[Phylobase-devl] [R-sig-phylo] Phylobase 0.4 Forge (installing issues in my old G4 powerBook)

Fri Mar 13 20:47:59 CET 2009

Dear Peter, Brian & Mark

Thanks for taking your time and your comments. Compilation process now
seems to be targeting OSX 10.4 after
Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4"). However after all the
compilation faile.

This red labeled output

ld: /Library/Frameworks/R.framework/../R.framework/R load command 14
unknown cmd field
/usr/bin/libtool: internal link edit command failed
make: *** [phylobase.so] Error 1
chmod: /Library/Frameworks/R.framework/Versions/2.8/Resources/library/phylobase/libs/ppc/*:
No such file or directory
ERROR: compilation failed for package 'phylobase'

I also noticed red labeled lines during initial stage of compilation as:

nxscharactersblock.cpp: In member function `virtual bool
NxsCharactersBlock::HandleNextState(NxsToken&, unsigned int, unsigned
int)':
nxscharactersblock.cpp:1412: warning: passing 'const double' for
converting 1 of 'std::vector<_Tp, _Alloc>::vector(size_t) [with _Tp =
double, _Alloc = std::allocator<double>]'

I already compiled phylobase in a newer OSX 10.5. However, I will
appreciate if you can help to make this old Power Book G4 to rock with
phylobase.

Raul Sedano

On Fri, Mar 13, 2009 at 6:11 AM, Mark Holder <mtholder at ku.edu> wrote:

> Hi,
>        Take this with a grain of salt, because I've never done any
> development in R, but...
>
>        I should be possible to compile and install NCL into a location on
> your system's LD_LIBRARY_PATH ( the DYLD_LIBRARY_PATH on Mac), such that
> phylobase picks up NCL from that location.  (note that LD_LIBRARY_PATH and
> DYLD_LIBRARY_PATH are environmental variables that can be set in your
> environment if you install in "non-standard" locations, if you install to
> /usr or /usr/local you usually do not have to set any variables).
>
>        You'd have to make sure that you install a version of NCL that has
> all of the functions that phylobase uses, but that should not be hard to do
> (I'd pull the NCL out of the phylobase distribution, if I were trying this).
>
>        If NCL itself (outside of phylobase) won't build on your PPC, then I
> should be able to help you with that.
>
>        Perhaps a more experienced R user can chime in on whether installing
> to a system location is going to cause problem for an R package.
>
>
> All the best,
> Mark
>
>
>
>
>
> On Mar 12, 2009, at 11:03 PM, Brian O'Meara wrote:
>
>  This error seems to have come up with another package (gee), and the
>> solution is setting an environmental variable. See thread at
>> https://stat.ethz.ch/pipermail/r-sig-mac/2008-October/005450.html
>>
>>> . Basically do Sys.setenv("MACOSX_DEPLOYMENT_TARGET"="10.4") so that
>>>
>> it targets 10.4 rather than 10.1.
>>
>> Brian
>>
>>
>> On Mar 12, 2009, at 10:41 PM, Raul Sedano wrote:
>>
>>  Thanks Brian,
>>> While your 4 steps did work in a Mac OSX 10.5, it did not work on my
>>> old PPC 10.4.11. This is what I got from R (newest version) in my
>>> old mac:
>>>
>>> After a long process of installation 10.4.11. systems, this is just
>>> the last part in red
>>>
>>> ld: flag: -undefined dynamic_lookup can't be used with
>>> MACOSX_DEPLOYMENT_TARGET environment variable set to: 10.1
>>> /usr/bin/libtool: internal link edit command failed
>>> make: *** [phylobase.so] Error 1
>>> chmod: ** Removing '/Library/Frameworks/R.framework/Versions/2.8/
>>> Resources/library/phylobase'
>>> /Library/Frameworks/R.framework/Versions/2.8/Resources/library/
>>> phylobase/libs/ppc/*: No such file or directory
>>> ERROR: compilation failed for package 'phylobase'
>>>
>>> The downloaded packages are in
>>>        /private/tmp/RtmpcBvRaE/downloaded_packages
>>> Updating HTML index of packages in '.Library'
>>> Warning message:
>>> In install.packages("phylobase", repos = "http://R-Forge.R-
>>> project.org",  :
>>>  installation of package 'phylobase' had non-zero exit status
>>>
>>> However, I was able to follow most of the Brian's four steps to
>>> remove phylobase and then re-install it but source compilation
>>> failed. Can you guys tell what is wrong with compilation? is this a
>>> issue just with OSX 10.4.11?
>>>
>>> Raul Sedano
>>>
>>>
>>> On Thu, Mar 12, 2009 at 3:13 PM, Brian O'Meara
>>> <bcomeara at nescent.org> wrote:
>>> Thanks, Peter and Roland, for  your emails. Installing from source
>>> with install.packages("phylobase",repos="http://R-Forge.R-
>>> project.org", type='source') worked. I think my problem earlier was
>>> that while I was using "R CMD REMOVE phylobase", I didn't restart R
>>> between attempted installs or unload and then load phylobase, so the
>>> version being used was never updated in memory. Peter, the reason I
>>> suspected a 10.4/10.5 was that my particular error, based on
>>> googling for it, occurs with code compiled on 10.5 without
>>> explicitly also being compiled for 10.4 (i.e., see <
>>> http://snipurl.com/crosscompile
>>>
>>>> ).
>>>>
>>>
>>> So, Raul, if you 1) Quit R, 2) Run "R CMD REMOVE phylobase" in
>>> Terminal, 3) type "install.packages("phylobase",repos="
>>> http://R-Forge.R-project.org
>>> ", type='source')" in R, 4) type "library(phylobase)", does
>>> everything work?
>>>
>>> Brian
>>>
>>>
>>>
>>> On Mar 12, 2009, at 5:54 PM, Peter Cowan wrote:
>>>
>>> On Mar 12, 2009, at 1:00 PM, Brian O'Meara wrote:
>>>
>>> Well, using 10.4.11 on an intel mac, with developer tools installed,
>>> running R 2.8.1, and got the error when trying to load phylobase
>>> (install appeared to work, just error on load):
>>>
>>>  install.packages("phylobase",repos="http://R-Forge.R-project.org")
>>>>
>>> trying URL '
>>> http://R-Forge.R-project.org/bin/macosx/universal/contrib/2.8/phylobase_0.4.tgz
>>> '
>>> Content type 'application/x-gzip' length 663910 bytes (648 Kb)
>>> opened URL
>>> ==================================================
>>> downloaded 648 Kb
>>>
>>>
>>> The downloaded packages are in
>>>      /tmp/RtmpFOnUD2/downloaded_packages
>>>
>>>  library(phylobase)
>>>>
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library '/Library/Frameworks/R.framework/
>>> Resources/library/phylobase/libs/i386/phylobase.so':
>>> dlopen(/Library/Frameworks/R.framework/Resources/library/phylobase/
>>> libs/i386/phylobase.so, 6): Symbol not found:
>>> Referenced from: /Library/Frameworks/R.framework/Resources/library/
>>> phylobase/libs/i386/phylobase.so
>>> Expected in: /usr/lib/libSystem.B.dylib
>>>
>>> Error in library(phylobase) : .First.lib failed for 'phylobase'
>>>
>>> So, it's not an issue of Raul not having developer tools (though I
>>> get a slightly different error, I'm assuming it is the same root
>>> cause). My error comes from the compiled version being made just for
>>> Mac OS 10.5, not cross-compiled for 10.4. My error persists when
>>> installing from source, though (after removing phylobase first),
>>> both from the 0.4 release and the trunk.
>>>
>>> How can you tell it is due to the 10.4/10.5 difference.  I'm no
>>> expert, but I would have guessed that they wouldn't differ when it
>>> comes to building R packages.
>>>
>>> Brian when you run
>>>
>>> install.packages("phylobase",repos="http://R-Forge.R-project.org",
>>> type='source')
>>>
>>> Do you get any errors?  Or is it when loading the package?
>>>
>>> Is this email helpful here:
>>>
>>> <
>>> http://lists.r-forge.r-project.org/pipermail/phylobase-devl/2008-July/000192.html
>>>
>>>>
>>>>
>>> We've run through this before with phylobase, I think the fix
>>> involved a makefile, but I wonder how it got broken again.
>>>
>>> This might add impetus to update NCL, I think that the building
>>> process might have been improved.
>>>
>>> peter
>>>
>>>
>>> Brian
>>>
>>>
>>> On Mar 12, 2009, at 12:32 AM, Peter Cowan wrote:
>>>
>>> Raul,
>>>
>>> I'm CCing r-sig-phylo and the phylobase-dev list as other people may
>>> be having the same problem.
>>>
>>> On Mar 11, 2009, at 8:10 PM, Raul Sedano wrote:
>>>
>>> Hi Peter, thanks for your comments, I already tried your suggestion.
>>> This is
>>> what I got when using install.packages("phylobase", repos="
>>> http://R-Forge.R-project.org")
>>> Error in library(phylobase) : .First.lib failed for 'phylobase'
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared library
>>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/
>>> phylobase/libs/ppc/phylobase.so':
>>> dlopen(/Library/Frameworks/R.framework/Versions/2.8/Resources/
>>> library/phylobase/libs/ppc/phylobase.so,
>>> 6): Symbol not found: __ZN8NxsBlock16GetImpliedBlocksEv
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Versions/2.8/Resources/library/
>>> phylobase/libs/ppc/phylobase.so
>>> Expected in: dynamic lookup
>>>
>>> This should have worked.  It works for me, however I'm using 10.5 on
>>> an intel computer.  Guessing from the error message you're using a
>>> PPC computer.
>>>
>>> Any ideas to solve this? I though the problem was related to the
>>> lack of
>>> compilers. I have tried multiple compilers including those you pointed
>>> through the website.
>>>
>>> Well we know appear to have two problems, one is that the build from
>>> R-forge doesn't work on your system (does any one on the list have a
>>> PPC with Mac os X 10.4, to confirm this).  The other problem is that
>>> it's not compiling either.
>>>
>>> Are you still getting the same errors even with the developer tools
>>> installed?
>>>
>>> Peter
>>>
>>>
>>> Raul Sedano
>>>
>>>
>>>
>>> On Wed, Mar 11, 2009 at 6:02 PM, Peter Cowan <pdc at berkeley.edu> wrote:
>>>
>>> Raul,
>>>
>>> Yes, you need to have the full developer tools package installed for
>>> compiling to work.  It's installs a bunch of programs necessary to
>>> build
>>> from source.  Out of curiosity, is there a reason why you're trying to
>>> install from source?
>>>
>>> You should be able to install the package using the following line
>>> in R:
>>>
>>> install.packages("phylobase", repos="http://R-Forge.R-project.org")
>>>
>>> Peter
>>>
>>>
>>>
>>> On Mar 11, 2009, at 5:10 PM, Raul Sedano wrote:
>>>
>>> Hey Peter, I got a different output from the terminal. Do you have any
>>> suggestion to correct this in my system? This might be the reason
>>> for my
>>> current problem installing phylobase.Raul:~ Milvago$ Make
>>> -bash: Make: command not found
>>> Raul:~ Milvago$
>>>
>>> Should I use installers from Apple Developer Tools package to solve
>>> this
>>> problem. Yes I did install gcc3.3 (but also tried gcc4.0) software
>>> from
>>> the
>>> Xcode Tools /Applications/Installers in my PowerBook.
>>>
>>> Thanks in advance,
>>>
>>> Raul Sedano
>>>
>>> On Wed, Mar 11, 2009 at 4:33 PM, Peter Cowan <pdc at berkeley.edu> wrote:
>>>
>>> Raul,
>>>
>>> When you say you installed the compilers in the R-FAQ, which ones do
>>> you
>>> mean?  Did you install the tools individually or as the Apple
>>> Developer
>>> Tools package?  For the mac the best guide to compliers for R stuff,
>>> is
>>> here:
>>>
>>> <http://r.research.att.com/tools/>
>>>
>>> When you open the terminal and run the command "make" what do you get?
>>>
>>> I see:
>>>
>>> Macintosh-7:~ peter$ make
>>> make: *** No targets specified and no makefile found.  Stop.
>>> Macintosh-7:~ peter$
>>>
>>> Peter
>>>
>>>
>>> On Mar 11, 2009, at 4:22 PM, Raul Sedano wrote:
>>>
>>> Hey,
>>>
>>> First, I want to thanks Phylobase developers for such flexible
>>> application,
>>> I look forward to squeeze phylobase capabilities. However I need some
>>> advice
>>> to install Phylobase 0.4 (source) in my old G4/10.4/mac. I have
>>> installed compilers as indicated in R-FAQ but still does not work. The
>>> same
>>> error show up  in multiple newer PowerBook machines. I got the
>>> following
>>> R
>>> "response" suggesting the lack of a Make command. I will appreciate
>>> any
>>> comments in such basic topic.
>>>
>>> Raul Sedano
>>>
>>>
>>>
>>> trying URL '
>>> http://r-forge.r-project.org/src/contrib/phylobase_0.4.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 771914 bytes (753 Kb)
>>> opened URL
>>> ==================================================
>>> downloaded 753 Kb
>>>
>>> WARNING: ignoring environment value of R_HOME
>>> * Installing *source* package 'phylobase' ...
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> /Library/Frameworks/R.framework/Resources/bin/config: line 1: make:
>>> command
>>> not found
>>> checking for g++... no
>>> checking for c++... no
>>> checking for gpp... no
>>> checking for aCC... no
>>> checking for CC... no
>>> checking for cxx... no
>>> checking for cc++... no
>>> checking for cl... no
>>> checking for FCC... no
>>> checking for KCC... no
>>> checking for RCC... no
>>> checking for xlC_r... no
>>> checking for xlC... no
>>> checking for C++ compiler default output file name... configure:
>>> error:
>>> C++
>>> compiler cannot create executables
>>> See `config.log' for more details.
>>> ERROR: configuration failed for package 'phylobase'
>>> ** Removing
>>>
>>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/
>>> phylobase'
>>> ** Restoring previous
>>>
>>> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/
>>> phylobase'
>>>
>>> The downloaded packages are in
>>> /private/tmp/RtmpMpRHQe/downloaded_packages
>>>
>>>
>>>
>>>  [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-phylo mailing list
>>> R-sig-phylo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> R-sig-phylo mailing list
>>> R-sig-phylo at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>>
>>>
>>> ________________________________
>>> Brian O'Meara
>>> NESCent
>>> Durham, NC
>>> http://www.brianomeara.info
>>> ________________________________
>>>
>>>
>>>
>>>
>>>
>>>
>>> ________________________________
>>> Brian O'Meara
>>> NESCent
>>> Durham, NC
>>> http://www.brianomeara.info
>>> ________________________________
>>>
>>>
>>>
>>>
>>>
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>
>
> Mark Holder
>
> mtholder at ku.edu
> http://www.people.ku.edu/~mtholder/
>
> ==============================================
> Department of Ecology and Evolutionary Biology
> University of Kansas
> 6031 Haworth Hall
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045
>
> lab phone:  785.864.5789
>
> fax (shared): 785.864.5860
> ==============================================
>
>
>
>
>
>
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>
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