[Debian-med-packaging] Debian Med package for MrBayes

Tue Jun 26 14:16:32 BST 2018

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
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