[Debian-med-packaging] Bug#906486: libseqlib: FTBFS in buster/sid (dh_makeshlibs fails)

Fri Aug 17 20:21:50 BST 2018

Package: src:libseqlib
Version: 1.1.2+dfsg-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
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT'
configure.ac:17: installing './compile'
configure.ac:19: installing './config.guess'
configure.ac:19: installing './config.sub'
configure.ac:4: installing './missing'

[... snipped ...]

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  _ZNSt6vectorIiSaIiEE12emplace_backIJiEEEvDpOT_ at Base 1.1.1+dfsg
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 1.1.1+dfsg
+ _ZNSt6vectorImSaImEE17_M_default_appendEm at Base 1.1.2+dfsg-1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.1.2+dfsg-1
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  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1.1+dfsg
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1.1+dfsg
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  _ZNSt7__cxx114listIN6SeqLib13GenomicRegionESaIS2_EE5mergeEOS4_ at Base 1.1.1+dfsg
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  _ZNSt8_Rb_treeIN12aho_corasick7ahoemitIcEES2_St9_IdentityIS2_ESt4lessIS2_ESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 1.1.1+dfsg
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@@ -387,6 +396,8 @@
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  _ZNSt8_Rb_treeIcSt4pairIKcSt10unique_ptrIN12aho_corasick5stateIcEESt14default_deleteIS5_EEESt10_Select1stIS9_ESt4lessIcESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E at Base 1.1.1+dfsg
  _ZNSt8__detail9_Map_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS6_N6SeqLib4_BamEESaISB_ENS_10_Select1stESt8equal_toIS6_ESt4hashIS6_ENS_18_Mod_range_hashingENS_20_Default_ranged_hashENS_20_Prime_rehash_policyENS_17_Hashtable_traitsILb1ELb0ELb1EEELb1EEixERS8_ at Base 1.1.1+dfsg
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+ _ZSt10__pop_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_SK_RT0_ at Base 1.1.2+dfsg-1
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_RT0_ at Base 1.1.1+dfsg
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_RT0_ at Base 1.1.1+dfsg
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@@ -395,6 +406,7 @@
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  _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEElS3_NS0_5__ops15_Iter_less_iterEEvT_T0_SC_T1_T2_ at Base 1.1.1+dfsg
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  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_T0_ at Base 1.1.1+dfsg
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  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 1.1.1+dfsg
dh_makeshlibs: failing due to earlier errors
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 with "dpkg-buildpackage -B" in my autobuilder.
Most probably, it also fails here in reproducible builds:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libseqlib.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.

