[Debichem-devel] Bug#921784: Bug#921784: gromacs: FTBFS (ld returned 1 exit status)

[Nicholas Breen]

On Sat, Feb 09, 2019 at 12:15:22AM +0000, Santiago Vila wrote:
> Package: src:gromacs
> Version: 2019-2
> Severity: serious
> Tags: ftbfs
> 
> Dear maintainer:
> 
> I tried to build this package in buster but it failed:
[...]
> /usr/bin/mpicxx.openmpi   -msse2   -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast      -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o  -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhwloc.so -lrt /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lm 
> collect2: error: ld returned 1 exit status
> make[4]: *** [src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make:190: bin/mdlib-test] Error 1
[...]

Hi Santiago,

I can't reproduce this build failure in a clean buster or sid chroot.
Both build successfully.

> The build was made in my autobuilder with "dpkg-buildpackage -A"
> and it also fails here:
> 
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/gromacs.html
> 
> where you can get a full build log if you need it.

This is actually a different error.  Is this running under pbuilder or a
derivative?  The test case that this build log failed on requires a
semi-functional network setup - it doesn't need (or attempt to use)
outside access, but it does at least need gethostbyname() to return a
reachable address for the system's hostname, with localhost being fine.
This does *not* work with the default pbuilder configuration, only with
USENETWORK=yes.  sbuild on the buildds works, as does a build outside a
constrained environment.  pbuilder also breaks further down the chain
for a few tests that don't allow running as root, unless BUILDUSERID is
also configured to a non-zero value.  It does make testing more
difficult!  If those constraints can't be met and pbuilder is essential,
it should be built with 'nocheck'.

Since it's no problem for either the buildds or users in their own
shell, I haven't considered those issues as serious bugs.



-- 
Nicholas Breen
nbreen at debian.org