[Debian-med-packaging] Bug#917591: libbpp-seq-omics: FTBFS (dh_makeshlibs fails)

[Santiago Vila]

Package: src:libbpp-seq-omics
Version: 2.4.1-1
Severity: serious
Tags: ftbfs

Dear maintainer:

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

--------------------------------------------------------------------------------
[...]
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
	cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
-- The CXX compiler identification is GNU 8.2.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- bpp-core 4.1.0 found:

[... snipped ...]

  _ZNK3bpp13AlphabetState5cloneEv at Base 2.4.1
  _ZNK3bpp13CodonAlphabet23getUnknownCharacterCodeEv at Base 2.4.1
  _ZNK3bpp14LetterAlphabet16isCharInAlphabetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
@@ -991,9 +991,9 @@
  _ZThn8_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZThn8_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorIiSaIiEE at Base 2.4.1
  _ZTv0_n112_NK3bpp23VectorSequenceContainer20getNumberOfSequencesEv at Base 2.4.1
- _ZTv0_n144_NK3bpp12SequenceMask7getTypeB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n144_NK3bpp12SequenceMask7getTypeB5cxx11Ev at Base 2.4.1
  _ZTv0_n144_NK3bpp15SequenceQuality7getTypeB5cxx11Ev at Base 2.4.1
- _ZTv0_n152_NK3bpp12SequenceMask11isValidWithERKNS_22SequenceWithAnnotationEb at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n152_NK3bpp12SequenceMask11isValidWithERKNS_22SequenceWithAnnotationEb at Base 2.4.1
  _ZTv0_n152_NK3bpp15SequenceQuality11isValidWithERKNS_22SequenceWithAnnotationEb at Base 2.4.1
  _ZTv0_n168_NK3bpp12EdSymbolListixEm at Base 2.4.1
  _ZTv0_n168_NK3bpp15BasicSymbolListixEm at Base 2.4.1
@@ -1003,7 +1003,7 @@
  _ZTv0_n24_N3bpp10BppIntegerD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp11MafSequenceD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp11MafSequenceD1Ev at Base 2.4.1
- _ZTv0_n24_N3bpp12SequenceMaskD0Ev at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n24_N3bpp12SequenceMaskD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13AlphabetStateD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
@@ -1142,7 +1142,7 @@
  _ZTv0_n48_N3bpp25SimpleMafStatisticsResult8setValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi at Base 2.4.1
  _ZTv0_n48_N3bpp36CsvStatisticsOutputIterationListener14iterationStopsEv at Base 2.4.1
  _ZTv0_n48_NK3bpp12EdSymbolList11getAlphabetEv at Base 2.4.1
- _ZTv0_n48_NK3bpp12SequenceMask11isRemovableEv at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n48_NK3bpp12SequenceMask11isRemovableEv at Base 2.4.1
  _ZTv0_n48_NK3bpp15SequenceQuality11isRemovableEv at Base 2.4.1
  _ZTv0_n48_NK3bpp21AbstractMafStatistics9getResultEv at Base 2.4.1
  _ZTv0_n48_NK3bpp22SequenceWithAnnotation7getNameB5cxx11Ev at Base 2.4.1
@@ -1162,7 +1162,7 @@
  _ZTv0_n56_N3bpp34SiteFrequencySpectrumMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_N3bpp37FourSpeciesPatternCountsMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_NK3bpp12EdSymbolList4sizeEv at Base 2.4.1
- _ZTv0_n56_NK3bpp12SequenceMask8isSharedEv at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n56_NK3bpp12SequenceMask8isSharedEv at Base 2.4.1
  _ZTv0_n56_NK3bpp15BasicSymbolList4sizeEv at Base 2.4.1
  _ZTv0_n56_NK3bpp15SequenceQuality8isSharedEv at Base 2.4.1
  _ZTv0_n64_N3bpp16GffFeatureReader21getFeaturesOfSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:15: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made in my autobuilder with "dpkg-buildpackage -B"
but it also fails here:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-seq-omics.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.