[Debian-med-packaging] Debian Med package for MrBayes
Andreas Tille
andreas at fam-tille.de
Tue Jun 26 16:26:38 BST 2018
Hi Andreas,
On Tue, Jun 26, 2018 at 04:11:26PM +0200, Andreas Kusalananda Kähäri wrote:
> Thanks for the log! Much appreciated!
>
> The error is due to a declaration in one of our header files. This
> declaration is commented out in our code on the 'develop' branch (since
> it's of a Beagle function and thus already declared in the Beagle
> header). This leads me to believe that you are in fact compiling the
> 'master' branch. Could you please retry with the 'develop' branch?
I admit I did not used any branch but downloaded
https://github.com/NBISweden/MrBayes/archive/pre-3.2.7.tar.gz
So you would recommend to rather use the latest clone on devel
branch and retry?
Kind regards
Andreas.
> On Tue, Jun 26, 2018 at 03:16:32PM +0200, Andreas Tille wrote:
> > Dear Johan,
> >
> > On Tue, Jun 26, 2018 at 11:22:35AM +0000, Johan Nylander wrote:
> > > Dear Andreas!
> > >
> > > The code for the MrBayes package is coming closer to a new release.
> > > Again, the previous release (currently on Debian) was hosted on
> > > sourceforge, but we now moved everything to github. During the move, we
> > > also did a major overhaul of the build system.
> >
> > Thanks a lot for the early warning about changes. That's really
> > appreciated.
> >
> > > Would it be OK for you to take a quick look at what we currently have,
> > > and maybe give us some pointers to what we can improve in order for the
> > > incorporation into debian repos to be as smooth as possible?
> > >
> > > Here is the repo for the the next upcoming release ("develop" branch):
> > >
> > > https://github.com/NBISweden/MrBayes
> >
> > I've checked this out, did some adaptations to the Debian build system
> > but finally I get a build error where I have no clue how to fix it:
> >
> > ...
> > gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -mabm -I/usr/include/libhmsbeagle-1 -g -O2 -std=c99 -pedantic -g -O2 -fdebug-prefix-map=/build/mrbayes-3.2.7~pre=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c
> > gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -mabm -I/usr/include/libhmsbeagle-1 -g -O2 -std=c99 -pedantic -g -O2 -fdebug-prefix-map=/build/mrbayes-3.2.7~pre=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-best.o `test -f 'best.c' || echo './'`best.c
> > gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mrdrnd -mbmi -mbmi2 -mabm -I/usr/include/libhmsbeagle-1 -g -O2 -std=c99 -pedantic -g -O2 -fdebug-prefix-map=/build/mrbayes-3.2.7~pre=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -c -o mb-command.o `test -f 'command.c' || echo './'`command.c
> > In file included from command.c:40:0:
> > mbbeagle.h:24:14: error: conflicting types for 'beagleGetVersion'
> > extern char *beagleGetVersion (void);
> > ^~~~~~~~~~~~~~~~
> > In file included from bayes.h:58:0,
> > from command.c:38:
> > /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h:240:30: note: previous declaration of 'beagleGetVersion' was here
> > BEAGLE_DLLEXPORT const char* beagleGetVersion(void);
> > ^~~~~~~~~~~~~~~~
> > command.c: In function 'FreeCharacters':
> > command.c:9050:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
> > if (numChar > numTaxa)
> > ^~
> > command.c:9052:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
> > tempSetNeg = (int *) SafeRealloc ((void *)tempSetNeg, (size_t)numTaxa*sizeof(int));
> > ^~~~~~~~~~
> > make[4]: *** [Makefile:463: mb-command.o] Error 1
> >
> >
> > I've attached the full debian build log - may be you scroll
> > down until "dh_auto_configure" or so.
> >
> >
> > > Thank you very much
> >
> > Thanks to you
> >
> > Andreas.
> >
> >
> > > Yours
> > >
> > > Johan Nylander & Andreas Kusalananda Kähäri
> > >
> > >
> > >
> > > On 2018-02-16 09:59, Andreas Tille wrote:
> > > > Dear Johan,
> > > >
> > > > On Thu, Feb 15, 2018 at 01:32:24PM +0000, Johan Nylander wrote:
> > > >> I saw on the Debian pages that you are involved in packaging the
> > > >> software MrBayes for Debian Med.
> > > >>
> > > >> I just wanted to inform you that we are currently in the process of
> > > >> moving all code base from SourceForge to Github.
> > > > Thanks a lot for this very helpful information! That's really welcome
> > > > since our automatic system to seek for new upstream versions would not
> > > > notice this.
> > > >
> > > >> The latest version of the code is in pre-release state at
> > > >> https://github.com/NBISweden/MrBayes, and we are hoping to complete the
> > > >> next release soon.
> > > > A short ping would be helpful to let us issue an updated package right
> > > > after this.
> > > >
> > > >> Furthermore, is there anything we can do in order for the building
> > > >> process to be as smooth as possible on your side?
> > > > There is one thing I should have probably reported earlier: In Debian
> > > > the "source" of all "binaries" is required which also affects the source
> > > > of PDF documentation. While this is part of your repository it was not
> > > > contained inside the release tarball. We fixed this by the following
> > > > extra code:
> > > >
> > > >
> > > > # remove PDF without source
> > > > rm -f $documentation/commref*.pdf
> > > > # fetch sources for remaining doc from SVN into temporary dir
> > > > svn export https://svn.code.sf.net/p/mrbayes/code/documentation tmp
> > > > # remove unneeded stuff from documentation SVN
> > > > rm -f tmp/Manual*.pdf
> > > > rm -f tmp/*.rtf
> > > > rm -f tmp/*.rb
> > > > rm -f tmp/Release_instructions.txt
> > > > # move remaining doc to source dir
> > > > mv tmp/* documentation
> > > > rmdir tmp
> > > >
> > > >
> > > > It would be really helpful if you would include all the sources that are
> > > > needed to build the PDF documents would be included into the download
> > > > tarball which would safe us the extra code. I realised that the
> > > > prerelease MrBayes-pre-3.2.7.tar.gz contains a restructured doc directory
> > > > including Makefile.{am,in} - may be you realised my request even before
> > > > I asked for it.
> > > >
> > > > Kind regards and thanks again
> > > >
> > > > Andreas.
> > > >
> > >
> > > --
> > >
> > > Johan A. A. Nylander, PhD.
> > > Department of Bioinformatics and Genetics
> > > Swedish Museum of Natural History
> > > BOX 50007, 10405 Stockholm, Sweden
> > > Visiting addr.: Frescativägen 40, 11418 Stockholm
> > > Ph.: +46(0)851954056, e-mail:Johan.Nylander at nrm.se
> >
> > --
> > http://fam-tille.de
>
>
>
> --
> Andreas Kusalananda Kähäri,
> National Bioinformatics Infrastructure Sweden (NBIS),
> Uppsala University, Sweden.
>
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