[Debian-med-packaging] Bug#906337: bioperl-run: FTBFS in buster/sid (autobuilder hangs)

[Santiago Vila]

Package: src:bioperl-run
Version: 1.7.2-3
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep
   dh_update_autotools_config -i
   dh_autoreconf -i
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --install_scripts 
	perl -I. Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" --install_scripts
Checking prerequisites...
  recommends:
    *  Bio::FeatureIO is not installed
    *  Config::Any is not installed
    *  File::Sort is not installed


[... snipped ...]

ok 106 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok 107 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok 108 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok 109 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok 110 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok 111 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeature::Generic'
ok
# Required executable for Bio::Tools::Run::Hmmer is not present
t/Hmmer.t ..................... 
1..27
ok 1 - use Bio::Tools::Run::Hmmer;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::AlignIO;
ok 4 - An object of class 'Bio::Tools::Run::Hmmer' isa 'Bio::Tools::Run::Hmmer'
ok 5
ok 6
ok 7
ok 8 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 9 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 10 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 11 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 12 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 13 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 14 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 15 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 16 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 17 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 18 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 19 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 20 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 21 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 22 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 23 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 24 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 25 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 26 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok 27 # skip Required executable for Bio::Tools::Run::Hmmer is not present
ok
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
E: Build killed with signal TERM after 60 minutes of inactivity
--------------------------------------------------------------------------------

The build was made with "dpkg-buildpackage -A" in my autobuilder.
Most probably, it also fails here in reproducible builds:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/bioperl-run.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.