[Debian-med-packaging] Bug#1015488: libgenome: ftbfs with LTO (link time optimization) enabled

Matthias Klose doko at debian.org
Tue Jul 19 17:54:54 BST 2022 

Package: src:libgenome
Version: 1.3.11+svn20110227.4616-4
Severity: minor
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-lto

This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled.  For a background
for LTO please see

https://wiki.debian.org/ToolChain/LTO

The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures.  The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.

To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:

export DEB_BUILD_MAINT_OPTIONS = optimize=+lto

Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:

export DEB_BUILD_MAINT_OPTIONS = optimize=-lto

or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/libgenome_1.3.11+svn20110227.4616-4_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 1.3.11+svn20110227.4616
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EES5_RKS8_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNK6genome9gnFeature5CloneEv at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNKSt5ctypeIcE8do_widenEc at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome12gnFileContigESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome12gnFileContigESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIN6genome10gnLocationESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS5_S7_EERSA_ at Base 1.3.11+svn20110227.4616
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+#MISSING: 1.3.11+svn20110227.4616-4# (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS2_S4_EERS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# (optional)_ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome15gnBaseQualifierESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome15gnBaseQualifierESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIySaIyEE17_M_realloc_insertIJyEEEvN9__gnu_cxx17__normal_iteratorIPyS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt7__cxx1110_List_baseINS_12basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt7__cxx1110_List_baseIPKN6genome12gnBaseFilterESaIS4_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE16_M_insert_uniqueISB_EES6_ISt17_Rb_tree_iteratorISB_EbEOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE20_Reuse_or_alloc_nodeclIRKS8_EEPSt13_Rb_tree_nodeIS8_EOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EES5_RKS8_ at Base 1.3.11+svn20110227.4616
  _ZTIN6genome10gnBaseSpecE at Base 1.3.11+svn20110227.4616
  _ZTIN6genome10gnLocationE at Base 1.3.11+svn20110227.4616
  _ZTIN6genome10gnSequenceE at Base 1.3.11+svn20110227.4616
@@ -738,8 +738,8 @@
  _ZTVN6genome10gnSequenceE at Base 1.3.11+svn20110227.4616
  _ZTVN6genome11gnFASSourceE at Base 1.3.11+svn20110227.4616
  _ZTVN6genome11gnGBKSourceE at Base 1.3.11+svn20110227.4616
- _ZTVN6genome11gnMultiSpecINS_12gnContigSpecEEE at Base 1.3.11+svn20110227.4616
- _ZTVN6genome11gnMultiSpecINS_14gnFragmentSpecEEE at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZTVN6genome11gnMultiSpecINS_12gnContigSpecEEE at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZTVN6genome11gnMultiSpecINS_14gnFragmentSpecEEE at Base 1.3.11+svn20110227.4616
  _ZTVN6genome11gnRAWSourceE at Base 1.3.11+svn20110227.4616
  _ZTVN6genome11gnSEQSourceE at Base 1.3.11+svn20110227.4616
  _ZTVN6genome12gnBaseFilterE at Base 1.3.11+svn20110227.4616
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

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