[Debichem-devel] Bug#752800: openbabel: diff for NMU version 2.3.2+dfsg-1.3

[Kurt Roeckx]

On Mon, Aug 11, 2014 at 02:40:03PM +0300, Damyan Ivanov wrote:
> -=| Damyan Ivanov, 11.08.2014 11:36:54 +0300 |=-
> > I've prepared an NMU for openbabel (versioned as 2.3.2+dfsg-1.3) and
> > uploaded it to unstable.
> 
> This failed to build on brahms/amd64 [1] with an IEC:
> 
>  [100%] Building CXX object 
>  scripts/CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o
>  cd /«BUILDDIR»/openbabel-2.3.2+dfsg/build/scripts && /usr/bin/c++   
>  -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_SHARED_POINTER 
>  -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -D_FILE_OFFSET_BITS=64 
>  -D_LARGE_FILES -D__WXGTK__ -Dbindings_perl_EXPORTS -g -O2 
>  -fstack-protector --param=ssp-buffer-size=4 -Wformat 
>  -Werror=format-security -D_FORTIFY_SOURCE=2  -pthread -fopenmp -fPIC 
>  -isystem 
>  /usr/lib/x86_64-linux-gnu/wx/include/gtk2-unicode-release-2.8 
>  -isystem /usr/include/wx-2.8 
>  -I/«BUILDDIR»/openbabel-2.3.2+dfsg/build/include 
>  -I/«BUILDDIR»/openbabel-2.3.2+dfsg/data 
>  -I/«BUILDDIR»/openbabel-2.3.2+dfsg/include -I/usr/include/eigen3 
>  -I/usr/include/python2.7 -I/usr/lib/perl/5.18/CORE    
>  -DOB_MODULE_PATH="\"/usr/lib/openbabel/2.3.2\"" -o 
>  CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o -c 
>  /«BUILDDIR»/openbabel-2.3.2+dfsg/scripts/perl/openbabel-perl.cpp
>  c++: internal compiler error: Killed (program cc1plus)
>  Please submit a full bug report,
>  with preprocessed source if appropriate.
>  See <file:///usr/share/doc/gcc-4.9/README.Bugs> for instructions.
>  make[4]: *** 
>  [scripts/CMakeFiles/bindings_perl.dir/perl/openbabel-perl.cpp.o] 
>  Error 4
> 
>  [1] https://buildd.debian.org/status/fetch.php?pkg=openbabel&arch=amd64&ver=2.3.2+dfsg-1.3&stamp=1407752332
> 
> I have built the package several times on amd64 (in a pbuilder chroot) 
> before uploading and I noticed that it takes some time to build, 
> especially when it comes to perl/python bindings (the IEC above is 
> when compiling the perl binding). Perhaps the buildd was constrained 
> in RAM/swap?

It only has 2 GB of RAM + 0.5 GB of swap.  I also found this in
the log:
[37098.081505] Out of memory: Kill process 19127 (cc1plus) score 447 or sacrifice child
[37098.081508] Killed process 19127 (cc1plus) total-vm:1213428kB, anon-rss:1042196kB, file-rss:0kB

> Buildd admins, can you re-schedule the build, possibly on another 
> host?

Done, and I've excluded that package on brahms.


Kurt