaud Gaujoux
> >> >> <renaud at mancala.cbio.uct.ac.za>
> >> >> wrote:
> >> >> > Couple of questions to understand what is going on:
> >> >> >
> >> >> >   * why does R CMD config --ldflags returns these extra '..' if
> they
> >> >> > are
> >> >> > incorrect?
> >> >> >   * why does the compilation work if the path is incorrect to R
> >> >> > library
> >> >> > is
> >> >> > incorrect?
> >> >> >   * why removing the dots should solve the malloc error?
> >> >> >
> >> >> >
> >> >> >
> >> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> R CMD config --ldflags
> >> >> >> yields
> >> >> >> -F/Library/Frameworks/R.framework/.. -framework R
> >> >> >>
> >> >> >> This needs to be hacked for mkoctfile to:
> >> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >> >> >> (no '..')
> >> >> >>
> >> >> >> Applying this to the github source fixes it for
> >> >> >> Mac OS X Mavericks provided the --no-test-load
> >> >> >> and octave_end tricks are used.
> >> >> >>
> >> >> >>
> >> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >> >> >>>
> >> >> >>> Not sure where the extra '..' would come from.
> >> >> >>> Are you installing the latest version from github?
> >> >> >>>
> >> >> >>> devtools::install_github('RcppOctave', 'renozao')
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
> >> >> >>> wrote:
> >> >> >>>>
> >> >> >>>> It appears that octave_end is not called at all under Mac OS X.
> >> >> >>>> But
> >> >> >>>> it
> >> >> >>>> is also not called under Linux! I inserted Rprintf statements to
> >> >> >>>> check.
> >> >> >>>>
> >> >> >>>> Perhaps the explanation is that failing to call octave_end under
> >> >> >>>> Linux
> >> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If
> >> >> >>>> this
> >> >> >>>> is so the Mac OS X behavior is less dangerous...
> >> >> >>>>
> >> >> >>>> If I do not use --no-test-load, I get the result in
> RcppOctave.log
> >> >> >>>> (attached)
> >
> >
>
-------------- next part --------------
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From renaud at mancala.cbio.uct.ac.za  Fri Nov  8 17:33:51 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 8 Nov 2013 18:33:51 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
Message-ID: <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>

Nice. Many thanks!

... and along the way we, or at least I, learnt that the hooks
.onUnload and .onDetach are actually not called when R quits and that
required cleanup procedures must be registered via reg.finalizer to be
sure they are called.

What is left:
  * check if a Mac binary package works fine on machine different than
the one it was built on.
  * get CRAN building machines geared with Octave so that binary
packages are available from CRAN. I will follow up with the CRAN
maintainer on this.

Bests,
Renaud



On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
> The biocLite windows binary install works (provided the user has Octave in
> PATH).
>
> The github (ref='develop') install works under Linux and Mac OS X
> (Mavericks).
>
> And by increasing the "biodiversity" (number of OS's supported) a hidden bug
> was
> uncovered and fixed (after 100 posts!).
>
> Cheers,
> Dominick
>
>
> On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux
> <renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> True :D
>> I thought of trying to get a neat sequence of flags without quote but
>> clearly did not work.
>> I updated the gh and myCRAN versions: they now contain your solution
>> for -Wl and also use mkoctfile rather than octave-config to retrieve
>> the include and linker flags.
>>
>> If possible, can anybody please try the windows binary from myCRAN:
>>
>> source('http://www.bioconductor.org/biocLite.R')
>> biocLite('RcppOctave', siteRepos =
>> 'http://web.cbio.uct.ac.za/~renaud/CRAN')
>>
>> Thank you.
>>
>> Bests,
>> Renaud
>>
>> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com> wrote:
>> > This solution yields:
>> >
>> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
>> >
>> > and the linker doesn't know that the last "R" belongs to the
>> > -framework option.
>> >
>> > To fix, simply add the 'g' qualifier to the sed command in
>> > configure.ac:
>> >
>> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
>> >
>> >
>> > My original solution works because the -Wl,"whatever"
>> > option causes mkoctfile to insert the string "whatever"
>> > into the linker command line without parsing. If instead
>> > mkoctfile used a form of exec(3) that expects tokenized
>> > options, the sed solution would be necessary.
>> >
>> >
>> >
>> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
>> > <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>
>> >> I changed configure.ac into:
>> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
>> >>
>> >> as I read/saw that multiple options must be comma separated.
>> >> This will break if the path to the R framework contains spaces though.
>> >> Can you please try again:
>> >>
>> >> install_github('RcppOctave', 'renozao', ref = 'develop')
>> >>
>> >> Thanks.
>> >>
>> >> Bests,
>> >> Renaud
>> >>
>> >> On 6 November 2013 22:37, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za>
>> >> wrote:
>> >> > Nice. It is indeed a better solution than changing the flags and
>> >> > their
>> >> > values. The sed command did not work probably because I forgot to
>> >> > double
>> >> > the
>> >> > square brackets, which is necessary to correctly pass configure's
>> >> > first
>> >> > string evaluation.
>> >> > I will incorporate the change tomorrow.
>> >> > Thanks!
>> >> >
>> >> > Bests,
>> >> > Renaud
>> >> >
>> >> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
>> >> >>
>> >> >> The reason we have been hacking away at '-F' vs '-L' instead of
>> >> >> letting 'R CMD config' figure things out is that mkoctfile does not
>> >> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
>> >> >> the -Wl,whatever option, which simply passes whatever down to
>> >> >> the linker.
>> >> >>
>> >> >> I have attached a modified configure.ac that uses this option
>> >> >> instead of using sed to hack the output of R CMD config --ldflags.
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi
>> >> >> <djsamperi at gmail.com>
>> >> >> wrote:
>> >> >>
>> >> >> Hello Renaud,
>> >> >>
>> >> >> So, this R technical issue (reg.finalizer) was the crux of the
>> >> >> problem
>> >> >> all
>> >> >> along. Good work!
>> >> >>
>> >> >> The '..' is still there and the build still fails without my hacked
>> >> >> Makefile.in, but
>> >> >> with this change everything works (no more install memory errors).
>> >> >>
>> >> >> The '..' in the output of R CMD config --ldflags is there for a
>> >> >> purpose,
>> >> >> because
>> >> >> the R framework is under /Library/Frameworks, and not under
>> >> >> /Library/Frameworks/R.framework. This is analogous to
>> >> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a
>> >> >> collection
>> >> >> of libraries (instead of frameworks), not just libfoo.so.
>> >> >> (A Mac OS framework is analogous to an R package.)
>> >> >>
>> >> >> Make sure '..' is not in the path supplied to '-L' and everything
>> >> >> should
>> >> >> work.
>> >> >>
>> >> >> Cheers,
>> >> >> Dominick
>> >> >>
>> >> >>
>> >> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
>> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >> >>
>> >> >> Hi,
>> >> >>
>> >> >> I made some changes available in the develop version, which should
>> >> >> hopefully solve both issues:
>> >> >>   * octave_end is now called on exit (via reg.finalizer: see my post
>> >> >> on r-devel
>> >> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>> >> >>   * the extra dots are removed by the sed in configure.ac, but I
>> >> >> think
>> >> >> we still need to figure out why these dots are there...
>> >> >>
>> >> >> To test:
>> >> >>
>> >> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>> >> >>
>> >> >> Thanks.
>> >> >>
>> >> >> Bests,
>> >> >> Renaud
>> >> >>
>> >> >> On 6 November 2013 11:15, Renaud Gaujoux
>> >> >> <renaud at mancala.cbio.uct.ac.za>
>> >> >> wrote:
>> >> >> > Couple of questions to understand what is going on:
>> >> >> >
>> >> >> >   * why does R CMD config --ldflags returns these extra '..' if
>> >> >> > they
>> >> >> > are
>> >> >> > incorrect?
>> >> >> >   * why does the compilation work if the path is incorrect to R
>> >> >> > library
>> >> >> > is
>> >> >> > incorrect?
>> >> >> >   * why removing the dots should solve the malloc error?
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> R CMD config --ldflags
>> >> >> >> yields
>> >> >> >> -F/Library/Frameworks/R.framework/.. -framework R
>> >> >> >>
>> >> >> >> This needs to be hacked for mkoctfile to:
>> >> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
>> >> >> >> (no '..')
>> >> >> >>
>> >> >> >> Applying this to the github source fixes it for
>> >> >> >> Mac OS X Mavericks provided the --no-test-load
>> >> >> >> and octave_end tricks are used.
>> >> >> >>
>> >> >> >>
>> >> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>> >> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >> >> >>>
>> >> >> >>> Not sure where the extra '..' would come from.
>> >> >> >>> Are you installing the latest version from github?
>> >> >> >>>
>> >> >> >>> devtools::install_github('RcppOctave', 'renozao')
>> >> >> >>>
>> >> >> >>>
>> >> >> >>>
>> >> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
>> >> >> >>> wrote:
>> >> >> >>>>
>> >> >> >>>> It appears that octave_end is not called at all under Mac OS X.
>> >> >> >>>> But
>> >> >> >>>> it
>> >> >> >>>> is also not called under Linux! I inserted Rprintf statements
>> >> >> >>>> to
>> >> >> >>>> check.
>> >> >> >>>>
>> >> >> >>>> Perhaps the explanation is that failing to call octave_end
>> >> >> >>>> under
>> >> >> >>>> Linux
>> >> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X?
>> >> >> >>>> If
>> >> >> >>>> this
>> >> >> >>>> is so the Mac OS X behavior is less dangerous...
>> >> >> >>>>
>> >> >> >>>> If I do not use --no-test-load, I get the result in
>> >> >> >>>> RcppOctave.log
>> >> >> >>>> (attached)
>> >
>> >
>
>

From renaud at mancala.cbio.uct.ac.za  Fri Nov  8 23:53:33 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sat, 9 Nov 2013 00:53:33 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
Message-ID: <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>

Ah, I forgot something:
  * running a full R CMD check --as-cran on Mac?
:D

On 8 November 2013 18:33, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> Nice. Many thanks!
>
> ... and along the way we, or at least I, learnt that the hooks
> .onUnload and .onDetach are actually not called when R quits and that
> required cleanup procedures must be registered via reg.finalizer to be
> sure they are called.
>
> What is left:
>   * check if a Mac binary package works fine on machine different than
> the one it was built on.
>   * get CRAN building machines geared with Octave so that binary
> packages are available from CRAN. I will follow up with the CRAN
> maintainer on this.
>
> Bests,
> Renaud
>
>
>
> On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
>> The biocLite windows binary install works (provided the user has Octave in
>> PATH).
>>
>> The github (ref='develop') install works under Linux and Mac OS X
>> (Mavericks).
>>
>> And by increasing the "biodiversity" (number of OS's supported) a hidden bug
>> was
>> uncovered and fixed (after 100 posts!).
>>
>> Cheers,
>> Dominick
>>
>>
>> On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux
>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>> True :D
>>> I thought of trying to get a neat sequence of flags without quote but
>>> clearly did not work.
>>> I updated the gh and myCRAN versions: they now contain your solution
>>> for -Wl and also use mkoctfile rather than octave-config to retrieve
>>> the include and linker flags.
>>>
>>> If possible, can anybody please try the windows binary from myCRAN:
>>>
>>> source('http://www.bioconductor.org/biocLite.R')
>>> biocLite('RcppOctave', siteRepos =
>>> 'http://web.cbio.uct.ac.za/~renaud/CRAN')
>>>
>>> Thank you.
>>>
>>> Bests,
>>> Renaud
>>>
>>> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com> wrote:
>>> > This solution yields:
>>> >
>>> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
>>> >
>>> > and the linker doesn't know that the last "R" belongs to the
>>> > -framework option.
>>> >
>>> > To fix, simply add the 'g' qualifier to the sed command in
>>> > configure.ac:
>>> >
>>> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
>>> >
>>> >
>>> > My original solution works because the -Wl,"whatever"
>>> > option causes mkoctfile to insert the string "whatever"
>>> > into the linker command line without parsing. If instead
>>> > mkoctfile used a form of exec(3) that expects tokenized
>>> > options, the sed solution would be necessary.
>>> >
>>> >
>>> >
>>> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
>>> > <renaud at mancala.cbio.uct.ac.za> wrote:
>>> >>
>>> >> I changed configure.ac into:
>>> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
>>> >>
>>> >> as I read/saw that multiple options must be comma separated.
>>> >> This will break if the path to the R framework contains spaces though.
>>> >> Can you please try again:
>>> >>
>>> >> install_github('RcppOctave', 'renozao', ref = 'develop')
>>> >>
>>> >> Thanks.
>>> >>
>>> >> Bests,
>>> >> Renaud
>>> >>
>>> >> On 6 November 2013 22:37, Renaud Gaujoux
>>> >> <renaud at mancala.cbio.uct.ac.za>
>>> >> wrote:
>>> >> > Nice. It is indeed a better solution than changing the flags and
>>> >> > their
>>> >> > values. The sed command did not work probably because I forgot to
>>> >> > double
>>> >> > the
>>> >> > square brackets, which is necessary to correctly pass configure's
>>> >> > first
>>> >> > string evaluation.
>>> >> > I will incorporate the change tomorrow.
>>> >> > Thanks!
>>> >> >
>>> >> > Bests,
>>> >> > Renaud
>>> >> >
>>> >> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
>>> >> >>
>>> >> >> The reason we have been hacking away at '-F' vs '-L' instead of
>>> >> >> letting 'R CMD config' figure things out is that mkoctfile does not
>>> >> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
>>> >> >> the -Wl,whatever option, which simply passes whatever down to
>>> >> >> the linker.
>>> >> >>
>>> >> >> I have attached a modified configure.ac that uses this option
>>> >> >> instead of using sed to hack the output of R CMD config --ldflags.
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi
>>> >> >> <djsamperi at gmail.com>
>>> >> >> wrote:
>>> >> >>
>>> >> >> Hello Renaud,
>>> >> >>
>>> >> >> So, this R technical issue (reg.finalizer) was the crux of the
>>> >> >> problem
>>> >> >> all
>>> >> >> along. Good work!
>>> >> >>
>>> >> >> The '..' is still there and the build still fails without my hacked
>>> >> >> Makefile.in, but
>>> >> >> with this change everything works (no more install memory errors).
>>> >> >>
>>> >> >> The '..' in the output of R CMD config --ldflags is there for a
>>> >> >> purpose,
>>> >> >> because
>>> >> >> the R framework is under /Library/Frameworks, and not under
>>> >> >> /Library/Frameworks/R.framework. This is analogous to
>>> >> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a
>>> >> >> collection
>>> >> >> of libraries (instead of frameworks), not just libfoo.so.
>>> >> >> (A Mac OS framework is analogous to an R package.)
>>> >> >>
>>> >> >> Make sure '..' is not in the path supplied to '-L' and everything
>>> >> >> should
>>> >> >> work.
>>> >> >>
>>> >> >> Cheers,
>>> >> >> Dominick
>>> >> >>
>>> >> >>
>>> >> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
>>> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>>> >> >>
>>> >> >> Hi,
>>> >> >>
>>> >> >> I made some changes available in the develop version, which should
>>> >> >> hopefully solve both issues:
>>> >> >>   * octave_end is now called on exit (via reg.finalizer: see my post
>>> >> >> on r-devel
>>> >> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
>>> >> >>   * the extra dots are removed by the sed in configure.ac, but I
>>> >> >> think
>>> >> >> we still need to figure out why these dots are there...
>>> >> >>
>>> >> >> To test:
>>> >> >>
>>> >> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
>>> >> >>
>>> >> >> Thanks.
>>> >> >>
>>> >> >> Bests,
>>> >> >> Renaud
>>> >> >>
>>> >> >> On 6 November 2013 11:15, Renaud Gaujoux
>>> >> >> <renaud at mancala.cbio.uct.ac.za>
>>> >> >> wrote:
>>> >> >> > Couple of questions to understand what is going on:
>>> >> >> >
>>> >> >> >   * why does R CMD config --ldflags returns these extra '..' if
>>> >> >> > they
>>> >> >> > are
>>> >> >> > incorrect?
>>> >> >> >   * why does the compilation work if the path is incorrect to R
>>> >> >> > library
>>> >> >> > is
>>> >> >> > incorrect?
>>> >> >> >   * why removing the dots should solve the malloc error?
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> R CMD config --ldflags
>>> >> >> >> yields
>>> >> >> >> -F/Library/Frameworks/R.framework/.. -framework R
>>> >> >> >>
>>> >> >> >> This needs to be hacked for mkoctfile to:
>>> >> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
>>> >> >> >> (no '..')
>>> >> >> >>
>>> >> >> >> Applying this to the github source fixes it for
>>> >> >> >> Mac OS X Mavericks provided the --no-test-load
>>> >> >> >> and octave_end tricks are used.
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
>>> >> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>>> >> >> >>>
>>> >> >> >>> Not sure where the extra '..' would come from.
>>> >> >> >>> Are you installing the latest version from github?
>>> >> >> >>>
>>> >> >> >>> devtools::install_github('RcppOctave', 'renozao')
>>> >> >> >>>
>>> >> >> >>>
>>> >> >> >>>
>>> >> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
>>> >> >> >>> wrote:
>>> >> >> >>>>
>>> >> >> >>>> It appears that octave_end is not called at all under Mac OS X.
>>> >> >> >>>> But
>>> >> >> >>>> it
>>> >> >> >>>> is also not called under Linux! I inserted Rprintf statements
>>> >> >> >>>> to
>>> >> >> >>>> check.
>>> >> >> >>>>
>>> >> >> >>>> Perhaps the explanation is that failing to call octave_end
>>> >> >> >>>> under
>>> >> >> >>>> Linux
>>> >> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X?
>>> >> >> >>>> If
>>> >> >> >>>> this
>>> >> >> >>>> is so the Mac OS X behavior is less dangerous...
>>> >> >> >>>>
>>> >> >> >>>> If I do not use --no-test-load, I get the result in
>>> >> >> >>>> RcppOctave.log
>>> >> >> >>>> (attached)
>>> >
>>> >
>>
>>

From djsamperi at gmail.com  Sat Nov  9 02:20:20 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 8 Nov 2013 20:20:20 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
 <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
Message-ID: <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>

I've attached the output of R CMD check --as-cran.
No errors, just a few NOTE's. (Suggested package
RUnit must be installed.)

There has been a lot of discussion about "NOTE"
on r-revel, and it is not clear to me if this is considered
to be an error or just a warning. I don't know if CRAN
will accept a package with NOTE's...



On Fri, Nov 8, 2013 at 5:53 PM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> Ah, I forgot something:
>   * running a full R CMD check --as-cran on Mac?
> :D
>
> On 8 November 2013 18:33, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
> > Nice. Many thanks!
> >
> > ... and along the way we, or at least I, learnt that the hooks
> > .onUnload and .onDetach are actually not called when R quits and that
> > required cleanup procedures must be registered via reg.finalizer to be
> > sure they are called.
> >
> > What is left:
> >   * check if a Mac binary package works fine on machine different than
> > the one it was built on.
> >   * get CRAN building machines geared with Octave so that binary
> > packages are available from CRAN. I will follow up with the CRAN
> > maintainer on this.
> >
> > Bests,
> > Renaud
> >
> >
> >
> > On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
> >> The biocLite windows binary install works (provided the user has Octave
> in
> >> PATH).
> >>
> >> The github (ref='develop') install works under Linux and Mac OS X
> >> (Mavericks).
> >>
> >> And by increasing the "biodiversity" (number of OS's supported) a
> hidden bug
> >> was
> >> uncovered and fixed (after 100 posts!).
> >>
> >> Cheers,
> >> Dominick
> >>
> >>
> >> On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux
> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>>
> >>> True :D
> >>> I thought of trying to get a neat sequence of flags without quote but
> >>> clearly did not work.
> >>> I updated the gh and myCRAN versions: they now contain your solution
> >>> for -Wl and also use mkoctfile rather than octave-config to retrieve
> >>> the include and linker flags.
> >>>
> >>> If possible, can anybody please try the windows binary from myCRAN:
> >>>
> >>> source('http://www.bioconductor.org/biocLite.R')
> >>> biocLite('RcppOctave', siteRepos =
> >>> 'http://web.cbio.uct.ac.za/~renaud/CRAN')
> >>>
> >>> Thank you.
> >>>
> >>> Bests,
> >>> Renaud
> >>>
> >>> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com>
> wrote:
> >>> > This solution yields:
> >>> >
> >>> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
> >>> >
> >>> > and the linker doesn't know that the last "R" belongs to the
> >>> > -framework option.
> >>> >
> >>> > To fix, simply add the 'g' qualifier to the sed command in
> >>> > configure.ac:
> >>> >
> >>> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
> >>> >
> >>> >
> >>> > My original solution works because the -Wl,"whatever"
> >>> > option causes mkoctfile to insert the string "whatever"
> >>> > into the linker command line without parsing. If instead
> >>> > mkoctfile used a form of exec(3) that expects tokenized
> >>> > options, the sed solution would be necessary.
> >>> >
> >>> >
> >>> >
> >>> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
> >>> > <renaud at mancala.cbio.uct.ac.za> wrote:
> >>> >>
> >>> >> I changed configure.ac into:
> >>> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
> >>> >>
> >>> >> as I read/saw that multiple options must be comma separated.
> >>> >> This will break if the path to the R framework contains spaces
> though.
> >>> >> Can you please try again:
> >>> >>
> >>> >> install_github('RcppOctave', 'renozao', ref = 'develop')
> >>> >>
> >>> >> Thanks.
> >>> >>
> >>> >> Bests,
> >>> >> Renaud
> >>> >>
> >>> >> On 6 November 2013 22:37, Renaud Gaujoux
> >>> >> <renaud at mancala.cbio.uct.ac.za>
> >>> >> wrote:
> >>> >> > Nice. It is indeed a better solution than changing the flags and
> >>> >> > their
> >>> >> > values. The sed command did not work probably because I forgot to
> >>> >> > double
> >>> >> > the
> >>> >> > square brackets, which is necessary to correctly pass configure's
> >>> >> > first
> >>> >> > string evaluation.
> >>> >> > I will incorporate the change tomorrow.
> >>> >> > Thanks!
> >>> >> >
> >>> >> > Bests,
> >>> >> > Renaud
> >>> >> >
> >>> >> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
> >>> >> >>
> >>> >> >> The reason we have been hacking away at '-F' vs '-L' instead of
> >>> >> >> letting 'R CMD config' figure things out is that mkoctfile does
> not
> >>> >> >> know about R frameworks ('-F' is invalid). But mkoctfile does
> have
> >>> >> >> the -Wl,whatever option, which simply passes whatever down to
> >>> >> >> the linker.
> >>> >> >>
> >>> >> >> I have attached a modified configure.ac that uses this option
> >>> >> >> instead of using sed to hack the output of R CMD config
> --ldflags.
> >>> >> >>
> >>> >> >>
> >>> >> >>
> >>> >> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi
> >>> >> >> <djsamperi at gmail.com>
> >>> >> >> wrote:
> >>> >> >>
> >>> >> >> Hello Renaud,
> >>> >> >>
> >>> >> >> So, this R technical issue (reg.finalizer) was the crux of the
> >>> >> >> problem
> >>> >> >> all
> >>> >> >> along. Good work!
> >>> >> >>
> >>> >> >> The '..' is still there and the build still fails without my
> hacked
> >>> >> >> Makefile.in, but
> >>> >> >> with this change everything works (no more install memory
> errors).
> >>> >> >>
> >>> >> >> The '..' in the output of R CMD config --ldflags is there for a
> >>> >> >> purpose,
> >>> >> >> because
> >>> >> >> the R framework is under /Library/Frameworks, and not under
> >>> >> >> /Library/Frameworks/R.framework. This is analogous to
> >>> >> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a
> >>> >> >> collection
> >>> >> >> of libraries (instead of frameworks), not just libfoo.so.
> >>> >> >> (A Mac OS framework is analogous to an R package.)
> >>> >> >>
> >>> >> >> Make sure '..' is not in the path supplied to '-L' and everything
> >>> >> >> should
> >>> >> >> work.
> >>> >> >>
> >>> >> >> Cheers,
> >>> >> >> Dominick
> >>> >> >>
> >>> >> >>
> >>> >> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
> >>> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>> >> >>
> >>> >> >> Hi,
> >>> >> >>
> >>> >> >> I made some changes available in the develop version, which
> should
> >>> >> >> hopefully solve both issues:
> >>> >> >>   * octave_end is now called on exit (via reg.finalizer: see my
> post
> >>> >> >> on r-devel
> >>> >> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html
> )
> >>> >> >>   * the extra dots are removed by the sed in configure.ac, but I
> >>> >> >> think
> >>> >> >> we still need to figure out why these dots are there...
> >>> >> >>
> >>> >> >> To test:
> >>> >> >>
> >>> >> >> devtools::install_github('RcppOctave', 'renozao', ref =
> 'develop')
> >>> >> >>
> >>> >> >> Thanks.
> >>> >> >>
> >>> >> >> Bests,
> >>> >> >> Renaud
> >>> >> >>
> >>> >> >> On 6 November 2013 11:15, Renaud Gaujoux
> >>> >> >> <renaud at mancala.cbio.uct.ac.za>
> >>> >> >> wrote:
> >>> >> >> > Couple of questions to understand what is going on:
> >>> >> >> >
> >>> >> >> >   * why does R CMD config --ldflags returns these extra '..' if
> >>> >> >> > they
> >>> >> >> > are
> >>> >> >> > incorrect?
> >>> >> >> >   * why does the compilation work if the path is incorrect to R
> >>> >> >> > library
> >>> >> >> > is
> >>> >> >> > incorrect?
> >>> >> >> >   * why removing the dots should solve the malloc error?
> >>> >> >> >
> >>> >> >> >
> >>> >> >> >
> >>> >> >> > On 5 November 2013 16:38, Dominick Samperi <
> djsamperi at gmail.com>
> >>> >> >> > wrote:
> >>> >> >> >>
> >>> >> >> >> R CMD config --ldflags
> >>> >> >> >> yields
> >>> >> >> >> -F/Library/Frameworks/R.framework/.. -framework R
> >>> >> >> >>
> >>> >> >> >> This needs to be hacked for mkoctfile to:
> >>> >> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >>> >> >> >> (no '..')
> >>> >> >> >>
> >>> >> >> >> Applying this to the github source fixes it for
> >>> >> >> >> Mac OS X Mavericks provided the --no-test-load
> >>> >> >> >> and octave_end tricks are used.
> >>> >> >> >>
> >>> >> >> >>
> >>> >> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >>> >> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>> >> >> >>>
> >>> >> >> >>> Not sure where the extra '..' would come from.
> >>> >> >> >>> Are you installing the latest version from github?
> >>> >> >> >>>
> >>> >> >> >>> devtools::install_github('RcppOctave', 'renozao')
> >>> >> >> >>>
> >>> >> >> >>>
> >>> >> >> >>>
> >>> >> >> >>> On 2 November 2013 07:00, Dominick Samperi <
> djsamperi at gmail.com>
> >>> >> >> >>> wrote:
> >>> >> >> >>>>
> >>> >> >> >>>> It appears that octave_end is not called at all under Mac
> OS X.
> >>> >> >> >>>> But
> >>> >> >> >>>> it
> >>> >> >> >>>> is also not called under Linux! I inserted Rprintf
> statements
> >>> >> >> >>>> to
> >>> >> >> >>>> check.
> >>> >> >> >>>>
> >>> >> >> >>>> Perhaps the explanation is that failing to call octave_end
> >>> >> >> >>>> under
> >>> >> >> >>>> Linux
> >>> >> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS
> X?
> >>> >> >> >>>> If
> >>> >> >> >>>> this
> >>> >> >> >>>> is so the Mac OS X behavior is less dangerous...
> >>> >> >> >>>>
> >>> >> >> >>>> If I do not use --no-test-load, I get the result in
> >>> >> >> >>>> RcppOctave.log
> >>> >> >> >>>> (attached)
> >>> >
> >>> >
> >>
> >>
>
-------------- next part --------------
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URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20131108/96587398/attachment-0001.html>
-------------- next part --------------
* using log directory ?/Users/dsamperi/Downloads/RcppOctave.Rcheck?
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* checking for file ?RcppOctave/DESCRIPTION? ... OK
* checking extension type ... Package
* this is package ?RcppOctave? version ?0.13.3?
* checking CRAN incoming feasibility ... OK
Maintainer: ?Renaud Gaujoux <renaud at tx.technion.ac.il>?
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: ?knitr? ?bibtex?
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .gitignore
  .project
  .settings
These were most likely included in error. See section ?Package
structure? in the ?Writing R Extensions? manual.

CRAN-pack knows about all of these
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ?RcppOctave? can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files found at top level:
  ?config.log? ?config.status? ?man-roxygen? ?pkg.Rproj? ?staticdocs?
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... NOTE
Package has both ?src/Makevars.in? and ?src/Makevars?.
Installation with --no-configure' is unlikely to work.  If you intended
?src/Makevars? to be used on Windows, rename it to ?src/Makevars.win?
otherwise remove it.  If ?configure? created ?src/Makevars?, you need a
?cleanup? script.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ?inst/doc? ... OK
* checking installed files from ?inst/doc? ... OK
* checking files in ?vignettes? ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ?doRUnit.R?
 OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ?/Users/dsamperi/Downloads/RcppOctave.Rcheck/00check.log?
for details.


From renaud at mancala.cbio.uct.ac.za  Sat Nov  9 08:21:20 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sat, 9 Nov 2013 09:21:20 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
 <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
 <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>
Message-ID: <CAHavPHE_m4iN21kkRAYai6ksb6-KsqgVvQrVLvk=JBkZ0gnUuA@mail.gmail.com>

This NOTEs won't pass CRAN policy, but should really not appear. Did you
run the check directly on the source tar.gz file or on the guthub directory
where you tested compilation?

Could you please try checking with all the suggested packages installed,
otherwise unit tests will not run. It's actually strange that no error was
thrown ar this step.
Thanks.

Bests,
Renaud


On Saturday, November 9, 2013, Dominick Samperi wrote:

> I've attached the output of R CMD check --as-cran.
> No errors, just a few NOTE's. (Suggested package
> RUnit must be installed.)
>
> There has been a lot of discussion about "NOTE"
> on r-revel, and it is not clear to me if this is considered
> to be an error or just a warning. I don't know if CRAN
> will accept a package with NOTE's...
>
>
>
> On Fri, Nov 8, 2013 at 5:53 PM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
> Ah, I forgot something:
>   * running a full R CMD check --as-cran on Mac?
> :D
>
> On 8 November 2013 18:33, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
> > Nice. Many thanks!
> >
> > ... and along the way we, or at least I, learnt that the hooks
> > .onUnload and .onDetach are actually not called when R quits and that
> > required cleanup procedures must be registered via reg.finalizer to be
> > sure they are called.
> >
> > What is left:
> >   * check if a Mac binary package works fine on machine different than
> > the one it was built on.
> >   * get CRAN building machines geared with Octave so that binary
> > packages are available from CRAN. I will follow up with the CRAN
> > maintainer on this.
> >
> > Bests,
> > Renaud
> >
> >
> >
> > On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
> >> The biocLite windows binary install works (provided the user has Octave
> in
> >> PATH).
> >>
> >> The github (ref='develop') install works under Linux and Mac OS X
> >> (Mavericks).
> >>
> >> And by increasing the "biodiversity" (number of OS's supported) a
> hidden bug
> >> was
> >> uncovered and fixed (after 100 posts!).
> >>
> >> Cheers,
> >> Dominick
> >>
> >>
> >> On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux
> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >>>
> >>> True :D
> >>> I thought of trying to get a neat sequence of flags without quote but
> >>> clearly did not work.
> >>> I updated the gh and myCRAN versions: they now contain your solution
> >>> for -Wl and also use mkoctfile rather than octave-config to retrieve
> >>> the include and linker flags.
> >>>
> >>> If possible, can anybody please try the windows binary from myCRAN:
> >>>
> >>> source('http://www.bioconductor.org/biocLite.R')
> >>> biocLite('RcppOctave', siteRepos =
> >>> 'http://web.cbio.uct.ac.za/~renaud/CRAN')
> >>>
> >>> Thank you.
> >>>
> >>> Bests,
> >>> Renaud
> >>>
> >>> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com>
> wrote:
> >>> > This solution yields:
> >>> >
> >>> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
> >>> >
> >>> > and the linker doesn't know that the last "R" belongs to the
> >>> > -framework option.
> >>> >
> >>> > To fix, simply add the 'g' qualifier to the sed command in
> >>> > configure.ac:
> >>> >
> >>> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
> >>> >
> >>> >
> >>> > My original solution works because the -Wl,"whatever"
> >>> > option causes mkoctfile to insert the string "whatever"
> >>> > into the linker command line without parsing. If instead
> >>> > mkoctfile used a form of exec(3) that expects tokenized
> >>> > options, the sed solution would be necessary.
> >>> >
> >>> >
> >>> >
> >>> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
> >>> > <renaud at mancala.cbio.uct.ac.za> wrote:
> >>> >>
> >>> >> I changed configure.ac into:
> >>> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
> >>> >>
> >>> >>
>
>
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From djsamperi at gmail.com  Sat Nov  9 22:13:06 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Sat, 9 Nov 2013 16:13:06 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHE_m4iN21kkRAYai6ksb6-KsqgVvQrVLvk=JBkZ0gnUuA@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
 <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
 <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>
 <CAHavPHE_m4iN21kkRAYai6ksb6-KsqgVvQrVLvk=JBkZ0gnUuA@mail.gmail.com>
Message-ID: <CADUbQ5j6rAsvvQH3E6XB6wcPGE5b3CccNq-3=_gi2k8_40aY9g@mail.gmail.com>

With all suggested packages installed I managed to get R CMD check --as-cran
to run clean (no errors, warnings, or notes), but a few "non-standard"
directories
had to be removed, cleanup had to be run explicitly, and RcppOctave.Rnw had
to be modified to use tryCatch instead of try. The attached shell script
was used
to generate the clean check.


On Sat, Nov 9, 2013 at 2:21 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> This NOTEs won't pass CRAN policy, but should really not appear. Did you
> run the check directly on the source tar.gz file or on the guthub directory
> where you tested compilation?
>
> Could you please try checking with all the suggested packages installed,
> otherwise unit tests will not run. It's actually strange that no error
> was thrown ar this step.
> Thanks.
>
> Bests,
> Renaud
>
>
> On Saturday, November 9, 2013, Dominick Samperi wrote:
>
>> I've attached the output of R CMD check --as-cran.
>> No errors, just a few NOTE's. (Suggested package
>> RUnit must be installed.)
>>
>> There has been a lot of discussion about "NOTE"
>> on r-revel, and it is not clear to me if this is considered
>> to be an error or just a warning. I don't know if CRAN
>> will accept a package with NOTE's...
>>
>>
>>
>> On Fri, Nov 8, 2013 at 5:53 PM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> Ah, I forgot something:
>>   * running a full R CMD check --as-cran on Mac?
>> :D
>>
>> On 8 November 2013 18:33, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>> > Nice. Many thanks!
>> >
>> > ... and along the way we, or at least I, learnt that the hooks
>> > .onUnload and .onDetach are actually not called when R quits and that
>> > required cleanup procedures must be registered via reg.finalizer to be
>> > sure they are called.
>> >
>> > What is left:
>> >   * check if a Mac binary package works fine on machine different than
>> > the one it was built on.
>> >   * get CRAN building machines geared with Octave so that binary
>> > packages are available from CRAN. I will follow up with the CRAN
>> > maintainer on this.
>> >
>> > Bests,
>> > Renaud
>> >
>> >
>> >
>> > On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
>> >> The biocLite windows binary install works (provided the user has
>> Octave in
>> >> PATH).
>> >>
>> >> The github (ref='develop') install works under Linux and Mac OS X
>> >> (Mavericks).
>> >>
>> >> And by increasing the "biodiversity" (number of OS's supported) a
>> hidden bug
>> >> was
>> >> uncovered and fixed (after 100 posts!).
>> >>
>> >> Cheers,
>> >> Dominick
>> >>
>> >>
>> >> On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux
>> >> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>>
>> >>> True :D
>> >>> I thought of trying to get a neat sequence of flags without quote but
>> >>> clearly did not work.
>> >>> I updated the gh and myCRAN versions: they now contain your solution
>> >>> for -Wl and also use mkoctfile rather than octave-config to retrieve
>> >>> the include and linker flags.
>> >>>
>> >>> If possible, can anybody please try the windows binary from myCRAN:
>> >>>
>> >>> source('http://www.bioconductor.org/biocLite.R')
>> >>> biocLite('RcppOctave', siteRepos =
>> >>> 'http://web.cbio.uct.ac.za/~renaud/CRAN')
>> >>>
>> >>> Thank you.
>> >>>
>> >>> Bests,
>> >>> Renaud
>> >>>
>> >>> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com>
>> wrote:
>> >>> > This solution yields:
>> >>> >
>> >>> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
>> >>> >
>> >>> > and the linker doesn't know that the last "R" belongs to the
>> >>> > -framework option.
>> >>> >
>> >>> > To fix, simply add the 'g' qualifier to the sed command in
>> >>> > configure.ac:
>> >>> >
>> >>> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
>> >>> >
>> >>> >
>> >>> > My original solution works because the -Wl,"whatever"
>> >>> > option causes mkoctfile to insert the string "whatever"
>> >>> > into the linker command line without parsing. If instead
>> >>> > mkoctfile used a form of exec(3) that expects tokenized
>> >>> > options, the sed solution would be necessary.
>> >>> >
>> >>> >
>> >>> >
>> >>> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
>> >>> > <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>> >>
>> >>> >> I changed configure.ac into:
>> >>> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
>> >>> >>
>> >>> >>
>>
>>
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From renaud at mancala.cbio.uct.ac.za  Sun Nov 10 12:42:56 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sun, 10 Nov 2013 13:42:56 +0200
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CADUbQ5j6rAsvvQH3E6XB6wcPGE5b3CccNq-3=_gi2k8_40aY9g@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
 <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
 <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>
 <CAHavPHE_m4iN21kkRAYai6ksb6-KsqgVvQrVLvk=JBkZ0gnUuA@mail.gmail.com>
 <CADUbQ5j6rAsvvQH3E6XB6wcPGE5b3CccNq-3=_gi2k8_40aY9g@mail.gmail.com>
Message-ID: <CAHavPHHMpCuVFuU1mFEAgat+4HS_H0=CkxkRyC8t6h4CXHbufw@mail.gmail.com>

Are you checking the tar.gz file?
R CMD chech --as-cran RcppOctave_0.13.3.tar.gz

This should not give you notes about the extra files and directories. The
try/tryCatch error is weird. I will have a look on Monday.

Renaud

On Saturday, November 9, 2013, Dominick Samperi wrote:

> With all suggested packages installed I managed to get R CMD check
> --as-cran
> to run clean (no errors, warnings, or notes), but a few "non-standard"
> directories
> had to be removed, cleanup had to be run explicitly, and RcppOctave.Rnw had
> to be modified to use tryCatch instead of try. The attached shell script
> was used
> to generate the clean check
>
-------------- next part --------------
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From djsamperi at gmail.com  Sun Nov 10 16:00:10 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Sun, 10 Nov 2013 10:00:10 -0500
Subject: [Rcppoctave-user] Apple Blues
In-Reply-To: <CAHavPHHMpCuVFuU1mFEAgat+4HS_H0=CkxkRyC8t6h4CXHbufw@mail.gmail.com>
References: <CADUbQ5hiJe-0HKQGsvctcJR2MuxeFuGeh8w++e+UT2eMnh+s9Q@mail.gmail.com>
 <CADUbQ5hBc+xD2VykLtc7C3e6nLtfx5H_tOXcRhYSxVWheTAdnQ@mail.gmail.com>
 <CADUbQ5iuyq=eUBqV8wgbqiiq3yP5QMiZgig0ad6AKQpZgsDUJw@mail.gmail.com>
 <CADUbQ5iUZg_jtgjtRNcO1XGW1A14co4xO+xQyZV1MN3tUMp76w@mail.gmail.com>
 <CADUbQ5jByCQyBjRE3e_5XRmBSFceSzHQSz58QHVAJ2k-gE01MQ@mail.gmail.com>
 <CAHavPHGvM7zAjH+Pbp4ddaaOadhbnqHbipnA4xMZk5PF7UuLzA@mail.gmail.com>
 <CADUbQ5jScyr7FcgeCX6aqz3RyYD7KwqnV6cq3J=KJeEsx3Et3g@mail.gmail.com>
 <CADUbQ5i7DDgdn05CzYzU1TeLaNsE0OFFkrbb7Mx-JaVLA8ne1A@mail.gmail.com>
 <CAHavPHHsdS=uCwZhbO-3sbN4D01bDk-Sa4oJnw8seugyD6XP3Q@mail.gmail.com>
 <CADUbQ5jdHrK-Vj7JXm3i+8_HDutwh3Lk84wT6etKPy4bSWa0Vg@mail.gmail.com>
 <CAHavPHG+V9dc=QAEPjA-UJrLoHkJ0-N5gu4HLtmGd-C5Jx5qtg@mail.gmail.com>
 <CADUbQ5gQ+tL0_XNMKiU3WVrem7Mf2Gj6qnRapaH8pOM5RaMi3w@mail.gmail.com>
 <CAHavPHE+aXp6+DJmMpf_MiBjtHFZBTdnHVRZfuczd07BtvhdRA@mail.gmail.com>
 <CADUbQ5hg_dF8VctowiYVWBy6GnH9vVbvmc=--wjdrVnWLKihOg@mail.gmail.com>
 <CAHavPHENP6EfG_bfsQPzbXR3BwOhHqKPJastXheuG0A+sXUW_Q@mail.gmail.com>
 <CAHavPHHVKQOcWRchnastTO9Ghhn_LaZvSuzKqSjOHp_rvj-t8w@mail.gmail.com>
 <CADUbQ5jWvdPTHWkffuZ9thMFcP=TFuAUv2wovhxRdjx24cuzWQ@mail.gmail.com>
 <CADUbQ5i7mSH1GAMLzU0at_JeS-dXjSOnoumW-abCYkPA+vLP7A@mail.gmail.com>
 <CAHavPHGsHRhMPb+AV_661eWvurrji4=av276fECpAtNFDHn5CA@mail.gmail.com>
 <CAHavPHG8+X+CuhAkMu-vxhmWqsT2ZCOyHghShe8ASscFGsz0yw@mail.gmail.com>
 <CADUbQ5jphuWdZtZV4ThYiGEC2Yz=MXv+1xONqsxECrPfG8N1Dg@mail.gmail.com>
 <CAHavPHEOzT6cM51kc038q77dn68dxDBBVi9bPGqyi5rT1oH45A@mail.gmail.com>
 <CADUbQ5giWGHiHBh_5ZCs_jQc1_5RvHE-4N+OyxhzqT6uwRXzng@mail.gmail.com>
 <CAHavPHEuYvC=CsxB23fqX=Q091EPsUE-PQ7L72iP2be7VCq8Fw@mail.gmail.com>
 <CAHavPHF8O3edntXbThkH+0gSAHeFwLgp_reSnU_O38g0C2fXWQ@mail.gmail.com>
 <CADUbQ5hiS5PMc=ULE1aUuXtVKfXGpoPnSO5uiiLyOTwY_weVPg@mail.gmail.com>
 <CAHavPHE_m4iN21kkRAYai6ksb6-KsqgVvQrVLvk=JBkZ0gnUuA@mail.gmail.com>
 <CADUbQ5j6rAsvvQH3E6XB6wcPGE5b3CccNq-3=_gi2k8_40aY9g@mail.gmail.com>
 <CAHavPHHMpCuVFuU1mFEAgat+4HS_H0=CkxkRyC8t6h4CXHbufw@mail.gmail.com>
Message-ID: <CADUbQ5jcdNLv0ph52vDb=hN2UNmYKczCW_c0AQdnGKeZ-Zyd6g@mail.gmail.com>

No I was checking using the checked-out directory. Using the
tar.gz archive eliminates the need for explicit cleanup and
deleting directories, but the try issue remains. (It seems to
me that R CMD check should call cleanup automatically,
but it doesn't, and there is no --clean option.)

Indeed, I cannot build the tar.gz file if I don't splice out the
try calls. I'm attaching the log for R CMD build RcppOctave.


On Sun, Nov 10, 2013 at 6:42 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> Are you checking the tar.gz file?
> R CMD chech --as-cran RcppOctave_0.13.3.tar.gz
>
> This should not give you notes about the extra files and directories. The
> try/tryCatch error is weird. I will have a look on Monday.
>
> Renaud
>
> On Saturday, November 9, 2013, Dominick Samperi wrote:
>
>> With all suggested packages installed I managed to get R CMD check
>> --as-cran
>> to run clean (no errors, warnings, or notes), but a few "non-standard"
>> directories
>> had to be removed, cleanup had to be run explicitly, and RcppOctave.Rnw
>> had
>> to be modified to use tryCatch instead of try. The attached shell script
>> was used
>> to generate the clean check
>>
>
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* checking for file ?RcppOctave/DESCRIPTION? ... OK
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* building the PDF package manual
Hmm ... looks like a package
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From yitping at mpe.mpg.de  Wed Nov 20 18:25:52 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Wed, 20 Nov 2013 18:25:52 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
Message-ID: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>

Hi RcppOctave users,

I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.

I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.

- I have Octave 3.6.4 installed.
- I managed to compile the shared library, RcppOctave.so.
- But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.

Error in dyn.load("RcppOctave.so") : 
  unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
  Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
  Expected in: flat namespace
 in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so

Any idea why it is so? Any help would be appreciated. Thanks very much.


Best regards,
Yitping
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From renaud at mancala.cbio.uct.ac.za  Wed Nov 20 20:26:38 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Wed, 20 Nov 2013 21:26:38 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
Message-ID: <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>

Hi Yitping,

thank you for your interest in the RcppOctave package, which will hopefully
provide what you need... once you get it working :D
It will be great to get your feedback on how things work from a Mac-Octave
user point of view.

The package should compile fine with the settings described in the README
file.
Can you please send more details on your R (output of sessionInfo() and
Sys.info) and Octave installation.
Did you fetch the latest version of the source package from github?

In R, try:

library(devtools)
install_github('RcppOctave', 'renozao', ref = 'develop')


Renaud


On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:

> Hi RcppOctave users,
>
> I have just found out about this R packages and I am very excited about
> it. I am an Octave user and would like to use more R. Therefore I think
> this package will be perfect for me.
>
> I also understand that the package still has some installation issues with
> Mac OS. However I tried to install the package on a Mac platform anyway for
> the sake of trying and this is what I got.
>
> - I have Octave 3.6.4 installed.
> - I managed to compile the shared library, RcppOctave.so.
> - But I cannot proceed (to generating the documentation part) because the
> library cannot be loaded. This is the error message I got.
>
> *Error in dyn.load("RcppOctave.so") : *
> *  unable to load shared object
> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':*
> *  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value*
> *  Referenced from:
> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
> *  Expected in: flat namespace*
> * in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>
> Any idea why it is so? Any help would be appreciated. Thanks very much.
>
>
> Best regards,
> Yitping
>
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>
>
>
>
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From renaud at mancala.cbio.uct.ac.za  Thu Nov 21 10:36:39 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 21 Nov 2013 11:36:39 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
Message-ID: <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>

Thanks for the details Yitping, forwarding now to the list.
Please remember to Cc the list in your replies, so that there is a record
for future public reference.

On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:

> Hi Renaud,
>
> Thanks for your prompt reply. I tried the install_github() method you
> suggested but to no success either. The error is similar to what I had
> earlier, which source codes downloaded from RcppOctave cran webpage. Below
> are the log and error messages in case it is helpful.
>
> I have also included the output of sessionInfo() and Sys.info(). My Octave
> installation was done through MacPorts (*octave*-devel
> @3.6.4_9+atlas+docs+gcc48).
>
> Thanks in advance.
>
> Yitping
>
> > library(devtools)
> > install_github('RcppOctave', 'renozao', ref = 'develop')
> *Installing github repo(s) RcppOctave/develop from renozao*
> *Downloading RcppOctave.zip from
> https://github.com/renozao/RcppOctave/archive/develop.zip
> <https://github.com/renozao/RcppOctave/archive/develop.zip>*
> *Installing package from
> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip*
> *Installing RcppOctave*
> *'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
> \*
> *
> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
> \*
> *
> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
> \*
> *  --with-keep.source --install-tests *
>
> * installing *source* package 'RcppOctave' ...
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking whether R is a shared library... yes
> checking type of Operating System... Darwin
> checking whether OS is Mac OS (Darwin)... yes
> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
> -framework R"
> Using mkoctfile with R_CPPFLAGS:
> -I/Library/Frameworks/R.framework/Resources/include
> checking for octave-config... /opt/local/bin/octave-config
> checking for mkoctfile... /opt/local/bin/mkoctfile
> checking Octave include flags...
> -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> checking Octave libraries... -loctinterp -loctave -lcruft
> checking Octave version... 3.6.4
> checking whether to infer output names for Octave function (>= 3.4.3)...
> yes
> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> -loctinterp -loctave -lcruft
> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1
> checking RcppOctave Octave module directory...
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
> configure: creating ./config.status
> config.status: creating src/Makevars
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating src/modules/Makefile
> ** libs
> "/opt/local/bin/mkoctfile" -v utils.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> -loctinterp -loctave -lcruft -arch x86_64
> "/opt/local/bin/mkoctfile" -v
> -I/Library/Frameworks/R.framework/Resources/include
> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -I/opt/local/include -pipe -Os -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> -arch x86_64
> # Copying Octave modules to directory
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
> llvm-g++-4.2 -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1 -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
> llvm-g++-4.2 -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1 -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
> rcpp_octave.o
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** tests
> ** preparing package for lazy loading
> ** help
> Error :
> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
> ERROR: installing Rd objects failed for package 'RcppOctave'
> * removing
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>
>
>
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>   sysname
>
>               "Darwin"
>
>                 release
>
>               "13.0.0"
>
>                 version
> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
> root:xnu-2422.1.72~6/RELEASE_X86_64"
>
>               nodename
>
>           "dooku.local"
>
>                 machine
>
>               "x86_64"
>
>                   login
>
>               "yitping"
>
>                   user
>
>               "yitping"
>
>         effective_user
>
>               ?yitping"
>
>
>
>
>
>
>
> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
>
> Hi Yitping,
>
> thank you for your interest in the RcppOctave package, which will
> hopefully provide what you need... once you get it working :D
> It will be great to get your feedback on how things work from a Mac-Octave
> user point of view.
>
> The package should compile fine with the settings described in the README
> file.
> Can you please send more details on your R (output of sessionInfo() and
> Sys.info) and Octave installation.
> Did you fetch the latest version of the source package from github?
>
> In R, try:
>
> library(devtools)
> install_github('RcppOctave', 'renozao', ref = 'develop')
>
>
> Renaud
>
>
> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>
>> Hi RcppOctave users,
>>
>> I have just found out about this R packages and I am very excited about
>> it. I am an Octave user and would like to use more R. Therefore I think
>> this package will be perfect for me.
>>
>> I also understand that the package still has some installation issues
>> with Mac OS. However I tried to install the package on a Mac platform
>> anyway for the sake of trying and this is what I got.
>>
>> - I have Octave 3.6.4 installed.
>> - I managed to compile the shared library, RcppOctave.so.
>> - But I cannot proceed (to generating the documentation part) because the
>> library cannot be loaded. This is the error message I got.
>>
>> *Error in dyn.load("RcppOctave.so") : *
>> *  unable to load shared object
>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':*
>> *  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value*
>> *  Referenced from:
>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>> *  Expected in: flat namespace*
>> * in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>>
>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>
>>
>> Best regards,
>> Yitping
>>
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>>
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>
>>
>>
>>
>
>
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From renaud at mancala.cbio.uct.ac.za  Thu Nov 21 10:49:21 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 21 Nov 2013 11:49:21 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
Message-ID: <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>

Hi Dominick,

Yitping is compiling (successfully) with macports, but there seem to be an
issue when actually calling the code.
I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
that be the origin of the problem?

Yitping, could you please try the following:

install.packages('RcppOctave', repos='http://web.cbio.uct.ac.za/~renaud/CRAN',
INSTALL_opts = '--no-docs --no-help')
library(RcppOctave)
OctaveConfig()
getLoadedDLLs()
o_runif(1)


Thank you

On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>wrote:

> Thanks for the details Yitping, forwarding now to the list.
> Please remember to Cc the list in your replies, so that there is a record
> for future public reference.
>
> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>
>> Hi Renaud,
>>
>> Thanks for your prompt reply. I tried the install_github() method you
>> suggested but to no success either. The error is similar to what I had
>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>> are the log and error messages in case it is helpful.
>>
>> I have also included the output of sessionInfo() and Sys.info(). My
>> Octave installation was done through MacPorts (*octave*-devel
>> @3.6.4_9+atlas+docs+gcc48).
>>
>> Thanks in advance.
>>
>> Yitping
>>
>> > library(devtools)
>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>> *Installing github repo(s) RcppOctave/develop from renozao*
>> *Downloading RcppOctave.zip from
>> https://github.com/renozao/RcppOctave/archive/develop.zip
>> <https://github.com/renozao/RcppOctave/archive/develop.zip>*
>> *Installing package from
>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip*
>> *Installing RcppOctave*
>> *'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>> \*
>> *
>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>> \*
>> *
>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>> \*
>> *  --with-keep.source --install-tests *
>>
>> * installing *source* package 'RcppOctave' ...
>> checking for gcc... gcc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for g++... g++
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether g++ accepts -g... yes
>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking whether R is a shared library... yes
>> checking type of Operating System... Darwin
>> checking whether OS is Mac OS (Darwin)... yes
>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>> -framework R"
>> Using mkoctfile with R_CPPFLAGS:
>> -I/Library/Frameworks/R.framework/Resources/include
>> checking for octave-config... /opt/local/bin/octave-config
>> checking for mkoctfile... /opt/local/bin/mkoctfile
>> checking Octave include flags...
>> -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> checking Octave libraries... -loctinterp -loctave -lcruft
>> checking Octave version... 3.6.4
>> checking whether to infer output names for Octave function (>= 3.4.3)...
>> yes
>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> -loctinterp -loctave -lcruft
>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1
>> checking RcppOctave Octave module directory...
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> config.status: creating src/modules/Makefile
>> ** libs
>> "/opt/local/bin/mkoctfile" -v utils.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> -loctinterp -loctave -lcruft -arch x86_64
>> "/opt/local/bin/mkoctfile" -v
>> -I/Library/Frameworks/R.framework/Resources/include
>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -I/opt/local/include -pipe -Os -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> -arch x86_64
>> # Copying Octave modules to directory
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>> llvm-g++-4.2 -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>> llvm-g++-4.2 -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>> rcpp_octave.o
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>> installing to
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>> ** R
>> ** demo
>> ** inst
>> ** tests
>> ** preparing package for lazy loading
>> ** help
>> Error :
>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>   Expected in: flat namespace
>>  in
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>> ERROR: installing Rd objects failed for package 'RcppOctave'
>> * removing
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>
>>
>>
>>
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>>   sysname
>>
>>                 "Darwin"
>>
>>                 release
>>
>>                 "13.0.0"
>>
>>                 version
>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>
>>                 nodename
>>
>>           "dooku.local"
>>
>>                 machine
>>
>>                 "x86_64"
>>
>>                   login
>>
>>               "yitping"
>>
>>                     user
>>
>>               "yitping"
>>
>>           effective_user
>>
>>               ?yitping"
>>
>>
>>
>>
>>
>>
>>
>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> Hi Yitping,
>>
>> thank you for your interest in the RcppOctave package, which will
>> hopefully provide what you need... once you get it working :D
>> It will be great to get your feedback on how things work from a
>> Mac-Octave user point of view.
>>
>> The package should compile fine with the settings described in the README
>> file.
>> Can you please send more details on your R (output of sessionInfo() and
>> Sys.info) and Octave installation.
>> Did you fetch the latest version of the source package from github?
>>
>> In R, try:
>>
>> library(devtools)
>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>
>>
>> Renaud
>>
>>
>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>
>>> Hi RcppOctave users,
>>>
>>> I have just found out about this R packages and I am very excited about
>>> it. I am an Octave user and would like to use more R. Therefore I think
>>> this package will be perfect for me.
>>>
>>> I also understand that the package still has some installation issues
>>> with Mac OS. However I tried to install the package on a Mac platform
>>> anyway for the sake of trying and this is what I got.
>>>
>>> - I have Octave 3.6.4 installed.
>>> - I managed to compile the shared library, RcppOctave.so.
>>> - But I cannot proceed (to generating the documentation part) because
>>> the library cannot be loaded. This is the error message I got.
>>>
>>> *Error in dyn.load("RcppOctave.so") : *
>>> *  unable to load shared object
>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':*
>>> *  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value*
>>> *  Referenced from:
>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>>> *  Expected in: flat namespace*
>>> * in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>>>
>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>
>>>
>>> Best regards,
>>> Yitping
>>>
>>> _______________________________________________
>>> Rcppoctave-user mailing list
>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>
>>>
>>>
>>>
>>
>>
>
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From yitping at mpe.mpg.de  Thu Nov 21 11:54:32 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Thu, 21 Nov 2013 11:54:32 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
Message-ID: <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>

Hi Renaud,

I tried your suggestion but R complains that the package is not available as a binary. This is the same error that led me to compile it from the command line in the first place. But trying it from the command line with RcppOctave_0.13.3.tar.gz from the suggested repository and using the suggested installation options did not work either. The output of is below.

Thanks again.

Yitping

[yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
* installing to library ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
* installing *source* package ?RcppOctave? ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
checking whether R is a shared library... yes
checking type of Operating System... Darwin
checking whether OS is Mac OS (Darwin)... yes
Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
checking for octave-config... /opt/local/bin/octave-config
checking for mkoctfile... /opt/local/bin/mkoctfile
checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
checking Octave libraries... -loctinterp -loctave -lcruft
checking Octave version... 3.6.4
checking whether to infer output names for Octave function (>= 3.4.3)... yes
Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/modules/Makefile
** libs
"/opt/local/bin/mkoctfile" -v utils.cc
/usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
/usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
"/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
/usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
/usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
# Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
** R
** demo
** inst
** preparing package for lazy loading
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?


On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> Hi Dominick, 
> 
> Yitping is compiling (successfully) with macports, but there seem to be an issue when actually calling the code. 
> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could that be the origin of the problem? 
> 
> Yitping, could you please try the following:
> 
> install.packages('RcppOctave', repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs --no-help')
> library(RcppOctave)
> OctaveConfig()
> getLoadedDLLs()
> o_runif(1)
> 
> 
> Thank you
> 
> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> Thanks for the details Yitping, forwarding now to the list.
> Please remember to Cc the list in your replies, so that there is a record for future public reference.
> 
> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
> Hi Renaud,
> 
> Thanks for your prompt reply. I tried the install_github() method you suggested but to no success either. The error is similar to what I had earlier, which source codes downloaded from RcppOctave cran webpage. Below are the log and error messages in case it is helpful.
> 
> I have also included the output of sessionInfo() and Sys.info(). My Octave installation was done through MacPorts (octave-devel @3.6.4_9+atlas+docs+gcc48). 
> 
> Thanks in advance.
> 
> Yitping
> 
> > library(devtools)
> > install_github('RcppOctave', 'renozao', ref = 'develop')
> Installing github repo(s) RcppOctave/develop from renozao
> Downloading RcppOctave.zip from https://github.com/renozao/RcppOctave/archive/develop.zip
> Installing package from /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
> Installing RcppOctave
> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
>   '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'  \
>   --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'  \
>   --with-keep.source --install-tests 
> 
> * installing *source* package 'RcppOctave' ...
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables... 
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking whether R is a shared library... yes
> checking type of Operating System... Darwin
> checking whether OS is Mac OS (Darwin)... yes
> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking for octave-config... /opt/local/bin/octave-config
> checking for mkoctfile... /opt/local/bin/mkoctfile
> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> checking Octave libraries... -loctinterp -loctave -lcruft
> checking Octave version... 3.6.4
> checking whether to infer output names for Octave function (>= 3.4.3)... yes
> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
> configure: creating ./config.status
> config.status: creating src/Makevars
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating src/modules/Makefile
> ** libs
> "/opt/local/bin/mkoctfile" -v utils.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** tests
> ** preparing package for lazy loading
> ** help
> Error : /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41: .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
> ERROR: installing Rd objects failed for package 'RcppOctave'
> * removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
> 
> 
> 
> 
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
>   sysname 
>                                                                                          "Darwin" 
>                                                                                           release 
>                                                                                          "13.0.0" 
>                                                                                           version 
> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64" 
>                                                                                          nodename 
>                                                                                     "dooku.local" 
>                                                                                           machine 
>                                                                                          "x86_64" 
>                                                                                             login 
>                                                                                         "yitping" 
>                                                                                              user 
>                                                                                         "yitping" 
>                                                                                    effective_user 
>                                                                                         ?yitping"
> 
> 
> 
> 
> 
> 
> 
> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> 
>> Hi Yitping,
>> 
>> thank you for your interest in the RcppOctave package, which will hopefully provide what you need... once you get it working :D
>> It will be great to get your feedback on how things work from a Mac-Octave user point of view.
>> 
>> The package should compile fine with the settings described in the README file.
>> Can you please send more details on your R (output of sessionInfo() and Sys.info) and Octave installation.
>> Did you fetch the latest version of the source package from github? 
>> 
>> In R, try:
>> 
>> library(devtools)
>> install_github('RcppOctave', 'renozao', ref = 'develop')
>> 
>> 
>> Renaud
>> 
>> 
>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> Hi RcppOctave users,
>> 
>> I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.
>> 
>> I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.
>> 
>> - I have Octave 3.6.4 installed.
>> - I managed to compile the shared library, RcppOctave.so.
>> - But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.
>> 
>> Error in dyn.load("RcppOctave.so") : 
>>   unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>   Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>   Expected in: flat namespace
>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>> 
>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>> 
>> 
>> Best regards,
>> Yitping
>> 
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>> 
>> 
>> 
>> 
> 
> 
> 

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From renaud at mancala.cbio.uct.ac.za  Thu Nov 21 12:02:29 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Thu, 21 Nov 2013 13:02:29 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
Message-ID: <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>

Ah, true, you would need to add type = 'source' to the install.packages
command.
Anyway this is not the actual problem.

It looks like the octave library are either not found or not loaded
correctly (maybe due to the compiler discrepancy).
Can you try this (not sure this is correct on Mac)

LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
RcppOctave_0.13.3.tar.gz

The idea is to put ensure the octave libraries are in the PATH.

Renaud


On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:

> Hi Renaud,
>
> I tried your suggestion but R complains that the package is not available
> as a binary. This is the same error that led me to compile it from the
> command line in the first place. But trying it from the command line with
> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
> suggested installation options did not work either. The output of is below.
>
> Thanks again.
>
> Yitping
>
> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
> * installing to library
> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> * installing *source* package ?RcppOctave? ...
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking whether R is a shared library... yes
> checking type of Operating System... Darwin
> checking whether OS is Mac OS (Darwin)... yes
> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
> -framework R"
> Using mkoctfile with R_CPPFLAGS:
> -I/Library/Frameworks/R.framework/Resources/include
> checking for octave-config... /opt/local/bin/octave-config
> checking for mkoctfile... /opt/local/bin/mkoctfile
> checking Octave include flags...
> -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> checking Octave libraries... -loctinterp -loctave -lcruft
> checking Octave version... 3.6.4
> checking whether to infer output names for Octave function (>= 3.4.3)...
> yes
> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> -loctinterp -loctave -lcruft
> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1
> checking RcppOctave Octave module directory...
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
> configure: creating ./config.status
> config.status: creating src/Makevars
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating src/modules/Makefile
> ** libs
> "/opt/local/bin/mkoctfile" -v utils.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> -loctinterp -loctave -lcruft -arch x86_64
> "/opt/local/bin/mkoctfile" -v
> -I/Library/Frameworks/R.framework/Resources/include
> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -I/opt/local/include -pipe -Os -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> -arch x86_64
> # Copying Octave modules to directory
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
> llvm-g++-4.2 -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1 -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
> llvm-g++-4.2 -arch x86_64
> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> -DOCT_POST_3_4_0=1 -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
> rcpp_octave.o
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>
>
> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux <
> renaud at mancala.cbio.uct.ac.za> wrote:
>
> Hi Dominick,
>
> Yitping is compiling (successfully) with macports, but there seem to be an
> issue when actually calling the code.
> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
> that be the origin of the problem?
>
> Yitping, could you please try the following:
>
> install.packages('RcppOctave', repos='
> http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
> --no-help')
> library(RcppOctave)
> OctaveConfig()
> getLoadedDLLs()
> o_runif(1)
>
>
> Thank you
>
> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>wrote:
>
>> Thanks for the details Yitping, forwarding now to the list.
>> Please remember to Cc the list in your replies, so that there is a record
>> for future public reference.
>>
>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>
>>> Hi Renaud,
>>>
>>> Thanks for your prompt reply. I tried the install_github() method you
>>> suggested but to no success either. The error is similar to what I had
>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>> are the log and error messages in case it is helpful.
>>>
>>> I have also included the output of sessionInfo() and Sys.info(). My
>>> Octave installation was done through MacPorts (*octave*-devel
>>> @3.6.4_9+atlas+docs+gcc48).
>>>
>>> Thanks in advance.
>>>
>>> Yitping
>>>
>>> > library(devtools)
>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>> *Installing github repo(s) RcppOctave/develop from renozao*
>>> *Downloading RcppOctave.zip from
>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>> <https://github.com/renozao/RcppOctave/archive/develop.zip>*
>>> *Installing package from
>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip*
>>> *Installing RcppOctave*
>>> *'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD
>>> INSTALL  \*
>>> *
>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>> \*
>>> *
>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>> \*
>>> *  --with-keep.source --install-tests *
>>>
>>> * installing *source* package 'RcppOctave' ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS:
>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>> Using mkoctfile with R_CPPFLAGS:
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags...
>>> -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>> -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>> yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory...
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> -loctinterp -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc<http://rrng.cc/>
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc<http://rrng.cc/>-o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -arch x86_64
>>> # Copying Octave modules to directory
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>> rcpp_octave.o
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>> installing to
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** tests
>>> ** preparing package for lazy loading
>>> ** help
>>> Error :
>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>   error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>> * removing
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>
>>>
>>>
>>>
>>> R version 3.0.2 (2013-09-25)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>>   sysname
>>>
>>>                 "Darwin"
>>>
>>>                   release
>>>
>>>                 "13.0.0"
>>>
>>>                   version
>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>
>>>                 nodename
>>>
>>>             "dooku.local"
>>>
>>>                   machine
>>>
>>>                 "x86_64"
>>>
>>>                     login
>>>
>>>                 "yitping"
>>>
>>>                     user
>>>
>>>                 "yitping"
>>>
>>>           effective_user
>>>
>>>                 ?yitping"
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <
>>> renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>> Hi Yitping,
>>>
>>> thank you for your interest in the RcppOctave package, which will
>>> hopefully provide what you need... once you get it working :D
>>> It will be great to get your feedback on how things work from a
>>> Mac-Octave user point of view.
>>>
>>> The package should compile fine with the settings described in the
>>> README file.
>>> Can you please send more details on your R (output of sessionInfo() and
>>> Sys.info) and Octave installation.
>>> Did you fetch the latest version of the source package from github?
>>>
>>> In R, try:
>>>
>>> library(devtools)
>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>
>>>
>>> Renaud
>>>
>>>
>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>
>>>> Hi RcppOctave users,
>>>>
>>>> I have just found out about this R packages and I am very excited about
>>>> it. I am an Octave user and would like to use more R. Therefore I think
>>>> this package will be perfect for me.
>>>>
>>>> I also understand that the package still has some installation issues
>>>> with Mac OS. However I tried to install the package on a Mac platform
>>>> anyway for the sake of trying and this is what I got.
>>>>
>>>> - I have Octave 3.6.4 installed.
>>>> - I managed to compile the shared library, RcppOctave.so.
>>>> - But I cannot proceed (to generating the documentation part) because
>>>> the library cannot be loaded. This is the error message I got.
>>>>
>>>> *Error in dyn.load("RcppOctave.so") : *
>>>> *  unable to load shared object
>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':*
>>>> *  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so,
>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value*
>>>> *  Referenced from:
>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>>>> *  Expected in: flat namespace*
>>>> * in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so*
>>>>
>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>
>>>>
>>>> Best regards,
>>>> Yitping
>>>>
>>>> _______________________________________________
>>>> Rcppoctave-user mailing list
>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>
>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>
>
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From djsamperi at gmail.com  Thu Nov 21 15:42:53 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Thu, 21 Nov 2013 09:42:53 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
Message-ID: <CADUbQ5gKs0GYRDDKCS61mshdg5ekbV4tb6KWvG=FSi=BEwTaBg@mail.gmail.com>

Under Mavericks (latest version of Mac OS) llvm-g++-4.2 no longer
works, and this is the source of the problem.
This OS update caused a lot of problems for non-Apple software packages.

By default packages builds use the compiler that was used to build R
(at CRAN). The work-around
(mentioned in an earlier thread) is to create ~/.R/Makevars containing
CC=clang
CXX=clang++

This specifies the compilers to use for package builds.

On Thu, Nov 21, 2013 at 4:49 AM, Renaud Gaujoux
<renaud at mancala.cbio.uct.ac.za> wrote:
> Hi Dominick,
>
> Yitping is compiling (successfully) with macports, but there seem to be an
> issue when actually calling the code.
> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
> that be the origin of the problem?
>
> Yitping, could you please try the following:
>
> install.packages('RcppOctave',
> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
> --no-help')
> library(RcppOctave)
> OctaveConfig()
> getLoadedDLLs()
> o_runif(1)
>
>
> Thank you
>
> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
>>
>> Thanks for the details Yitping, forwarding now to the list.
>> Please remember to Cc the list in your replies, so that there is a record
>> for future public reference.
>>
>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>
>>> Hi Renaud,
>>>
>>> Thanks for your prompt reply. I tried the install_github() method you
>>> suggested but to no success either. The error is similar to what I had
>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>> are the log and error messages in case it is helpful.
>>>
>>> I have also included the output of sessionInfo() and Sys.info(). My
>>> Octave installation was done through MacPorts (octave-devel
>>> @3.6.4_9+atlas+docs+gcc48).
>>>
>>> Thanks in advance.
>>>
>>> Yitping
>>>
>>> > library(devtools)
>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>> Installing github repo(s) RcppOctave/develop from renozao
>>> Downloading RcppOctave.zip from
>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>> Installing package from
>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>> Installing RcppOctave
>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>> \
>>>
>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>> \
>>>
>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>> \
>>>   --with-keep.source --install-tests
>>>
>>> * installing *source* package 'RcppOctave' ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>>> -framework R"
>>> Using mkoctfile with R_CPPFLAGS:
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags...
>>> -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>> -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>> yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory...
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>> -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -arch x86_64
>>> # Copying Octave modules to directory
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>> rcpp_octave.o
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>> installing to
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** tests
>>> ** preparing package for lazy loading
>>> ** help
>>> Error :
>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>   error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>> * removing
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>
>>>
>>>
>>>
>>> R version 3.0.2 (2013-09-25)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>>   sysname
>>>
>>> "Darwin"
>>>
>>> release
>>>
>>> "13.0.0"
>>>
>>> version
>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>
>>> nodename
>>>
>>> "dooku.local"
>>>
>>> machine
>>>
>>> "x86_64"
>>>
>>> login
>>>
>>> "yitping"
>>>
>>> user
>>>
>>> "yitping"
>>>
>>> effective_user
>>>
>>> ?yitping"
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>> Hi Yitping,
>>>
>>> thank you for your interest in the RcppOctave package, which will
>>> hopefully provide what you need... once you get it working :D
>>> It will be great to get your feedback on how things work from a
>>> Mac-Octave user point of view.
>>>
>>> The package should compile fine with the settings described in the README
>>> file.
>>> Can you please send more details on your R (output of sessionInfo() and
>>> Sys.info) and Octave installation.
>>> Did you fetch the latest version of the source package from github?
>>>
>>> In R, try:
>>>
>>> library(devtools)
>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>
>>>
>>> Renaud
>>>
>>>
>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>
>>>> Hi RcppOctave users,
>>>>
>>>> I have just found out about this R packages and I am very excited about
>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>> package will be perfect for me.
>>>>
>>>> I also understand that the package still has some installation issues
>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>> for the sake of trying and this is what I got.
>>>>
>>>> - I have Octave 3.6.4 installed.
>>>> - I managed to compile the shared library, RcppOctave.so.
>>>> - But I cannot proceed (to generating the documentation part) because
>>>> the library cannot be loaded. This is the error message I got.
>>>>
>>>> Error in dyn.load("RcppOctave.so") :
>>>>   unable to load shared object
>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>   Referenced from:
>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>   Expected in: flat namespace
>>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>
>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>
>>>>
>>>> Best regards,
>>>> Yitping
>>>>
>>>> _______________________________________________
>>>> Rcppoctave-user mailing list
>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>
>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>
>>>>
>>>>
>>>
>>>
>>
>

From yitping at mpe.mpg.de  Thu Nov 21 15:44:12 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Thu, 21 Nov 2013 15:44:12 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
Message-ID: <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>

Hi Renaud,

But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was reported not found in the error message belongs to RcppOctave.so instead of to liboctave.

[yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
                 U __Z22bind_internal_variableRKSsRK12octave_value

[yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep __Z22bind_internal_variable 

I tried your suggestion anyway but similar error returned.

Yitping


On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> Ah, true, you would need to add type = 'source' to the install.packages command.
> Anyway this is not the actual problem. 
> 
> It looks like the octave library are either not found or not loaded correctly (maybe due to the compiler discrepancy).
> Can you try this (not sure this is correct on Mac)
> 
> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL RcppOctave_0.13.3.tar.gz
> 
> The idea is to put ensure the octave libraries are in the PATH.
> 
> Renaud
> 
> 
> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
> Hi Renaud,
> 
> I tried your suggestion but R complains that the package is not available as a binary. This is the same error that led me to compile it from the command line in the first place. But trying it from the command line with RcppOctave_0.13.3.tar.gz from the suggested repository and using the suggested installation options did not work either. The output of is below.
> 
> Thanks again.
> 
> Yitping
> 
> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
> * installing to library ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
> * installing *source* package ?RcppOctave? ...
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables... 
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for g++... g++
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking whether R is a shared library... yes
> checking type of Operating System... Darwin
> checking whether OS is Mac OS (Darwin)... yes
> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
> checking for octave-config... /opt/local/bin/octave-config
> checking for mkoctfile... /opt/local/bin/mkoctfile
> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
> checking Octave libraries... -loctinterp -loctave -lcruft
> checking Octave version... 3.6.4
> checking whether to infer output names for Octave function (>= 3.4.3)... yes
> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
> configure: creating ./config.status
> config.status: creating src/Makevars
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating src/modules/Makefile
> ** libs
> "/opt/local/bin/mkoctfile" -v utils.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
> 
> 
> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> 
>> Hi Dominick, 
>> 
>> Yitping is compiling (successfully) with macports, but there seem to be an issue when actually calling the code. 
>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could that be the origin of the problem? 
>> 
>> Yitping, could you please try the following:
>> 
>> install.packages('RcppOctave', repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs --no-help')
>> library(RcppOctave)
>> OctaveConfig()
>> getLoadedDLLs()
>> o_runif(1)
>> 
>> 
>> Thank you
>> 
>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>> Thanks for the details Yitping, forwarding now to the list.
>> Please remember to Cc the list in your replies, so that there is a record for future public reference.
>> 
>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> Hi Renaud,
>> 
>> Thanks for your prompt reply. I tried the install_github() method you suggested but to no success either. The error is similar to what I had earlier, which source codes downloaded from RcppOctave cran webpage. Below are the log and error messages in case it is helpful.
>> 
>> I have also included the output of sessionInfo() and Sys.info(). My Octave installation was done through MacPorts (octave-devel @3.6.4_9+atlas+docs+gcc48). 
>> 
>> Thanks in advance.
>> 
>> Yitping
>> 
>> > library(devtools)
>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>> Installing github repo(s) RcppOctave/develop from renozao
>> Downloading RcppOctave.zip from https://github.com/renozao/RcppOctave/archive/develop.zip
>> Installing package from /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>> Installing RcppOctave
>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
>>   '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'  \
>>   --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'  \
>>   --with-keep.source --install-tests 
>> 
>> * installing *source* package 'RcppOctave' ...
>> checking for gcc... gcc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables... 
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for g++... g++
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether g++ accepts -g... yes
>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking whether R is a shared library... yes
>> checking type of Operating System... Darwin
>> checking whether OS is Mac OS (Darwin)... yes
>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking for octave-config... /opt/local/bin/octave-config
>> checking for mkoctfile... /opt/local/bin/mkoctfile
>> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> checking Octave libraries... -loctinterp -loctave -lcruft
>> checking Octave version... 3.6.4
>> checking whether to infer output names for Octave function (>= 3.4.3)... yes
>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
>> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> config.status: creating src/modules/Makefile
>> ** libs
>> "/opt/local/bin/mkoctfile" -v utils.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>> ** R
>> ** demo
>> ** inst
>> ** tests
>> ** preparing package for lazy loading
>> ** help
>> Error : /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41: .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>   Expected in: flat namespace
>>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>> ERROR: installing Rd objects failed for package 'RcppOctave'
>> * removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>> 
>> 
>> 
>> 
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> 
>>   sysname 
>>                                                                                          "Darwin" 
>>                                                                                           release 
>>                                                                                          "13.0.0" 
>>                                                                                           version 
>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64" 
>>                                                                                          nodename 
>>                                                                                     "dooku.local" 
>>                                                                                           machine 
>>                                                                                          "x86_64" 
>>                                                                                             login 
>>                                                                                         "yitping" 
>>                                                                                              user 
>>                                                                                         "yitping" 
>>                                                                                    effective_user 
>>                                                                                         ?yitping"
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>> 
>>> Hi Yitping,
>>> 
>>> thank you for your interest in the RcppOctave package, which will hopefully provide what you need... once you get it working :D
>>> It will be great to get your feedback on how things work from a Mac-Octave user point of view.
>>> 
>>> The package should compile fine with the settings described in the README file.
>>> Can you please send more details on your R (output of sessionInfo() and Sys.info) and Octave installation.
>>> Did you fetch the latest version of the source package from github? 
>>> 
>>> In R, try:
>>> 
>>> library(devtools)
>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>> 
>>> 
>>> Renaud
>>> 
>>> 
>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> Hi RcppOctave users,
>>> 
>>> I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.
>>> 
>>> I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.
>>> 
>>> - I have Octave 3.6.4 installed.
>>> - I managed to compile the shared library, RcppOctave.so.
>>> - But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.
>>> 
>>> Error in dyn.load("RcppOctave.so") : 
>>>   unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>> 
>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>> 
>>> 
>>> Best regards,
>>> Yitping
>>> 
>>> _______________________________________________
>>> Rcppoctave-user mailing list
>>> Rcppoctave-user at lists.r-forge.r-project.org
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>> 
>>> 
>>> 
>>> 
>> 
>> 
>> 
> 
> 

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From yitping at mpe.mpg.de  Fri Nov 22 09:25:14 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Fri, 22 Nov 2013 09:25:14 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
Message-ID: <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>

Hi all,

I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and I got a different symbol not found. This symbol and the previous one are indeed in RcppOctave.so but why is R not loading it? I have also tried setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.

Any suggestions would be very welcome. Thanks in advance again.

Yitping

Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
  Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so




On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:

> Hi Renaud,
> 
> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was reported not found in the error message belongs to RcppOctave.so instead of to liboctave.
> 
> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>                  U __Z22bind_internal_variableRKSsRK12octave_value
> 
> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep __Z22bind_internal_variable 
> 
> I tried your suggestion anyway but similar error returned.
> 
> Yitping
> 
> 
> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> 
>> Ah, true, you would need to add type = 'source' to the install.packages command.
>> Anyway this is not the actual problem. 
>> 
>> It looks like the octave library are either not found or not loaded correctly (maybe due to the compiler discrepancy).
>> Can you try this (not sure this is correct on Mac)
>> 
>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL RcppOctave_0.13.3.tar.gz
>> 
>> The idea is to put ensure the octave libraries are in the PATH.
>> 
>> Renaud
>> 
>> 
>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> Hi Renaud,
>> 
>> I tried your suggestion but R complains that the package is not available as a binary. This is the same error that led me to compile it from the command line in the first place. But trying it from the command line with RcppOctave_0.13.3.tar.gz from the suggested repository and using the suggested installation options did not work either. The output of is below.
>> 
>> Thanks again.
>> 
>> Yitping
>> 
>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>> * installing to library ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>> * installing *source* package ?RcppOctave? ...
>> checking for gcc... gcc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables... 
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for g++... g++
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether g++ accepts -g... yes
>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking whether R is a shared library... yes
>> checking type of Operating System... Darwin
>> checking whether OS is Mac OS (Darwin)... yes
>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking for octave-config... /opt/local/bin/octave-config
>> checking for mkoctfile... /opt/local/bin/mkoctfile
>> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> checking Octave libraries... -loctinterp -loctave -lcruft
>> checking Octave version... 3.6.4
>> checking whether to infer output names for Octave function (>= 3.4.3)... yes
>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
>> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> config.status: creating src/modules/Makefile
>> ** libs
>> "/opt/local/bin/mkoctfile" -v utils.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** building package indices
>> ** installing vignettes
>> ** testing if installed package can be loaded
>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>   Expected in: flat namespace
>>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>> 
>> 
>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>> 
>>> Hi Dominick, 
>>> 
>>> Yitping is compiling (successfully) with macports, but there seem to be an issue when actually calling the code. 
>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could that be the origin of the problem? 
>>> 
>>> Yitping, could you please try the following:
>>> 
>>> install.packages('RcppOctave', repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs --no-help')
>>> library(RcppOctave)
>>> OctaveConfig()
>>> getLoadedDLLs()
>>> o_runif(1)
>>> 
>>> 
>>> Thank you
>>> 
>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>>> Thanks for the details Yitping, forwarding now to the list.
>>> Please remember to Cc the list in your replies, so that there is a record for future public reference.
>>> 
>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> Hi Renaud,
>>> 
>>> Thanks for your prompt reply. I tried the install_github() method you suggested but to no success either. The error is similar to what I had earlier, which source codes downloaded from RcppOctave cran webpage. Below are the log and error messages in case it is helpful.
>>> 
>>> I have also included the output of sessionInfo() and Sys.info(). My Octave installation was done through MacPorts (octave-devel @3.6.4_9+atlas+docs+gcc48). 
>>> 
>>> Thanks in advance.
>>> 
>>> Yitping
>>> 
>>> > library(devtools)
>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>> Installing github repo(s) RcppOctave/develop from renozao
>>> Downloading RcppOctave.zip from https://github.com/renozao/RcppOctave/archive/develop.zip
>>> Installing package from /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>> Installing RcppOctave
>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
>>>   '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'  \
>>>   --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'  \
>>>   --with-keep.source --install-tests 
>>> 
>>> * installing *source* package 'RcppOctave' ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables... 
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)... yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>>> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** tests
>>> ** preparing package for lazy loading
>>> ** help
>>> Error : /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41: .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>> * removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>> 
>>> 
>>> 
>>> 
>>> R version 3.0.2 (2013-09-25)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> 
>>> 
>>>   sysname 
>>>                                                                                          "Darwin" 
>>>                                                                                           release 
>>>                                                                                          "13.0.0" 
>>>                                                                                           version 
>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64" 
>>>                                                                                          nodename 
>>>                                                                                     "dooku.local" 
>>>                                                                                           machine 
>>>                                                                                          "x86_64" 
>>>                                                                                             login 
>>>                                                                                         "yitping" 
>>>                                                                                              user 
>>>                                                                                         "yitping" 
>>>                                                                                    effective_user 
>>>                                                                                         ?yitping"
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>>> 
>>>> Hi Yitping,
>>>> 
>>>> thank you for your interest in the RcppOctave package, which will hopefully provide what you need... once you get it working :D
>>>> It will be great to get your feedback on how things work from a Mac-Octave user point of view.
>>>> 
>>>> The package should compile fine with the settings described in the README file.
>>>> Can you please send more details on your R (output of sessionInfo() and Sys.info) and Octave installation.
>>>> Did you fetch the latest version of the source package from github? 
>>>> 
>>>> In R, try:
>>>> 
>>>> library(devtools)
>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>> 
>>>> 
>>>> Renaud
>>>> 
>>>> 
>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>> Hi RcppOctave users,
>>>> 
>>>> I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.
>>>> 
>>>> I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.
>>>> 
>>>> - I have Octave 3.6.4 installed.
>>>> - I managed to compile the shared library, RcppOctave.so.
>>>> - But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.
>>>> 
>>>> Error in dyn.load("RcppOctave.so") : 
>>>>   unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>   Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>   Expected in: flat namespace
>>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>> 
>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>> 
>>>> 
>>>> Best regards,
>>>> Yitping
>>>> 
>>>> _______________________________________________
>>>> Rcppoctave-user mailing list
>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>> 
>> 
> 
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user

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From yitping at mpe.mpg.de  Fri Nov 22 14:39:57 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Fri, 22 Nov 2013 14:39:57 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
Message-ID: <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>

Hi all again,


I have successfully compile, install and load RcppOctave on my Mac (running Mavericks). In order to do this I have to reinstall Rcpp with customized ~/.R/Makevars (CC=clang, etc). I can load the library from the command line R but not from the GUI. It should be something related to the search path because octave-config could not be found. I will post it here if I find a way. In the meantime, any suggestions would be very welcome. Thanks very much.

Yitping



From the command line:
> library(RcppOctave)
Loading required package: Rcpp
Loading required package: pkgmaker
Loading required package: registry
RcppOctave [0.13.3] - Octave 3.6.4-api-v48+ (x86_64-apple-darwin13.0.0)
Octave path: /opt/local/bin

From the GUI:
> library(RcppOctave)
Loading required package: Rcpp
Loading required package: pkgmaker
Loading required package: registry
RcppOctave [0.13.3] - Octave (not configured)
NOTE: Octave binaries were probably not found. See ?octave_config.
Warning messages:
1: In value[[3L]](cond) :
  Failed loading Octave configuration: Error in base::system(..., intern = TRUE): error in running command

2: In value[[3L]](cond) :
  Failed loading Octave configuration: Error in base::system(..., intern = TRUE): error in running command

sh: octave-config: command not found
sh: octave-config: command not found
>


On Nov 22, 2013, at 9:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:

> Hi all,
> 
> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and I got a different symbol not found. This symbol and the previous one are indeed in RcppOctave.so but why is R not loading it? I have also tried setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
> 
> Any suggestions would be very welcome. Thanks in advance again.
> 
> Yitping
> 
> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
> 
> 
> 
> 
> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
> 
>> Hi Renaud,
>> 
>> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was reported not found in the error message belongs to RcppOctave.so instead of to liboctave.
>> 
>> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>>                  U __Z22bind_internal_variableRKSsRK12octave_value
>> 
>> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep __Z22bind_internal_variable 
>> 
>> I tried your suggestion anyway but similar error returned.
>> 
>> Yitping
>> 
>> 
>> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>> 
>>> Ah, true, you would need to add type = 'source' to the install.packages command.
>>> Anyway this is not the actual problem. 
>>> 
>>> It looks like the octave library are either not found or not loaded correctly (maybe due to the compiler discrepancy).
>>> Can you try this (not sure this is correct on Mac)
>>> 
>>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL RcppOctave_0.13.3.tar.gz
>>> 
>>> The idea is to put ensure the octave libraries are in the PATH.
>>> 
>>> Renaud
>>> 
>>> 
>>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> Hi Renaud,
>>> 
>>> I tried your suggestion but R complains that the package is not available as a binary. This is the same error that led me to compile it from the command line in the first place. But trying it from the command line with RcppOctave_0.13.3.tar.gz from the suggested repository and using the suggested installation options did not work either. The output of is below.
>>> 
>>> Thanks again.
>>> 
>>> Yitping
>>> 
>>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>>> * installing to library ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>>> * installing *source* package ?RcppOctave? ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables... 
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)... yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>>> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>>> 
>>> 
>>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>>> 
>>>> Hi Dominick, 
>>>> 
>>>> Yitping is compiling (successfully) with macports, but there seem to be an issue when actually calling the code. 
>>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could that be the origin of the problem? 
>>>> 
>>>> Yitping, could you please try the following:
>>>> 
>>>> install.packages('RcppOctave', repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs --no-help')
>>>> library(RcppOctave)
>>>> OctaveConfig()
>>>> getLoadedDLLs()
>>>> o_runif(1)
>>>> 
>>>> 
>>>> Thank you
>>>> 
>>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>>>> Thanks for the details Yitping, forwarding now to the list.
>>>> Please remember to Cc the list in your replies, so that there is a record for future public reference.
>>>> 
>>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>> Hi Renaud,
>>>> 
>>>> Thanks for your prompt reply. I tried the install_github() method you suggested but to no success either. The error is similar to what I had earlier, which source codes downloaded from RcppOctave cran webpage. Below are the log and error messages in case it is helpful.
>>>> 
>>>> I have also included the output of sessionInfo() and Sys.info(). My Octave installation was done through MacPorts (octave-devel @3.6.4_9+atlas+docs+gcc48). 
>>>> 
>>>> Thanks in advance.
>>>> 
>>>> Yitping
>>>> 
>>>> > library(devtools)
>>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>> Downloading RcppOctave.zip from https://github.com/renozao/RcppOctave/archive/develop.zip
>>>> Installing package from /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>> Installing RcppOctave
>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
>>>>   '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'  \
>>>>   --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'  \
>>>>   --with-keep.source --install-tests 
>>>> 
>>>> * installing *source* package 'RcppOctave' ...
>>>> checking for gcc... gcc
>>>> checking whether the C compiler works... yes
>>>> checking for C compiler default output file name... a.out
>>>> checking for suffix of executables... 
>>>> checking whether we are cross compiling... no
>>>> checking for suffix of object files... o
>>>> checking whether we are using the GNU C compiler... yes
>>>> checking whether gcc accepts -g... yes
>>>> checking for gcc option to accept ISO C89... none needed
>>>> checking for g++... g++
>>>> checking whether we are using the GNU C++ compiler... yes
>>>> checking whether g++ accepts -g... yes
>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>> checking whether R is a shared library... yes
>>>> checking type of Operating System... Darwin
>>>> checking whether OS is Mac OS (Darwin)... yes
>>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>>> Using mkoctfile with R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>> checking for octave-config... /opt/local/bin/octave-config
>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>> checking Octave include flags... -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>> checking Octave version... 3.6.4
>>>> checking whether to infer output names for Octave function (>= 3.4.3)... yes
>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1
>>>> checking RcppOctave Octave module directory... /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> config.status: creating src/modules/Makefile
>>>> ** libs
>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>>> "/opt/local/bin/mkoctfile" -v -I/Library/Frameworks/R.framework/Resources/include -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -I/opt/local/include -pipe -Os -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -arch x86_64
>>>> # Copying Octave modules to directory '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>> llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/.. -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include -DOCT_POST_3_4_0=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o rcpp_octave.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
>>>> installing to /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>> ** R
>>>> ** demo
>>>> ** inst
>>>> ** tests
>>>> ** preparing package for lazy loading
>>>> ** help
>>>> Error : /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41: .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>   dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>   Expected in: flat namespace
>>>>  in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>> * removing '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>> 
>>>> 
>>>> 
>>>> 
>>>> R version 3.0.2 (2013-09-25)
>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>> 
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>> 
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> 
>>>>   sysname 
>>>>                                                                                          "Darwin" 
>>>>                                                                                           release 
>>>>                                                                                          "13.0.0" 
>>>>                                                                                           version 
>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64" 
>>>>                                                                                          nodename 
>>>>                                                                                     "dooku.local" 
>>>>                                                                                           machine 
>>>>                                                                                          "x86_64" 
>>>>                                                                                             login 
>>>>                                                                                         "yitping" 
>>>>                                                                                              user 
>>>>                                                                                         "yitping" 
>>>>                                                                                    effective_user 
>>>>                                                                                         ?yitping"
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>>>> 
>>>>> Hi Yitping,
>>>>> 
>>>>> thank you for your interest in the RcppOctave package, which will hopefully provide what you need... once you get it working :D
>>>>> It will be great to get your feedback on how things work from a Mac-Octave user point of view.
>>>>> 
>>>>> The package should compile fine with the settings described in the README file.
>>>>> Can you please send more details on your R (output of sessionInfo() and Sys.info) and Octave installation.
>>>>> Did you fetch the latest version of the source package from github? 
>>>>> 
>>>>> In R, try:
>>>>> 
>>>>> library(devtools)
>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>> 
>>>>> 
>>>>> Renaud
>>>>> 
>>>>> 
>>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>> Hi RcppOctave users,
>>>>> 
>>>>> I have just found out about this R packages and I am very excited about it. I am an Octave user and would like to use more R. Therefore I think this package will be perfect for me.
>>>>> 
>>>>> I also understand that the package still has some installation issues with Mac OS. However I tried to install the package on a Mac platform anyway for the sake of trying and this is what I got.
>>>>> 
>>>>> - I have Octave 3.6.4 installed.
>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>> - But I cannot proceed (to generating the documentation part) because the library cannot be loaded. This is the error message I got.
>>>>> 
>>>>> Error in dyn.load("RcppOctave.so") : 
>>>>>   unable to load shared object '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>   Referenced from: /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>   Expected in: flat namespace
>>>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>> 
>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>> 
>>>>> 
>>>>> Best regards,
>>>>> Yitping
>>>>> 
>>>>> _______________________________________________
>>>>> Rcppoctave-user mailing list
>>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
> 

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From renaud at mancala.cbio.uct.ac.za  Fri Nov 22 14:57:08 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Fri, 22 Nov 2013 15:57:08 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>
Message-ID: <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>

>
> I have successfully compile, install and load RcppOctave on my Mac
> (running Mavericks). In order to do this I have to reinstall Rcpp with
> customized ~/.R/Makevars (CC=clang, etc).
>

Nice!


> I can load the library from the command line R but not from the GUI. It
> should be something related to the search path because octave-config could
> not be found. I will post it here if I find a way. In the meantime, any
> suggestions would be very welcome.
>

Interesting. Can you please try directly loading the library with:

library.dynam(RcppOctave, RcppOctave, dirname(path.package('RcppOctave)))

I am wondering if the library could still load despite octave-config not
being in the path.

Please let me know if calling Octave functions work fine.
Ideally, you would also run the following to make a complete check (from
command line), you may need to install the Suggests dependencies:

R CMD check --as-cran RcppOctave_0.13.3.tar.gz

Thank you.

Bests,
Renaud
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From yitping at mpe.mpg.de  Fri Nov 22 15:36:27 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Fri, 22 Nov 2013 15:36:27 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>
 <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>
Message-ID: <5145D85F-F3FD-453B-B6DE-ECDBBE4C4AB6@mpe.mpg.de>

Hi Renaud and all,

Thanks for the suggestions. Here are some two more logs for sharing.


(1) From the R GUI, I have to load the shared library manually first before calling library(?RcppOctave?). See log below.

> library.dynam('RcppOctave', 'RcppOctave', lib.loc=.libPaths(), verbose=TRUE)
now dyn.load("/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so") ...
> library('RcppOctave')
Loading required package: Rcpp
Loading required package: pkgmaker
Loading required package: registry
RcppOctave [0.13.3] - Octave 3.6.4-api-v48+ (x86_64-apple-darwin13.0.0)
Octave path: /opt/local/bin
> .CallOctave('version')
[1] "3.6.4"
> .CallOctave('sqrt', 10)
[1] 3.162278



(2) Checking the RcppOctave package from the command line failed at the ?examples? level. See log below.

[yitping at dooku src]$ R CMD check --as-cran RcppOctave_0.13.3.tar.gz 
* using log directory ?/Users/yitping/Toolbox/R/src/RcppOctave.Rcheck?
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* checking for file ?RcppOctave/DESCRIPTION? ... OK
* checking extension type ... Package
* this is package ?RcppOctave? version ?0.13.3?
* checking CRAN incoming feasibility ... OK
Maintainer: ?Renaud Gaujoux <renaud at tx.technion.ac.il>?
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ?RcppOctave? can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ?inst/doc? ... OK
* checking installed files from ?inst/doc? ... OK
* checking files in ?vignettes? ... OK
* checking examples ... ERROR
Running examples in ?RcppOctave-Ex.R? failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: o_ls
> ### Title: Listing Objects from the Current Octave Session
> ### Aliases: o_ls
> 
> ### ** Examples
> 
> ## Don't show: 
>  o_clear(all=TRUE) 
> ## End Don't show
> 
> # only variables
> o_assign(list(a=1, b=2, c=5))
> o_ls()
Error in .CallOctave("exist", NAME, ...) : 
  RcppOctave - error in Octave function `exist`:
  error: caught execution error in library function
Calls: o_ls -> sapply -> lapply -> FUN -> .CallOctave -> .Call
Execution halted


Thanks very much.

Yitping

On Nov 22, 2013, at 2:57 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> 
> 
> I have successfully compile, install and load RcppOctave on my Mac (running Mavericks). In order to do this I have to reinstall Rcpp with customized ~/.R/Makevars (CC=clang, etc).
> 
> Nice!
>  
> I can load the library from the command line R but not from the GUI. It should be something related to the search path because octave-config could not be found. I will post it here if I find a way. In the meantime, any suggestions would be very welcome. 
> 
> Interesting. Can you please try directly loading the library with:
> 
> library.dynam(RcppOctave, RcppOctave, dirname(path.package('RcppOctave)))
> 
> I am wondering if the library could still load despite octave-config not being in the path.
> 
> Please let me know if calling Octave functions work fine.
> Ideally, you would also run the following to make a complete check (from command line), you may need to install the Suggests dependencies:
> 
> R CMD check --as-cran RcppOctave_0.13.3.tar.gz
> 
> Thank you.
> 
> Bests,
> Renaud

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From djsamperi at gmail.com  Fri Nov 22 17:18:15 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 22 Nov 2013 11:18:15 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
Message-ID: <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>

Make sure to reinstall both Rcpp and RcppOctave from source after
configuring ~/.R/Makevars. Have you upgraded to Mavericks?
If you installed Octave using Homebrew then clang/clang++ will
be used as needed. This may not be the case if MacPorts is
used to install.

You could also try using gcc/g++ instead of clang/clang++ (not
llvm-gcc-4.2/llvm-g++-4.2), assuming that you are using
Mavericks.


On Fri, Nov 22, 2013 at 3:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
> Hi all,
>
> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and
> I got a different symbol not found. This symbol and the previous one are
> indeed in RcppOctave.so but why is R not loading it? I have also tried
> setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
>
> Any suggestions would be very welcome. Thanks in advance again.
>
> Yitping
>
> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
> 6): Symbol not found:
> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>   Expected in: flat namespace
>  in
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>
>
>
>
> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>
> Hi Renaud,
>
> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was
> reported not found in the error message belongs to RcppOctave.so instead of
> to liboctave.
>
> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>                  U __Z22bind_internal_variableRKSsRK12octave_value
>
> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep
> __Z22bind_internal_variable
>
> I tried your suggestion anyway but similar error returned.
>
> Yitping
>
>
> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
> wrote:
>
> Ah, true, you would need to add type = 'source' to the install.packages
> command.
> Anyway this is not the actual problem.
>
> It looks like the octave library are either not found or not loaded
> correctly (maybe due to the compiler discrepancy).
> Can you try this (not sure this is correct on Mac)
>
> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
> RcppOctave_0.13.3.tar.gz
>
> The idea is to put ensure the octave libraries are in the PATH.
>
> Renaud
>
>
> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>
>> Hi Renaud,
>>
>> I tried your suggestion but R complains that the package is not available
>> as a binary. This is the same error that led me to compile it from the
>> command line in the first place. But trying it from the command line with
>> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
>> suggested installation options did not work either. The output of is below.
>>
>> Thanks again.
>>
>> Yitping
>>
>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>> * installing to library
>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>> * installing *source* package ?RcppOctave? ...
>> checking for gcc... gcc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for g++... g++
>> checking whether we are using the GNU C++ compiler... yes
>> checking whether g++ accepts -g... yes
>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>> checking whether R is a shared library... yes
>> checking type of Operating System... Darwin
>> checking whether OS is Mac OS (Darwin)... yes
>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>> -framework R"
>> Using mkoctfile with R_CPPFLAGS:
>> -I/Library/Frameworks/R.framework/Resources/include
>> checking for octave-config... /opt/local/bin/octave-config
>> checking for mkoctfile... /opt/local/bin/mkoctfile
>> checking Octave include flags...
>> -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> checking Octave libraries... -loctinterp -loctave -lcruft
>> checking Octave version... 3.6.4
>> checking whether to infer output names for Octave function (>= 3.4.3)...
>> yes
>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>> -loctinterp -loctave -lcruft
>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1
>> checking RcppOctave Octave module directory...
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> config.status: creating src/modules/Makefile
>> ** libs
>> "/opt/local/bin/mkoctfile" -v utils.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>> -loctave -lcruft -arch x86_64
>> "/opt/local/bin/mkoctfile" -v
>> -I/Library/Frameworks/R.framework/Resources/include
>> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -I/opt/local/include -pipe -Os -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> -arch x86_64
>> # Copying Octave modules to directory
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>> llvm-g++-4.2 -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>> llvm-g++-4.2 -arch x86_64
>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>> rcpp_octave.o
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>> installing to
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** building package indices
>> ** installing vignettes
>> ** testing if installed package can be loaded
>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>   Expected in: flat namespace
>>  in
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> * removing
>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>>
>>
>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux
>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> Hi Dominick,
>>
>> Yitping is compiling (successfully) with macports, but there seem to be an
>> issue when actually calling the code.
>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
>> that be the origin of the problem?
>>
>> Yitping, could you please try the following:
>>
>> install.packages('RcppOctave',
>> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
>> --no-help')
>> library(RcppOctave)
>> OctaveConfig()
>> getLoadedDLLs()
>> o_runif(1)
>>
>>
>> Thank you
>>
>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>>>
>>> Thanks for the details Yitping, forwarding now to the list.
>>> Please remember to Cc the list in your replies, so that there is a record
>>> for future public reference.
>>>
>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>
>>>> Hi Renaud,
>>>>
>>>> Thanks for your prompt reply. I tried the install_github() method you
>>>> suggested but to no success either. The error is similar to what I had
>>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>>> are the log and error messages in case it is helpful.
>>>>
>>>> I have also included the output of sessionInfo() and Sys.info(). My
>>>> Octave installation was done through MacPorts (octave-devel
>>>> @3.6.4_9+atlas+docs+gcc48).
>>>>
>>>> Thanks in advance.
>>>>
>>>> Yitping
>>>>
>>>> > library(devtools)
>>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>> Downloading RcppOctave.zip from
>>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>>> Installing package from
>>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>> Installing RcppOctave
>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>>> \
>>>>
>>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>>> \
>>>>
>>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>>> \
>>>>   --with-keep.source --install-tests
>>>>
>>>> * installing *source* package 'RcppOctave' ...
>>>> checking for gcc... gcc
>>>> checking whether the C compiler works... yes
>>>> checking for C compiler default output file name... a.out
>>>> checking for suffix of executables...
>>>> checking whether we are cross compiling... no
>>>> checking for suffix of object files... o
>>>> checking whether we are using the GNU C compiler... yes
>>>> checking whether gcc accepts -g... yes
>>>> checking for gcc option to accept ISO C89... none needed
>>>> checking for g++... g++
>>>> checking whether we are using the GNU C++ compiler... yes
>>>> checking whether g++ accepts -g... yes
>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>> checking whether R is a shared library... yes
>>>> checking type of Operating System... Darwin
>>>> checking whether OS is Mac OS (Darwin)... yes
>>>> Using mkoctfile with R_LDFLAGS:
>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>>> Using mkoctfile with R_CPPFLAGS:
>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>> checking for octave-config... /opt/local/bin/octave-config
>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>> checking Octave include flags...
>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>>> -L/opt/local/lib
>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>> checking Octave version... 3.6.4
>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>> yes
>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> -loctinterp -loctave -lcruft
>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1
>>>> checking RcppOctave Octave module directory...
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> config.status: creating src/modules/Makefile
>>>> ** libs
>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>> -loctave -lcruft -arch x86_64
>>>> "/opt/local/bin/mkoctfile" -v
>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -arch x86_64
>>>> # Copying Octave modules to directory
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>> llvm-g++-4.2 -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>> llvm-g++-4.2 -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>>> rcpp_octave.o
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>> -Wl,CoreFoundation
>>>> installing to
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>> ** R
>>>> ** demo
>>>> ** inst
>>>> ** tests
>>>> ** preparing package for lazy loading
>>>> ** help
>>>> Error :
>>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>   error: unable to load shared object
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>
>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>   Referenced from:
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>   Expected in: flat namespace
>>>>  in
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>> * removing
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>>
>>>>
>>>>
>>>>
>>>> R version 3.0.2 (2013-09-25)
>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>>
>>>>   sysname
>>>>
>>>> "Darwin"
>>>>
>>>> release
>>>>
>>>> "13.0.0"
>>>>
>>>> version
>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>>
>>>> nodename
>>>>
>>>> "dooku.local"
>>>>
>>>> machine
>>>>
>>>> "x86_64"
>>>>
>>>> login
>>>>
>>>> "yitping"
>>>>
>>>> user
>>>>
>>>> "yitping"
>>>>
>>>> effective_user
>>>>
>>>> ?yitping"
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>
>>>> Hi Yitping,
>>>>
>>>> thank you for your interest in the RcppOctave package, which will
>>>> hopefully provide what you need... once you get it working :D
>>>> It will be great to get your feedback on how things work from a
>>>> Mac-Octave user point of view.
>>>>
>>>> The package should compile fine with the settings described in the
>>>> README file.
>>>> Can you please send more details on your R (output of sessionInfo() and
>>>> Sys.info) and Octave installation.
>>>> Did you fetch the latest version of the source package from github?
>>>>
>>>> In R, try:
>>>>
>>>> library(devtools)
>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>
>>>>
>>>> Renaud
>>>>
>>>>
>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>
>>>>> Hi RcppOctave users,
>>>>>
>>>>> I have just found out about this R packages and I am very excited about
>>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>>> package will be perfect for me.
>>>>>
>>>>> I also understand that the package still has some installation issues
>>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>>> for the sake of trying and this is what I got.
>>>>>
>>>>> - I have Octave 3.6.4 installed.
>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>> - But I cannot proceed (to generating the documentation part) because
>>>>> the library cannot be loaded. This is the error message I got.
>>>>>
>>>>> Error in dyn.load("RcppOctave.so") :
>>>>>   unable to load shared object
>>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>   Referenced from:
>>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>   Expected in: flat namespace
>>>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>
>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>>
>>>>>
>>>>> Best regards,
>>>>> Yitping
>>>>>
>>>>> _______________________________________________
>>>>> Rcppoctave-user mailing list
>>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>>
>>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>
>
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>
>
>
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>

From djsamperi at gmail.com  Fri Nov 22 17:22:51 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 22 Nov 2013 11:22:51 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>
Message-ID: <CADUbQ5gseoKgqq96TvKaLHc760A5GkCx3HrXv3DAdiNqWc+MwA@mail.gmail.com>

Hi Yitping,

I'm not sure how I missed your posts announcing that you got it working.
Congratulations!

Dominick



On Fri, Nov 22, 2013 at 11:18 AM, Dominick Samperi <djsamperi at gmail.com> wrote:
> Make sure to reinstall both Rcpp and RcppOctave from source after
> configuring ~/.R/Makevars. Have you upgraded to Mavericks?
> If you installed Octave using Homebrew then clang/clang++ will
> be used as needed. This may not be the case if MacPorts is
> used to install.
>
> You could also try using gcc/g++ instead of clang/clang++ (not
> llvm-gcc-4.2/llvm-g++-4.2), assuming that you are using
> Mavericks.
>
>
> On Fri, Nov 22, 2013 at 3:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> Hi all,
>>
>> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and
>> I got a different symbol not found. This symbol and the previous one are
>> indeed in RcppOctave.so but why is R not loading it? I have also tried
>> setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
>>
>> Any suggestions would be very welcome. Thanks in advance again.
>>
>> Yitping
>>
>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>
>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>> 6): Symbol not found:
>> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>>   Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>   Expected in: flat namespace
>>  in
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>
>>
>>
>>
>> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>
>> Hi Renaud,
>>
>> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was
>> reported not found in the error message belongs to RcppOctave.so instead of
>> to liboctave.
>>
>> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>>                  U __Z22bind_internal_variableRKSsRK12octave_value
>>
>> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep
>> __Z22bind_internal_variable
>>
>> I tried your suggestion anyway but similar error returned.
>>
>> Yitping
>>
>>
>> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>>
>> Ah, true, you would need to add type = 'source' to the install.packages
>> command.
>> Anyway this is not the actual problem.
>>
>> It looks like the octave library are either not found or not loaded
>> correctly (maybe due to the compiler discrepancy).
>> Can you try this (not sure this is correct on Mac)
>>
>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
>> RcppOctave_0.13.3.tar.gz
>>
>> The idea is to put ensure the octave libraries are in the PATH.
>>
>> Renaud
>>
>>
>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>
>>> Hi Renaud,
>>>
>>> I tried your suggestion but R complains that the package is not available
>>> as a binary. This is the same error that led me to compile it from the
>>> command line in the first place. But trying it from the command line with
>>> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
>>> suggested installation options did not work either. The output of is below.
>>>
>>> Thanks again.
>>>
>>> Yitping
>>>
>>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>>> * installing to library
>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>>> * installing *source* package ?RcppOctave? ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>>> -framework R"
>>> Using mkoctfile with R_CPPFLAGS:
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags...
>>> -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>> yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory...
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>> -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -arch x86_64
>>> # Copying Octave modules to directory
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>> rcpp_octave.o
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>> installing to
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>   error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>   Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>   Expected in: flat namespace
>>>  in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing
>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>>>
>>>
>>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux
>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>
>>> Hi Dominick,
>>>
>>> Yitping is compiling (successfully) with macports, but there seem to be an
>>> issue when actually calling the code.
>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
>>> that be the origin of the problem?
>>>
>>> Yitping, could you please try the following:
>>>
>>> install.packages('RcppOctave',
>>> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
>>> --no-help')
>>> library(RcppOctave)
>>> OctaveConfig()
>>> getLoadedDLLs()
>>> o_runif(1)
>>>
>>>
>>> Thank you
>>>
>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>> wrote:
>>>>
>>>> Thanks for the details Yitping, forwarding now to the list.
>>>> Please remember to Cc the list in your replies, so that there is a record
>>>> for future public reference.
>>>>
>>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>
>>>>> Hi Renaud,
>>>>>
>>>>> Thanks for your prompt reply. I tried the install_github() method you
>>>>> suggested but to no success either. The error is similar to what I had
>>>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>>>> are the log and error messages in case it is helpful.
>>>>>
>>>>> I have also included the output of sessionInfo() and Sys.info(). My
>>>>> Octave installation was done through MacPorts (octave-devel
>>>>> @3.6.4_9+atlas+docs+gcc48).
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Yitping
>>>>>
>>>>> > library(devtools)
>>>>> > install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>>> Downloading RcppOctave.zip from
>>>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>>>> Installing package from
>>>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>>> Installing RcppOctave
>>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>>>> \
>>>>>
>>>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>>>> \
>>>>>
>>>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>>>> \
>>>>>   --with-keep.source --install-tests
>>>>>
>>>>> * installing *source* package 'RcppOctave' ...
>>>>> checking for gcc... gcc
>>>>> checking whether the C compiler works... yes
>>>>> checking for C compiler default output file name... a.out
>>>>> checking for suffix of executables...
>>>>> checking whether we are cross compiling... no
>>>>> checking for suffix of object files... o
>>>>> checking whether we are using the GNU C compiler... yes
>>>>> checking whether gcc accepts -g... yes
>>>>> checking for gcc option to accept ISO C89... none needed
>>>>> checking for g++... g++
>>>>> checking whether we are using the GNU C++ compiler... yes
>>>>> checking whether g++ accepts -g... yes
>>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>>> checking whether R is a shared library... yes
>>>>> checking type of Operating System... Darwin
>>>>> checking whether OS is Mac OS (Darwin)... yes
>>>>> Using mkoctfile with R_LDFLAGS:
>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>>>> Using mkoctfile with R_CPPFLAGS:
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> checking for octave-config... /opt/local/bin/octave-config
>>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>>> checking Octave include flags...
>>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>>>> -L/opt/local/lib
>>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>>> checking Octave version... 3.6.4
>>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>>> yes
>>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>>> -loctinterp -loctave -lcruft
>>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1
>>>>> checking RcppOctave Octave module directory...
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> config.status: creating src/modules/Makefile
>>>>> ** libs
>>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>>> -loctave -lcruft -arch x86_64
>>>>> "/opt/local/bin/mkoctfile" -v
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>> -arch x86_64
>>>>> # Copying Octave modules to directory
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>>> llvm-g++-4.2 -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>>> llvm-g++-4.2 -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>>>> rcpp_octave.o
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>>> -Wl,CoreFoundation
>>>>> installing to
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>>> ** R
>>>>> ** demo
>>>>> ** inst
>>>>> ** tests
>>>>> ** preparing package for lazy loading
>>>>> ** help
>>>>> Error :
>>>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>>   error: unable to load shared object
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>>
>>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>   Referenced from:
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>   Expected in: flat namespace
>>>>>  in
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>>> * removing
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> R version 3.0.2 (2013-09-25)
>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>
>>>>> locale:
>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>
>>>>>
>>>>>   sysname
>>>>>
>>>>> "Darwin"
>>>>>
>>>>> release
>>>>>
>>>>> "13.0.0"
>>>>>
>>>>> version
>>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>>>
>>>>> nodename
>>>>>
>>>>> "dooku.local"
>>>>>
>>>>> machine
>>>>>
>>>>> "x86_64"
>>>>>
>>>>> login
>>>>>
>>>>> "yitping"
>>>>>
>>>>> user
>>>>>
>>>>> "yitping"
>>>>>
>>>>> effective_user
>>>>>
>>>>> ?yitping"
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>>
>>>>> Hi Yitping,
>>>>>
>>>>> thank you for your interest in the RcppOctave package, which will
>>>>> hopefully provide what you need... once you get it working :D
>>>>> It will be great to get your feedback on how things work from a
>>>>> Mac-Octave user point of view.
>>>>>
>>>>> The package should compile fine with the settings described in the
>>>>> README file.
>>>>> Can you please send more details on your R (output of sessionInfo() and
>>>>> Sys.info) and Octave installation.
>>>>> Did you fetch the latest version of the source package from github?
>>>>>
>>>>> In R, try:
>>>>>
>>>>> library(devtools)
>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>>
>>>>>
>>>>> Renaud
>>>>>
>>>>>
>>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>>
>>>>>> Hi RcppOctave users,
>>>>>>
>>>>>> I have just found out about this R packages and I am very excited about
>>>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>>>> package will be perfect for me.
>>>>>>
>>>>>> I also understand that the package still has some installation issues
>>>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>>>> for the sake of trying and this is what I got.
>>>>>>
>>>>>> - I have Octave 3.6.4 installed.
>>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>>> - But I cannot proceed (to generating the documentation part) because
>>>>>> the library cannot be loaded. This is the error message I got.
>>>>>>
>>>>>> Error in dyn.load("RcppOctave.so") :
>>>>>>   unable to load shared object
>>>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>>   dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>   Referenced from:
>>>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>   Expected in: flat namespace
>>>>>>  in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>
>>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>>>
>>>>>>
>>>>>> Best regards,
>>>>>> Yitping
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rcppoctave-user mailing list
>>>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>>>
>>>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>
>>
>>
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>

From yitping at mpe.mpg.de  Fri Nov 22 17:26:27 2013
From: yitping at mpe.mpg.de (Yitping Kok)
Date: Fri, 22 Nov 2013 17:26:27 +0100
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>
Message-ID: <52D94549-5B23-47F7-B150-BC76A3F981DB@mpe.mpg.de>

That is what I did. Reinstall both Rcpp and RcppOctave from the source. Yes, I am using Mavericks.

I think the problem I have right now is related to how the code is checking for the Octave related environment during library loading. I could be wrong but I think the /bin/sh script that is calling octave-config is not reading the user?s shell environment settings therefore not able finding the Octave binary.

Check out this the Sys.getenv(?PATH?) from the R GUI. It is quite obvious that the search is a standard one instead of a user customized one. MacPorts binaries are stored (by default) in /opt/local/bin.

> Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"

Please advise.

On Nov 22, 2013, at 5:18 PM, Dominick Samperi <djsamperi at gmail.com> wrote:

> Make sure to reinstall both Rcpp and RcppOctave from source after
> configuring ~/.R/Makevars. Have you upgraded to Mavericks?
> If you installed Octave using Homebrew then clang/clang++ will
> be used as needed. This may not be the case if MacPorts is
> used to install.
> 
> You could also try using gcc/g++ instead of clang/clang++ (not
> llvm-gcc-4.2/llvm-g++-4.2), assuming that you are using
> Mavericks.
> 
> 
> On Fri, Nov 22, 2013 at 3:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> Hi all,
>> 
>> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and
>> I got a different symbol not found. This symbol and the previous one are
>> indeed in RcppOctave.so but why is R not loading it? I have also tried
>> setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
>> 
>> Any suggestions would be very welcome. Thanks in advance again.
>> 
>> Yitping
>> 
>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>  error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>> 
>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>> 6): Symbol not found:
>> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>>  Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>  Expected in: flat namespace
>> in
>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>> 
>> 
>> 
>> 
>> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>> 
>> Hi Renaud,
>> 
>> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was
>> reported not found in the error message belongs to RcppOctave.so instead of
>> to liboctave.
>> 
>> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>>                 U __Z22bind_internal_variableRKSsRK12octave_value
>> 
>> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep
>> __Z22bind_internal_variable
>> 
>> I tried your suggestion anyway but similar error returned.
>> 
>> Yitping
>> 
>> 
>> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>> wrote:
>> 
>> Ah, true, you would need to add type = 'source' to the install.packages
>> command.
>> Anyway this is not the actual problem.
>> 
>> It looks like the octave library are either not found or not loaded
>> correctly (maybe due to the compiler discrepancy).
>> Can you try this (not sure this is correct on Mac)
>> 
>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
>> RcppOctave_0.13.3.tar.gz
>> 
>> The idea is to put ensure the octave libraries are in the PATH.
>> 
>> Renaud
>> 
>> 
>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> 
>>> Hi Renaud,
>>> 
>>> I tried your suggestion but R complains that the package is not available
>>> as a binary. This is the same error that led me to compile it from the
>>> command line in the first place. But trying it from the command line with
>>> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
>>> suggested installation options did not work either. The output of is below.
>>> 
>>> Thanks again.
>>> 
>>> Yitping
>>> 
>>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>>> * installing to library
>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>>> * installing *source* package ?RcppOctave? ...
>>> checking for gcc... gcc
>>> checking whether the C compiler works... yes
>>> checking for C compiler default output file name... a.out
>>> checking for suffix of executables...
>>> checking whether we are cross compiling... no
>>> checking for suffix of object files... o
>>> checking whether we are using the GNU C compiler... yes
>>> checking whether gcc accepts -g... yes
>>> checking for gcc option to accept ISO C89... none needed
>>> checking for g++... g++
>>> checking whether we are using the GNU C++ compiler... yes
>>> checking whether g++ accepts -g... yes
>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>> checking whether R is a shared library... yes
>>> checking type of Operating System... Darwin
>>> checking whether OS is Mac OS (Darwin)... yes
>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>>> -framework R"
>>> Using mkoctfile with R_CPPFLAGS:
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> checking for octave-config... /opt/local/bin/octave-config
>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>> checking Octave include flags...
>>> -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>> checking Octave version... 3.6.4
>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>> yes
>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>> -loctinterp -loctave -lcruft
>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1
>>> checking RcppOctave Octave module directory...
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> configure: creating ./config.status
>>> config.status: creating src/Makevars
>>> config.status: creating src/modules/Makefile
>>> ** libs
>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>> -loctave -lcruft -arch x86_64
>>> "/opt/local/bin/mkoctfile" -v
>>> -I/Library/Frameworks/R.framework/Resources/include
>>> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -I/opt/local/include -pipe -Os -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -arch x86_64
>>> # Copying Octave modules to directory
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>> llvm-g++-4.2 -arch x86_64
>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>> rcpp_octave.o
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>> -Wl,CoreFoundation
>>> installing to
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>> ** R
>>> ** demo
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** building package indices
>>> ** installing vignettes
>>> ** testing if installed package can be loaded
>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>  error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>> 
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>  Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>  Expected in: flat namespace
>>> in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing
>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>>> 
>>> 
>>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux
>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>> 
>>> Hi Dominick,
>>> 
>>> Yitping is compiling (successfully) with macports, but there seem to be an
>>> issue when actually calling the code.
>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
>>> that be the origin of the problem?
>>> 
>>> Yitping, could you please try the following:
>>> 
>>> install.packages('RcppOctave',
>>> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
>>> --no-help')
>>> library(RcppOctave)
>>> OctaveConfig()
>>> getLoadedDLLs()
>>> o_runif(1)
>>> 
>>> 
>>> Thank you
>>> 
>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>> wrote:
>>>> 
>>>> Thanks for the details Yitping, forwarding now to the list.
>>>> Please remember to Cc the list in your replies, so that there is a record
>>>> for future public reference.
>>>> 
>>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>> 
>>>>> Hi Renaud,
>>>>> 
>>>>> Thanks for your prompt reply. I tried the install_github() method you
>>>>> suggested but to no success either. The error is similar to what I had
>>>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>>>> are the log and error messages in case it is helpful.
>>>>> 
>>>>> I have also included the output of sessionInfo() and Sys.info(). My
>>>>> Octave installation was done through MacPorts (octave-devel
>>>>> @3.6.4_9+atlas+docs+gcc48).
>>>>> 
>>>>> Thanks in advance.
>>>>> 
>>>>> Yitping
>>>>> 
>>>>>> library(devtools)
>>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>>> Downloading RcppOctave.zip from
>>>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>>>> Installing package from
>>>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>>> Installing RcppOctave
>>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>>>> \
>>>>> 
>>>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>>>> \
>>>>> 
>>>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>>>> \
>>>>>  --with-keep.source --install-tests
>>>>> 
>>>>> * installing *source* package 'RcppOctave' ...
>>>>> checking for gcc... gcc
>>>>> checking whether the C compiler works... yes
>>>>> checking for C compiler default output file name... a.out
>>>>> checking for suffix of executables...
>>>>> checking whether we are cross compiling... no
>>>>> checking for suffix of object files... o
>>>>> checking whether we are using the GNU C compiler... yes
>>>>> checking whether gcc accepts -g... yes
>>>>> checking for gcc option to accept ISO C89... none needed
>>>>> checking for g++... g++
>>>>> checking whether we are using the GNU C++ compiler... yes
>>>>> checking whether g++ accepts -g... yes
>>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>>> checking whether R is a shared library... yes
>>>>> checking type of Operating System... Darwin
>>>>> checking whether OS is Mac OS (Darwin)... yes
>>>>> Using mkoctfile with R_LDFLAGS:
>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>>>> Using mkoctfile with R_CPPFLAGS:
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> checking for octave-config... /opt/local/bin/octave-config
>>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>>> checking Octave include flags...
>>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>>>> -L/opt/local/lib
>>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>>> checking Octave version... 3.6.4
>>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>>> yes
>>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>>> -loctinterp -loctave -lcruft
>>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1
>>>>> checking RcppOctave Octave module directory...
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> configure: creating ./config.status
>>>>> config.status: creating src/Makevars
>>>>> config.status: creating src/modules/Makefile
>>>>> ** libs
>>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>>> -loctave -lcruft -arch x86_64
>>>>> "/opt/local/bin/mkoctfile" -v
>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>> -arch x86_64
>>>>> # Copying Octave modules to directory
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>>> llvm-g++-4.2 -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>>> llvm-g++-4.2 -arch x86_64
>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>>>> rcpp_octave.o
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>>> -Wl,CoreFoundation
>>>>> installing to
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>>> ** R
>>>>> ** demo
>>>>> ** inst
>>>>> ** tests
>>>>> ** preparing package for lazy loading
>>>>> ** help
>>>>> Error :
>>>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>>  error: unable to load shared object
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>> 
>>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>  Referenced from:
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>  Expected in: flat namespace
>>>>> in
>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>>> * removing
>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> R version 3.0.2 (2013-09-25)
>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>> 
>>>>> locale:
>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>> 
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>> 
>>>>> 
>>>>>  sysname
>>>>> 
>>>>> "Darwin"
>>>>> 
>>>>> release
>>>>> 
>>>>> "13.0.0"
>>>>> 
>>>>> version
>>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>>> 
>>>>> nodename
>>>>> 
>>>>> "dooku.local"
>>>>> 
>>>>> machine
>>>>> 
>>>>> "x86_64"
>>>>> 
>>>>> login
>>>>> 
>>>>> "yitping"
>>>>> 
>>>>> user
>>>>> 
>>>>> "yitping"
>>>>> 
>>>>> effective_user
>>>>> 
>>>>> ?yitping"
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>> 
>>>>> Hi Yitping,
>>>>> 
>>>>> thank you for your interest in the RcppOctave package, which will
>>>>> hopefully provide what you need... once you get it working :D
>>>>> It will be great to get your feedback on how things work from a
>>>>> Mac-Octave user point of view.
>>>>> 
>>>>> The package should compile fine with the settings described in the
>>>>> README file.
>>>>> Can you please send more details on your R (output of sessionInfo() and
>>>>> Sys.info) and Octave installation.
>>>>> Did you fetch the latest version of the source package from github?
>>>>> 
>>>>> In R, try:
>>>>> 
>>>>> library(devtools)
>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>> 
>>>>> 
>>>>> Renaud
>>>>> 
>>>>> 
>>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>> 
>>>>>> Hi RcppOctave users,
>>>>>> 
>>>>>> I have just found out about this R packages and I am very excited about
>>>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>>>> package will be perfect for me.
>>>>>> 
>>>>>> I also understand that the package still has some installation issues
>>>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>>>> for the sake of trying and this is what I got.
>>>>>> 
>>>>>> - I have Octave 3.6.4 installed.
>>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>>> - But I cannot proceed (to generating the documentation part) because
>>>>>> the library cannot be loaded. This is the error message I got.
>>>>>> 
>>>>>> Error in dyn.load("RcppOctave.so") :
>>>>>>  unable to load shared object
>>>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>>  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>  Referenced from:
>>>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>  Expected in: flat namespace
>>>>>> in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>> 
>>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>>> 
>>>>>> 
>>>>>> Best regards,
>>>>>> Yitping
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Rcppoctave-user mailing list
>>>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>>> 
>>>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>> 
>> 
>> 
>> _______________________________________________
>> Rcppoctave-user mailing list
>> Rcppoctave-user at lists.r-forge.r-project.org
>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>> 

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From djsamperi at gmail.com  Fri Nov 22 17:42:40 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 22 Nov 2013 11:42:40 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <52D94549-5B23-47F7-B150-BC76A3F981DB@mpe.mpg.de>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <CADUbQ5h6mNuaHbQJ+vikmJ6M+kgumRbwmqbUNi98F71+c14qSQ@mail.gmail.com>
 <52D94549-5B23-47F7-B150-BC76A3F981DB@mpe.mpg.de>
Message-ID: <CADUbQ5hwURHsJ_WXHCrM9ZA8CaMk-VW-r8t9nhHaB1ZJ-xB-ug@mail.gmail.com>

I am not seeing this behavior. RcppOctave works the same from
the command line or from the R GUI, and in the GUI I get:

> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/Cellar/octave/3.6.4/bin:/usr/local/Cellar/octave/3.6.4/libexec/octave/3.6.4/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/api-v48+/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/site/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/libexec/octave/3.6.4/exec/x86_64-apple-darwin13.0.0:/usr/local/Cellar/octave/3.6.4/bin"

On Fri, Nov 22, 2013 at 11:26 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
> That is what I did. Reinstall both Rcpp and RcppOctave from the source. Yes, I am using Mavericks.
>
> I think the problem I have right now is related to how the code is checking for the Octave related environment during library loading. I could be wrong but I think the /bin/sh script that is calling octave-config is not reading the user?s shell environment settings therefore not able finding the Octave binary.
>
> Check out this the Sys.getenv(?PATH?) from the R GUI. It is quite obvious that the search is a standard one instead of a user customized one. MacPorts binaries are stored (by default) in /opt/local/bin.
>
>> Sys.getenv('PATH')
> [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
>
> Please advise.
>
> On Nov 22, 2013, at 5:18 PM, Dominick Samperi <djsamperi at gmail.com> wrote:
>
>> Make sure to reinstall both Rcpp and RcppOctave from source after
>> configuring ~/.R/Makevars. Have you upgraded to Mavericks?
>> If you installed Octave using Homebrew then clang/clang++ will
>> be used as needed. This may not be the case if MacPorts is
>> used to install.
>>
>> You could also try using gcc/g++ instead of clang/clang++ (not
>> llvm-gcc-4.2/llvm-g++-4.2), assuming that you are using
>> Mavericks.
>>
>>
>> On Fri, Nov 22, 2013 at 3:25 AM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>> Hi all,
>>>
>>> I tried compiling with CC=clang and CXX=clang++ added into ~/.R/Makevars and
>>> I got a different symbol not found. This symbol and the previous one are
>>> indeed in RcppOctave.so but why is R not loading it? I have also tried
>>> setting LD_LIBRARY_PATH and DYLD_LIBRARY_PATH before compiling, jus in case.
>>>
>>> Any suggestions would be very welcome. Thanks in advance again.
>>>
>>> Yitping
>>>
>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>  error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>> 6): Symbol not found:
>>> __ZN4Rcpp11EnvironmentixERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEE
>>>  Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>  Expected in: flat namespace
>>> in
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>
>>>
>>>
>>>
>>> On Nov 21, 2013, at 3:44 PM, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>
>>> Hi Renaud,
>>>
>>> But the symbol (__Z22bind_internal_variableRKSsRK12octave_value) that was
>>> reported not found in the error message belongs to RcppOctave.so instead of
>>> to liboctave.
>>>
>>> [yitping at dooku src]$ nm RcppOctave.so | grep __Z22bind_internal_variable
>>>                 U __Z22bind_internal_variableRKSsRK12octave_value
>>>
>>> [yitping at dooku src]$ nm /opt/local/lib/octave/3.6.4/liboctave.dylib | grep
>>> __Z22bind_internal_variable
>>>
>>> I tried your suggestion anyway but similar error returned.
>>>
>>> Yitping
>>>
>>>
>>> On Nov 21, 2013, at 12:02 PM, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>> wrote:
>>>
>>> Ah, true, you would need to add type = 'source' to the install.packages
>>> command.
>>> Anyway this is not the actual problem.
>>>
>>> It looks like the octave library are either not found or not loaded
>>> correctly (maybe due to the compiler discrepancy).
>>> Can you try this (not sure this is correct on Mac)
>>>
>>> LD_LIBRARY_PATH=/opt/local/lib/octave/3.6.4 R CMD INSTALL
>>> RcppOctave_0.13.3.tar.gz
>>>
>>> The idea is to put ensure the octave libraries are in the PATH.
>>>
>>> Renaud
>>>
>>>
>>> On 21 November 2013 12:54, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>
>>>> Hi Renaud,
>>>>
>>>> I tried your suggestion but R complains that the package is not available
>>>> as a binary. This is the same error that led me to compile it from the
>>>> command line in the first place. But trying it from the command line with
>>>> RcppOctave_0.13.3.tar.gz from the suggested repository and using the
>>>> suggested installation options did not work either. The output of is below.
>>>>
>>>> Thanks again.
>>>>
>>>> Yitping
>>>>
>>>> [yitping at dooku src]$ R CMD INSTALL --no-docs --no-help RcppOctave
>>>> * installing to library
>>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library?
>>>> * installing *source* package ?RcppOctave? ...
>>>> checking for gcc... gcc
>>>> checking whether the C compiler works... yes
>>>> checking for C compiler default output file name... a.out
>>>> checking for suffix of executables...
>>>> checking whether we are cross compiling... no
>>>> checking for suffix of object files... o
>>>> checking whether we are using the GNU C compiler... yes
>>>> checking whether gcc accepts -g... yes
>>>> checking for gcc option to accept ISO C89... none needed
>>>> checking for g++... g++
>>>> checking whether we are using the GNU C++ compiler... yes
>>>> checking whether g++ accepts -g... yes
>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>> checking whether R is a shared library... yes
>>>> checking type of Operating System... Darwin
>>>> checking whether OS is Mac OS (Darwin)... yes
>>>> Using mkoctfile with R_LDFLAGS: -Wl,"-F/Library/Frameworks/R.framework/..
>>>> -framework R"
>>>> Using mkoctfile with R_CPPFLAGS:
>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>> checking for octave-config... /opt/local/bin/octave-config
>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>> checking Octave include flags...
>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>> checking Octave version... 3.6.4
>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>> yes
>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>> -loctinterp -loctave -lcruft
>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1
>>>> checking RcppOctave Octave module directory...
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> configure: creating ./config.status
>>>> config.status: creating src/Makevars
>>>> config.status: creating src/modules/Makefile
>>>> ** libs
>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>> -loctave -lcruft -arch x86_64
>>>> "/opt/local/bin/mkoctfile" -v
>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>> -L/Library/Frameworks/R.framework/Libraries -lR Rrng.cc
>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>> Rrng.oct Rrng.o -L/Library/Frameworks/R.framework/Libraries -lR
>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -arch x86_64
>>>> # Copying Octave modules to directory
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>> llvm-g++-4.2 -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>> llvm-g++-4.2 -arch x86_64
>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>>> rcpp_octave.o
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>> -Wl,CoreFoundation
>>>> installing to
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>> ** R
>>>> ** demo
>>>> ** inst
>>>> ** preparing package for lazy loading
>>>> ** building package indices
>>>> ** installing vignettes
>>>> ** testing if installed package can be loaded
>>>> Error : .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>  error: unable to load shared object
>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>
>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>  Referenced from:
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>  Expected in: flat namespace
>>>> in
>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>> Error: loading failed
>>>> Execution halted
>>>> ERROR: loading failed
>>>> * removing
>>>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave?
>>>>
>>>>
>>>> On Nov 21, 2013, at 10:49 AM, Renaud Gaujoux
>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>
>>>> Hi Dominick,
>>>>
>>>> Yitping is compiling (successfully) with macports, but there seem to be an
>>>> issue when actually calling the code.
>>>> I see in the log that mkoctfile uses clang, while R calls llvm-g++, could
>>>> that be the origin of the problem?
>>>>
>>>> Yitping, could you please try the following:
>>>>
>>>> install.packages('RcppOctave',
>>>> repos='http://web.cbio.uct.ac.za/~renaud/CRAN', INSTALL_opts = '--no-docs
>>>> --no-help')
>>>> library(RcppOctave)
>>>> OctaveConfig()
>>>> getLoadedDLLs()
>>>> o_runif(1)
>>>>
>>>>
>>>> Thank you
>>>>
>>>> On 21 November 2013 11:36, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>
>>>> wrote:
>>>>>
>>>>> Thanks for the details Yitping, forwarding now to the list.
>>>>> Please remember to Cc the list in your replies, so that there is a record
>>>>> for future public reference.
>>>>>
>>>>> On 20 November 2013 22:20, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>>
>>>>>> Hi Renaud,
>>>>>>
>>>>>> Thanks for your prompt reply. I tried the install_github() method you
>>>>>> suggested but to no success either. The error is similar to what I had
>>>>>> earlier, which source codes downloaded from RcppOctave cran webpage. Below
>>>>>> are the log and error messages in case it is helpful.
>>>>>>
>>>>>> I have also included the output of sessionInfo() and Sys.info(). My
>>>>>> Octave installation was done through MacPorts (octave-devel
>>>>>> @3.6.4_9+atlas+docs+gcc48).
>>>>>>
>>>>>> Thanks in advance.
>>>>>>
>>>>>> Yitping
>>>>>>
>>>>>>> library(devtools)
>>>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>>> Installing github repo(s) RcppOctave/develop from renozao
>>>>>> Downloading RcppOctave.zip from
>>>>>> https://github.com/renozao/RcppOctave/archive/develop.zip
>>>>>> Installing package from
>>>>>> /var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T//Rtmp4VW5GA/RcppOctave.zip
>>>>>> Installing RcppOctave
>>>>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL
>>>>>> \
>>>>>>
>>>>>> '/private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop'
>>>>>> \
>>>>>>
>>>>>> --library='/Library/Frameworks/R.framework/Versions/3.0/Resources/library'
>>>>>> \
>>>>>>  --with-keep.source --install-tests
>>>>>>
>>>>>> * installing *source* package 'RcppOctave' ...
>>>>>> checking for gcc... gcc
>>>>>> checking whether the C compiler works... yes
>>>>>> checking for C compiler default output file name... a.out
>>>>>> checking for suffix of executables...
>>>>>> checking whether we are cross compiling... no
>>>>>> checking for suffix of object files... o
>>>>>> checking whether we are using the GNU C compiler... yes
>>>>>> checking whether gcc accepts -g... yes
>>>>>> checking for gcc option to accept ISO C89... none needed
>>>>>> checking for g++... g++
>>>>>> checking whether we are using the GNU C++ compiler... yes
>>>>>> checking whether g++ accepts -g... yes
>>>>>> Original R_LDFLAGS: -F/Library/Frameworks/R.framework/.. -framework R
>>>>>> Original R_CPPFLAGS: -I/Library/Frameworks/R.framework/Resources/include
>>>>>> checking whether R is a shared library... yes
>>>>>> checking type of Operating System... Darwin
>>>>>> checking whether OS is Mac OS (Darwin)... yes
>>>>>> Using mkoctfile with R_LDFLAGS:
>>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R"
>>>>>> Using mkoctfile with R_CPPFLAGS:
>>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>>> checking for octave-config... /opt/local/bin/octave-config
>>>>>> checking for mkoctfile... /opt/local/bin/mkoctfile
>>>>>> checking Octave include flags...
>>>>>> -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> checking Octave -L flags... -L/opt/local/lib/octave/3.6.4
>>>>>> -L/opt/local/lib
>>>>>> checking Octave libraries... -loctinterp -loctave -lcruft
>>>>>> checking Octave version... 3.6.4
>>>>>> checking whether to infer output names for Octave function (>= 3.4.3)...
>>>>>> yes
>>>>>> Using Octave LDFLAGS: -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib
>>>>>> -loctinterp -loctave -lcruft
>>>>>> Using Octave CPPFLAGS: -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1
>>>>>> checking RcppOctave Octave module directory...
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules
>>>>>> configure: creating ./config.status
>>>>>> config.status: creating src/Makevars
>>>>>> configure: creating ./config.status
>>>>>> config.status: creating src/Makevars
>>>>>> config.status: creating src/modules/Makefile
>>>>>> ** libs
>>>>>> "/opt/local/bin/mkoctfile" -v utils.cc
>>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -I/opt/local/include -pipe -Os -arch x86_64 utils.cc -o utils.o
>>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>>> utils.oct utils.o -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp
>>>>>> -loctave -lcruft -arch x86_64
>>>>>> "/opt/local/bin/mkoctfile" -v
>>>>>> -I/Library/Frameworks/R.framework/Resources/include
>>>>>> -Wl,"-F/Library/Frameworks/R.framework/.. -framework R" Rrng.cc
>>>>>> /usr/bin/clang++ -c -fPIC -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -I/opt/local/include -pipe -Os -arch x86_64
>>>>>> -I/Library/Frameworks/R.framework/Resources/include Rrng.cc -o Rrng.o
>>>>>> /usr/bin/clang++ -bundle -bundle_loader /opt/local/bin/octave-3.6.4 -o
>>>>>> Rrng.oct Rrng.o -Wl,-F/Library/Frameworks/R.framework/.. -framework R
>>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>>> -arch x86_64
>>>>>> # Copying Octave modules to directory
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/modules'
>>>>>> llvm-g++-4.2 -arch x86_64
>>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>>> -fPIC  -I/opt/local/include -c conversion.cpp -o conversion.o
>>>>>> llvm-g++-4.2 -arch x86_64
>>>>>> -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>>>>> `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e
>>>>>> "Rcpp:::CxxFlags()"` -I/opt/local/include/octave-3.6.4/octave/..
>>>>>> -I/opt/local/include/octave-3.6.4/octave -I/opt/local/include
>>>>>> -DOCT_POST_3_4_0=1 -I/usr/local/include
>>>>>> -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"
>>>>>> -fPIC  -I/opt/local/include -c rcpp_octave.cpp -o rcpp_octave.o
>>>>>> llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
>>>>>> -undefined dynamic_lookup -single_module -multiply_defined suppress
>>>>>> -L/usr/local/lib -L/usr/local/lib -o RcppOctave.so conversion.o
>>>>>> rcpp_octave.o
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
>>>>>> -L/opt/local/lib/octave/3.6.4 -L/opt/local/lib -loctinterp -loctave -lcruft
>>>>>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>>>>> -Wl,CoreFoundation
>>>>>> installing to
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
>>>>>> ** R
>>>>>> ** demo
>>>>>> ** inst
>>>>>> ** tests
>>>>>> ** preparing package for lazy loading
>>>>>> ** help
>>>>>> Error :
>>>>>> /private/var/folders/8x/g0dbm9yd1pz5n54vh5vdsmv40000gr/T/Rtmp4VW5GA/RcppOctave-develop/man/o_addpath.Rd:41:
>>>>>> .onLoad failed in loadNamespace() for 'RcppOctave', details:
>>>>>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>>>>>>  error: unable to load shared object
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so':
>>>>>>
>>>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so,
>>>>>> 6): Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>  Referenced from:
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>>  Expected in: flat namespace
>>>>>> in
>>>>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave/libs/RcppOctave.so
>>>>>> ERROR: installing Rd objects failed for package 'RcppOctave'
>>>>>> * removing
>>>>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppOctave'
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> R version 3.0.2 (2013-09-25)
>>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>
>>>>>>
>>>>>>  sysname
>>>>>>
>>>>>> "Darwin"
>>>>>>
>>>>>> release
>>>>>>
>>>>>> "13.0.0"
>>>>>>
>>>>>> version
>>>>>> "Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
>>>>>> root:xnu-2422.1.72~6/RELEASE_X86_64"
>>>>>>
>>>>>> nodename
>>>>>>
>>>>>> "dooku.local"
>>>>>>
>>>>>> machine
>>>>>>
>>>>>> "x86_64"
>>>>>>
>>>>>> login
>>>>>>
>>>>>> "yitping"
>>>>>>
>>>>>> user
>>>>>>
>>>>>> "yitping"
>>>>>>
>>>>>> effective_user
>>>>>>
>>>>>> ?yitping"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Nov 20, 2013, at 8:26 PM, Renaud Gaujoux
>>>>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>>>>>>
>>>>>> Hi Yitping,
>>>>>>
>>>>>> thank you for your interest in the RcppOctave package, which will
>>>>>> hopefully provide what you need... once you get it working :D
>>>>>> It will be great to get your feedback on how things work from a
>>>>>> Mac-Octave user point of view.
>>>>>>
>>>>>> The package should compile fine with the settings described in the
>>>>>> README file.
>>>>>> Can you please send more details on your R (output of sessionInfo() and
>>>>>> Sys.info) and Octave installation.
>>>>>> Did you fetch the latest version of the source package from github?
>>>>>>
>>>>>> In R, try:
>>>>>>
>>>>>> library(devtools)
>>>>>> install_github('RcppOctave', 'renozao', ref = 'develop')
>>>>>>
>>>>>>
>>>>>> Renaud
>>>>>>
>>>>>>
>>>>>> On 20 November 2013 19:25, Yitping Kok <yitping at mpe.mpg.de> wrote:
>>>>>>>
>>>>>>> Hi RcppOctave users,
>>>>>>>
>>>>>>> I have just found out about this R packages and I am very excited about
>>>>>>> it. I am an Octave user and would like to use more R. Therefore I think this
>>>>>>> package will be perfect for me.
>>>>>>>
>>>>>>> I also understand that the package still has some installation issues
>>>>>>> with Mac OS. However I tried to install the package on a Mac platform anyway
>>>>>>> for the sake of trying and this is what I got.
>>>>>>>
>>>>>>> - I have Octave 3.6.4 installed.
>>>>>>> - I managed to compile the shared library, RcppOctave.so.
>>>>>>> - But I cannot proceed (to generating the documentation part) because
>>>>>>> the library cannot be loaded. This is the error message I got.
>>>>>>>
>>>>>>> Error in dyn.load("RcppOctave.so") :
>>>>>>>  unable to load shared object
>>>>>>> '/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so':
>>>>>>>  dlopen(/Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so, 6):
>>>>>>> Symbol not found: __Z22bind_internal_variableRKSsRK12octave_value
>>>>>>>  Referenced from:
>>>>>>> /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>>  Expected in: flat namespace
>>>>>>> in /Users/yitping/Toolbox/R/src/RcppOctave/src/RcppOctave.so
>>>>>>>
>>>>>>> Any idea why it is so? Any help would be appreciated. Thanks very much.
>>>>>>>
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Yitping
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Rcppoctave-user mailing list
>>>>>>> Rcppoctave-user at lists.r-forge.r-project.org
>>>>>>>
>>>>>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Rcppoctave-user mailing list
>>> Rcppoctave-user at lists.r-forge.r-project.org
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>
>>>
>>>
>>> _______________________________________________
>>> Rcppoctave-user mailing list
>>> Rcppoctave-user at lists.r-forge.r-project.org
>>> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>>>
>

From djsamperi at gmail.com  Fri Nov 22 18:14:48 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Fri, 22 Nov 2013 12:14:48 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>
 <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>
Message-ID: <CADUbQ5iiZU-qbFb1gCaLngoa8pBxqz0z1MmiSV9K+gXUy7QMaw@mail.gmail.com>

Renaud,

Looks like you don't have a Mac yet.

Under Mac OS X you can get the installed version using
sw_vers -productVersion

The result is 10.9 for Mavericks.

You can check for this and when true insert the definitions for
CC and CXX into the package Makevars.

Yitping's problem might be due to the fact that Homebrew binaries
are installed into /usr/local/bin (already on his minimal path), but
MacPorts binaries go into /opt/local/bin (not on his minimal path).

Dominick


On Fri, Nov 22, 2013 at 8:57 AM, Renaud Gaujoux
<renaud at mancala.cbio.uct.ac.za> wrote:
>
>>
>> I have successfully compile, install and load RcppOctave on my Mac
>> (running Mavericks). In order to do this I have to reinstall Rcpp with
>> customized ~/.R/Makevars (CC=clang, etc).
>
>
> Nice!
>
>>
>> I can load the library from the command line R but not from the GUI. It
>> should be something related to the search path because octave-config could
>> not be found. I will post it here if I find a way. In the meantime, any
>> suggestions would be very welcome.
>
>
> Interesting. Can you please try directly loading the library with:
>
> library.dynam(RcppOctave, RcppOctave, dirname(path.package('RcppOctave)))
>
> I am wondering if the library could still load despite octave-config not
> being in the path.
>
> Please let me know if calling Octave functions work fine.
> Ideally, you would also run the following to make a complete check (from
> command line), you may need to install the Suggests dependencies:
>
> R CMD check --as-cran RcppOctave_0.13.3.tar.gz
>
> Thank you.
>
> Bests,
> Renaud
>
> _______________________________________________
> Rcppoctave-user mailing list
> Rcppoctave-user at lists.r-forge.r-project.org
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>

From renaud at mancala.cbio.uct.ac.za  Sat Nov 23 05:41:18 2013
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Sat, 23 Nov 2013 06:41:18 +0200
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
In-Reply-To: <CADUbQ5iDTrxVnWKKhE35FAsy1wRamR76n+0CRcWBOKW0KeATtA@mail.gmail.com>
References: <FD75426D-601C-4FDE-A7A4-BAC199C349AC@mpe.mpg.de>
 <CAHavPHFJXi2sd6aq7Rh6_m6bOyNr=G7gO0PK8MqnS0ozpJE9SA@mail.gmail.com>
 <E623E40C-0762-47B5-A0A4-3297E5FA981D@mpe.mpg.de>
 <CAHavPHGNiSNq8Tw4m9QaOJJRiSrxsCODFRgt-dNO=WR6haahTw@mail.gmail.com>
 <CAHavPHHpH6owGtcn_cnyGr13H1Pwc-kcUZEAN0umNnVS3kHi6A@mail.gmail.com>
 <11C0706A-EC80-4617-86A4-9B16AEC730F3@mpe.mpg.de>
 <CAHavPHGKqdDNy8hjzfL=NHaQGJqoZhWJGX9nTqkYeND_cgexow@mail.gmail.com>
 <797AA9FE-78B6-4B1D-892C-EAC7686943C9@mpe.mpg.de>
 <EB5B07F7-32BC-4430-AF4E-1ECEB866E004@mpe.mpg.de>
 <E2D429D7-537F-457A-BC90-DD6C8BF2B4A6@mpe.mpg.de>
 <CAHavPHHycmmDbyxPDrw5gC11T660MjLtaQLKa2yeAkExGFN55w@mail.gmail.com>
 <CADUbQ5iiZU-qbFb1gCaLngoa8pBxqz0z1MmiSV9K+gXUy7QMaw@mail.gmail.com>
 <CADUbQ5iDTrxVnWKKhE35FAsy1wRamR76n+0CRcWBOKW0KeATtA@mail.gmail.com>
Message-ID: <CAHavPHEA1Owiyx4p4jFjjLLyAvn060H3cJxjsJWOCfFy_wntgA@mail.gmail.com>

I thought of a work around for this: if deemed necessary by the configure
script based on the compiler used by Rcpp/R one would recompile Rcpp as a
static library, include it in the RcppOctave libs/ directory and link
against it. Que tal?

The path issue is actually easy to fix, I think.

Renaud

On Friday, November 22, 2013, Dominick Samperi wrote:

> On second thought the sw_vers trick will not work unless it
> is also implemented by the Rcpp package...
>
> On Fri, Nov 22, 2013 at 12:14 PM, Dominick Samperi <djsamperi at gmail.com<javascript:;>>
> wrote:
> > Renaud,
> >
> > Looks like you don't have a Mac yet.
> >
> > Under Mac OS X you can get the installed version using
> > sw_vers -productVersion
> >
> > The result is 10.9 for Mavericks.
> >
> > You can check for this and when true insert the definitions for
> > CC and CXX into the package Makevars.
> >
> > Yitping's problem might be due to the fact that Homebrew binaries
> > are installed into /usr/local/bin (already on his minimal path), but
> > MacPorts binaries go into /opt/local/bin (not on his minimal path).
> >
> > Dominick
> >
> >
> > On Fri, Nov 22, 2013 at 8:57 AM, Renaud Gaujoux
> > <renaud at mancala.cbio.uct.ac.za <javascript:;>> wrote:
> >>
> >>>
> >>> I have successfully compile, install and load RcppOctave on my Mac
> >>> (running Mavericks). In order to do this I have to reinstall Rcpp with
> >>> customized ~/.R/Makevars (CC=clang, etc).
> >>
> >>
> >> Nice!
> >>
> >>>
> >>> I can load the library from the command line R but not from the GUI. It
> >>> should be something related to the search path because octave-config
> could
> >>> not be found. I will post it here if I find a way. In the meantime, any
> >>> suggestions would be very welcome.
> >>
> >>
> >> Interesting. Can you please try directly loading the library with:
> >>
> >> library.dynam(RcppOctave, RcppOctave,
> dirname(path.package('RcppOctave)))
> >>
> >> I am wondering if the library could still load despite octave-config not
> >> being in the path.
> >>
> >> Please let me know if calling Octave functions work fine.
> >> Ideally, you would also run the following to make a complete check (from
> >> command line), you may need to install the Suggests dependencies:
> >>
> >> R CMD check --as-cran RcppOctave_0.13.3.tar.gz
> >>
> >> Thank you.
> >>
> >> Bests,
> >> Renaud
> >>
> >> _______________________________________________
> >> Rcppoctave-user mailing list
> >> Rcppoctave-user at lists.r-forge.r-project.org <javascript:;>
> >>
> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
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From djsamperi at gmail.com  Sat Nov 23 07:21:35 2013
From: djsamperi at gmail.com (Dominick Samperi)
Date: Sat, 23 Nov 2013 01:21:35 -0500
Subject: [Rcppoctave-user] Cannot load RcppOctave.so onto Mac OS
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Recompiling Rcpp as needed could work, but this is not a very elegant
solution, and the problem will probably disappear when the next version
of R is released. There has been much discussion on R-SIG-Mac about
Mavericks issues, and I suspect a fix will be included in the next release.

This could be as simple as using gcc/g++ for the compilers instead of
llvm-gcc-4.2/llvm-g++-4.2. Under Mavericks gcc/g++ are aliases for
clang/clang++, and for users of pre-Mavericks releases gcc/g++ can
also be used provided symbolic links are defined as needed.

I don't know what the plans are though.

On Fri, Nov 22, 2013 at 11:41 PM, Renaud Gaujoux
<renaud at mancala.cbio.uct.ac.za> wrote:
> I thought of a work around for this: if deemed necessary by the configure
> script based on the compiler used by Rcpp/R one would recompile Rcpp as a
> static library, include it in the RcppOctave libs/ directory and link
> against it. Que tal?
>
> The path issue is actually easy to fix, I think.
>
> Renaud
>
>
> On Friday, November 22, 2013, Dominick Samperi wrote:
>>
>> On second thought the sw_vers trick will not work unless it
>> is also implemented by the Rcpp package...
>>
>> On Fri, Nov 22, 2013 at 12:14 PM, Dominick Samperi <djsamperi at gmail.com>
>> wrote:
>> > Renaud,
>> >
>> > Looks like you don't have a Mac yet.
>> >
>> > Under Mac OS X you can get the installed version using
>> > sw_vers -productVersion
>> >
>> > The result is 10.9 for Mavericks.
>> >
>> > You can check for this and when true insert the definitions for
>> > CC and CXX into the package Makevars.
>> >
>> > Yitping's problem might be due to the fact that Homebrew binaries
>> > are installed into /usr/local/bin (already on his minimal path), but
>> > MacPorts binaries go into /opt/local/bin (not on his minimal path).
>> >
>> > Dominick
>> >
>> >
>> > On Fri, Nov 22, 2013 at 8:57 AM, Renaud Gaujoux
>> > <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>
>> >>>
>> >>> I have successfully compile, install and load RcppOctave on my Mac
>> >>> (running Mavericks). In order to do this I have to reinstall Rcpp with
>> >>> customized ~/.R/Makevars (CC=clang, etc).
>> >>
>> >>
>> >> Nice!
>> >>
>> >>>
>> >>> I can load the library from the command line R but not from the GUI.
>> >>> It
>> >>> should be something related to the search path because octave-config
>> >>> could
>> >>> not be found. I will post it here if I find a way. In the meantime,
>> >>> any
>> >>> suggestions would be very welcome.
>> >>
>> >>
>> >> Interesting. Can you please try directly loading the library with:
>> >>
>> >> library.dynam(RcppOctave, RcppOctave,
>> >> dirname(path.package('RcppOctave)))
>> >>
>> >> I am wondering if the library could still load despite octave-config
>> >> not
>> >> being in the path.
>> >>
>> >> Please let me know if calling Octave functions work fine.
>> >> Ideally, you would also run the following to make a complete check
>> >> (from
>> >> command line), you may need to install the Suggests dependencies:
>> >>
>> >> R CMD check --as-cran RcppOctave_0.13.3.tar.gz
>> >>
>> >> Thank you.
>> >>
>> >> Bests,
>> >> Renaud
>> >>
>> >> _______________________________________________
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>> >> Rcppoctave-user at lists.r-forge.r-project.org
>> >>
>> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user
>> >>
>>
>