From kammon101 at hotmail.ca  Sat Mar  1 19:41:46 2014
From: kammon101 at hotmail.ca (kam kammon)
Date: Sat, 1 Mar 2014 13:41:46 -0500
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
 Linux)
In-Reply-To: <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>,
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>,
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>,
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>,
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>,
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
Message-ID: <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>

Hi,

It installed correctly without mpi but it still doesn't work with mpi. Not sure if it has anything to do with whether octave was compiled with mpi (in both cases they were, the two Ubuntu systems are clones) The only difference is that in one system (the one where rcppoctave now works) I have removed the hdf5 packages with mpi enabled and replaced them with the version without mpi. So it is a hdf5 issue.

There is a thread on the shogun-toolbox forum which may be of interest (no solution, but the same issue apparently)

https://github.com/shogun-toolbox/shogun/issues/1856

Thanks

Date: Fri, 28 Feb 2014 14:21:21 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org


Hi,

I have just pushed a fix for this issue, at least when installing on Octave compiled without MPI.
Can you please try:

library(devtools)

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


Thanks.

Renaud



On 27 February 2014 22:45, kam kammon <kammon101 at hotmail.ca> wrote:





Hello, 

I tried installed rcppoctave  from git with and without  mpi. The failure logs are attached.
They were from git on Feb 23

Thanks

BernardDate: Wed, 12 Feb 2014 15:19:51 +0200

Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca


Putting rcppoctave-user at lists.r-forge.r-project.org in Cc of all your emails should do the trick (not changing the email Subject).



Renaud


On 12 February 2014 14:52, kam kammon <kammon101 at hotmail.ca> wrote:




Hi Renaud,

Thanks for the reply. I am currently unable to reproduce the log without mpi because if I remove the mpi packages it would remove a bunch of other things as well. But I can create a partial clone of my current system elsewhere and remove the mpi packages there. Since you are busy at the moment this can wait for a week or so.



I am kind of new to this and I am not sure how to reply to you on the mailing list on the same thread. There is no option to "reply" apparently and I don't want to create a new thread by sending  another email to rcppoctave-user at lists.r-forge.r-project.org. Please advice. 



Thanks

Bernard
Date: Sun, 9 Feb 2014 10:50:05 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za


To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org



Hi Bernard,

thank you for reporting this.
It looks like there are 2 different issues here:
  * with mpi: this issue is due to Octave trying to compile modules with MPI support. I have seen this before and am not yet sure why/how to fix it.



  * without mpi: this seems to be due to incompatibilities with 3.8, on which I have not tested RcppOctave

I cannot look into these errors now, but will do in the next couple of weeks.




Just to get a log of these errors for the latest dev version, can you please run the same installations using the version on github:

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




Thank you.

Bests,
Renaud



On 8 February 2014 04:45, kam kammon <kammon101 at hotmail.ca> wrote:






Hi, I am trying to install Rcppoctave from R with install.packages('RcppOctave') without success.

My OS is Ubuntu 13.10. R version 3.0.2, Octave version 3.8.0 (Octave is compiled from source with prefix=/usr/local)




I have tried installing hdf5  with mpi (libhdf5-mpi-dev, libhdf5-openmpi-dev and libhdf5-openmpi-7 from repository ) and without mpi (libhdf5-dev and libhdf5-7 from repository) and in both cases RcppOctave would not install. 




When libgdf5 is installed with mpi the install log shows "/usr/include/H5public.h:63:20: fatal error: mpi.h: No such file or directory"  while without mpi it shows a different error. 


I am attaching the installation log for both instances for further investigations.




Not sure if this is relevant, but when hdf5 is installed with mpi Octave needs to be recompiled  with 

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

Otherwise some octave-forge packages don't install.




http://octave.1599824.n4.nabble.com/Error-installing-package-on-classdef-tip-td4658542.html#a4658460




Thanks,

Bernard
 		 	   		  



_______________________________________________

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







 		 	   		  



 		 	   		  



 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140301/6250fa52/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: rcppoctave-no-mpi
Type: application/octet-stream
Size: 5097 bytes
Desc: not available
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140301/6250fa52/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: rcppoctave-with-mpi
Type: application/octet-stream
Size: 5096 bytes
Desc: not available
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140301/6250fa52/attachment-0001.obj>

From renaud at mancala.cbio.uct.ac.za  Mon Mar  3 09:05:22 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Mon, 3 Mar 2014 10:05:22 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
Message-ID: <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>

Good.
The MPI issue seems to be due to some compilation flags not being carried
over when compiling RcppOctave library.
The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX
-DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules,
so these flags should be available from octave-config.
Will look into it later.
Thanks.

Bests,
Renaud
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/5ea67b23/attachment.html>

From renaud at mancala.cbio.uct.ac.za  Mon Mar  3 09:16:24 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Mon, 3 Mar 2014 10:16:24 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>
Message-ID: <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>

Actually, the flags are most likely to be found in mkoctfile config.
Currently I use the flags returned by:

mkoctfile -p INCFLAGS

Might be easier if you could look if those effectively appear in this
variable or any other (do mkoctfile --help to list all variables). They
have to come from somewhere...
Thanks.

Renaud



On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> Good.
> The MPI issue seems to be due to some compilation flags not being carried
> over when compiling RcppOctave library.
> The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX
> -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules,
> so these flags should be available from octave-config.
> Will look into it later.
> Thanks.
>
> Bests,
> Renaud
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/a43c7e13/attachment.html>

From renaud at mancala.cbio.uct.ac.za  Mon Mar  3 09:30:50 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Mon, 3 Mar 2014 10:30:50 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>
 <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>
Message-ID: <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>

One more thought: have you tried installing after doing

export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

?



On 3 March 2014 10:16, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> Actually, the flags are most likely to be found in mkoctfile config.
> Currently I use the flags returned by:
>
> mkoctfile -p INCFLAGS
>
> Might be easier if you could look if those effectively appear in this
> variable or any other (do mkoctfile --help to list all variables). They
> have to come from somewhere...
> Thanks.
>
> Renaud
>
>
>
> On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>wrote:
>
>> Good.
>> The MPI issue seems to be due to some compilation flags not being carried
>> over when compiling RcppOctave library.
>> The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX
>> -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules,
>> so these flags should be available from octave-config.
>> Will look into it later.
>> Thanks.
>>
>> Bests,
>> Renaud
>>
>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/1053539b/attachment.html>

From renaud at mancala.cbio.uct.ac.za  Mon Mar  3 12:03:25 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Mon, 3 Mar 2014 13:03:25 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>
 <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>
 <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>
Message-ID: <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>

Hi,

can you please try again (from branch 'develop'). I have pushed a fix that
should solve the issue.
The MPI flags were stored in CPPFLAGS, which I now append to INCFLAGS

mkoctfile -p INCFLAGS
mkoctfile -p CPPFLAGS

Please flag this thread as SOLVED if this fixes the issue.
Thanks.

Bests,
Renaud


On 3 March 2014 10:30, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

> One more thought: have you tried installing after doing
>
>
> export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"
>
> ?
>
>
>
> On 3 March 2014 10:16, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>wrote:
>
>> Actually, the flags are most likely to be found in mkoctfile config.
>> Currently I use the flags returned by:
>>
>> mkoctfile -p INCFLAGS
>>
>> Might be easier if you could look if those effectively appear in this
>> variable or any other (do mkoctfile --help to list all variables). They
>> have to come from somewhere...
>> Thanks.
>>
>> Renaud
>>
>>
>>
>> On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>wrote:
>>
>>> Good.
>>> The MPI issue seems to be due to some compilation flags not being
>>> carried over when compiling RcppOctave library.
>>> The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX
>>> -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules,
>>> so these flags should be available from octave-config.
>>> Will look into it later.
>>> Thanks.
>>>
>>> Bests,
>>> Renaud
>>>
>>>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/e76d24c2/attachment.html>

From kammon101 at hotmail.ca  Mon Mar  3 22:56:58 2014
From: kammon101 at hotmail.ca (kam kammon)
Date: Mon, 3 Mar 2014 16:56:58 -0500
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
 Linux)
In-Reply-To: <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>,
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>,
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>,
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>,
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>,
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>,
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>,
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>,
 <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>,
 <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>,
 <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>
Message-ID: <BAY174-W35813C1A9B4B516D464CE3978F0@phx.gbl>

Hi,

Still doesn't work but with a different error which doesn't seem to involve mpi this time. It says it is an octave error but I have no idea what it may be.

Date: Mon, 3 Mar 2014 13:03:25 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org

Hi,

can you please try again (from branch 'develop'). I have pushed a fix that should solve the issue.
The MPI flags were stored in CPPFLAGS, which I now append to INCFLAGS


mkoctfile -p INCFLAGS
mkoctfile -p CPPFLAGS

Please flag this thread as SOLVED if this fixes the issue.
Thanks.

Bests,
Renaud



On 3 March 2014 10:30, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

One more thought: have you tried installing after doing

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

?





On 3 March 2014 10:16, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:


Actually, the flags are most likely to be found in mkoctfile config.
Currently I use the flags returned by:

mkoctfile -p INCFLAGS

Might be easier if you could look if those effectively appear in this variable or any other (do mkoctfile --help to list all variables). They have to come from somewhere...



Thanks.

Renaud




On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

Good.
The MPI issue seems to be due to some compilation flags not being carried over when compiling RcppOctave library. 



The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules, so these flags should be available from octave-config.

Will look into it later.
Thanks.

Bests,
Renaud









 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/603dbdf8/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: rcppoctave
Type: application/octet-stream
Size: 1061 bytes
Desc: not available
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140303/603dbdf8/attachment.obj>

From kammon101 at hotmail.ca  Sun Mar 16 09:25:42 2014
From: kammon101 at hotmail.ca (kam kammon)
Date: Sun, 16 Mar 2014 04:25:42 -0400
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
 Linux)
In-Reply-To: <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>,
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>,
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>,
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>,
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>,
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>,
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>,
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>,
 <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>,
 <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>,
 <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>
Message-ID: <BAY174-W2824B58C44C6EB65C4C26297720@phx.gbl>

Hi, Renaud

Tonight I had a chance to upgrade to Octave 3.8.1. RcppOctave from the stable branch installed fine (installed with just install.packages() in R)  so I suppose RcppOctave has been updated.
Thanks for the great work.

I am not sure how to mark the thread as solved though. 

Bernard

P.S This is unrelated but installing from the current development version return "! LaTeX Error: File `biblatex.sty' not found", hope that is helpful
Date: Mon, 3 Mar 2014 13:03:25 +0200
Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8 Linux)
From: renaud at mancala.cbio.uct.ac.za
To: kammon101 at hotmail.ca
CC: rcppoctave-user at lists.r-forge.r-project.org

Hi,

can you please try again (from branch 'develop'). I have pushed a fix that should solve the issue.
The MPI flags were stored in CPPFLAGS, which I now append to INCFLAGS


mkoctfile -p INCFLAGS
mkoctfile -p CPPFLAGS

Please flag this thread as SOLVED if this fixes the issue.
Thanks.

Bests,
Renaud



On 3 March 2014 10:30, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

One more thought: have you tried installing after doing

export  CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"

?





On 3 March 2014 10:16, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:


Actually, the flags are most likely to be found in mkoctfile config.
Currently I use the flags returned by:

mkoctfile -p INCFLAGS

Might be easier if you could look if those effectively appear in this variable or any other (do mkoctfile --help to list all variables). They have to come from somewhere...



Thanks.

Renaud




On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:

Good.
The MPI issue seems to be due to some compilation flags not being carried over when compiling RcppOctave library. 



The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules, so these flags should be available from octave-config.

Will look into it later.
Thanks.

Bests,
Renaud









 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/attachments/20140316/93457ca1/attachment.html>

From renaud at mancala.cbio.uct.ac.za  Mon Mar 17 08:32:48 2014
From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux)
Date: Mon, 17 Mar 2014 09:32:48 +0200
Subject: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
	Linux)
In-Reply-To: <BAY174-W2824B58C44C6EB65C4C26297720@phx.gbl>
References: <BAY174-W319FEA470397542F3020F097960@phx.gbl>
 <CAHavPHF1gOp47rM9ep+GNa=QFVEODwhwo_wOO0e+xXuzvByCkA@mail.gmail.com>
 <BAY174-W505F4C372C24DE91104EE097920@phx.gbl>
 <CAHavPHG-+2v2XAYcEGZ5DDs_gdvWmEUDohJed-cDTa1o543dww@mail.gmail.com>
 <BAY174-W15D37E7214554FD369ED5997830@phx.gbl>
 <CAHavPHEhG2XD9hWfaaJj-CpGY3pn9wWumKkz3mfEQd2ZBi=5+A@mail.gmail.com>
 <BAY174-W480F86B9B77947A1CD7F83978D0@phx.gbl>
 <CAHavPHH10tGBWK7Db7Rw3f9r=9CaTk=XeptJCckDDL3aRNyz2w@mail.gmail.com>
 <CAHavPHHyDdFxiYFvf=QnuzxMg=EMwamFxWKajeA7HZokpd57rg@mail.gmail.com>
 <CAHavPHEoshS_U8Ja7dgPi39iR5efDb_Fwiw78GOD53Q4-UnPZw@mail.gmail.com>
 <CAHavPHHrydVDduLH85BeMatce8GpPEYqVWo-QSEoxbHJcKSAAA@mail.gmail.com>
 <BAY174-W2824B58C44C6EB65C4C26297720@phx.gbl>
Message-ID: <CAHavPHEfwdhDFx8VUfWvFnTiyGFrhtyujRt=qLmTRo--ydAKHg@mail.gmail.com>

This is good news!
I think you can flag this as solved by pre-pending "[SOLVED]" to the subject.

The error from the develop branch is weird, but could come from a
vignette not having been properly pre-built. Will check that.

Bests,
Renaud


On 16 March 2014 10:25, kam kammon <kammon101 at hotmail.ca> wrote:
> Hi, Renaud
>
> Tonight I had a chance to upgrade to Octave 3.8.1. RcppOctave from the
> stable branch installed fine (installed with just install.packages() in R)
> so I suppose RcppOctave has been updated.
> Thanks for the great work.
>
> I am not sure how to mark the thread as solved though.
>
> Bernard
>
> P.S This is unrelated but installing from the current development version
> return "! LaTeX Error: File `biblatex.sty' not found", hope that is helpful
> ________________________________
> Date: Mon, 3 Mar 2014 13:03:25 +0200
>
> Subject: Re: [Rcppoctave-user] unable to install RcppOctave (Octave 3.8
> Linux)
> From: renaud at mancala.cbio.uct.ac.za
> To: kammon101 at hotmail.ca
> CC: rcppoctave-user at lists.r-forge.r-project.org
>
> Hi,
>
> can you please try again (from branch 'develop'). I have pushed a fix that
> should solve the issue.
> The MPI flags were stored in CPPFLAGS, which I now append to INCFLAGS
>
> mkoctfile -p INCFLAGS
> mkoctfile -p CPPFLAGS
>
> Please flag this thread as SOLVED if this fixes the issue.
> Thanks.
>
> Bests,
> Renaud
>
>
> On 3 March 2014 10:30, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>
> One more thought: have you tried installing after doing
>
>
> export CPPFLAGS="-I/usr/include/mpi -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX"
>
> ?
>
>
>
> On 3 March 2014 10:16, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>
> Actually, the flags are most likely to be found in mkoctfile config.
> Currently I use the flags returned by:
>
> mkoctfile -p INCFLAGS
>
> Might be easier if you could look if those effectively appear in this
> variable or any other (do mkoctfile --help to list all variables). They have
> to come from somewhere...
> Thanks.
>
> Renaud
>
>
>
> On 3 March 2014 10:05, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
>
> Good.
> The MPI issue seems to be due to some compilation flags not being carried
> over when compiling RcppOctave library.
> The MPI specific flags "-I/usr/include/mpi -DMPICH_SKIP_MPICXX
> -DOMPI_SKIP_MPICXX" are correctly used when compiling the Octave modules, so
> these flags should be available from octave-config.
> Will look into it later.
> Thanks.
>
> Bests,
> Renaud
>
>
>
>
>
>