Your message dated Wed, 21 Aug 2019 07:04:31 +0000
with message-id <[email protected]>
and subject line Bug#925733: fixed in libbpp-popgen 2.4.1-2
has caused the Debian Bug report #925733,
regarding libbpp-popgen: ftbfs with GCC-9
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
925733: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925733
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libbpp-popgen
Version: 2.4.1-1
Severity: normal
Tags: sid bullseye
User: [email protected]
Usertags: ftbfs-gcc-9
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/libbpp-popgen_2.4.1-1_unstable_gcc9.log
The last lines of the build log are at the end of this report.
To build with GCC 9, either set CC=gcc-9 CXX=g++-9 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-9/porting_to.html
GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.
[...]
+ _ZNK3bpp20AbstractCoreSequence7getNameB5cxx11Ev@Base 2.4.1-1
_ZNK3bpp20AbstractOutputStream12getPrecisionEv@Base 2.4.1
_ZNK3bpp20AbstractOutputStream27isScientificNotationEnabledEv@Base 2.4.1
_ZNK3bpp20MapSequenceContainer20getNumberOfSequencesEv@Base 2.4.1
@@ -905,12 +909,14 @@
_ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_@Base
2.4.1
_ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_@Base
2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi@Base 2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixERS3_@Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi@Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixERS3_@Base 2.4.1
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base
2.4.1
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base
2.4.1
_ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
_ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
2.4.1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED1Ev@Base 2.4.1-1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED2Ev@Base 2.4.1-1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
2.4.1
@@ -953,7 +959,7 @@
_ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base
2.4.1
_ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base
2.4.1
_ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE@Base
2.4.1
- _ZNSt6vectorImSaImEE9push_backERKm@Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt6vectorImSaImEE9push_backERKm@Base 2.4.1
_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIN9__gnu_cxx17__normal_iteratorIPcS4_EEEEvT_SA_St20forward_iterator_tag@Base
2.4.1
_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag@Base
2.4.1
_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag@Base
2.4.1
@@ -983,6 +989,8 @@
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base
2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E@Base
2.4.1
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base
2.4.1
+
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base
2.4.1-1
+
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base
2.4.1-1
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base
2.4.1
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base
2.4.1
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base
2.4.1
@@ -1020,7 +1028,7 @@
_ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_@Base
2.4.1
_ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_@Base
2.4.1
_ZSt5fixedRSt8ios_base@Base 2.4.1
-
_ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops16_Iter_equals_valIKmEEET_SB_SB_T0_St26random_access_iterator_tag@Base
2.4.1
+#MISSING: 2.4.1-1#
_ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops16_Iter_equals_valIKmEEET_SB_SB_T0_St26random_access_iterator_tag@Base
2.4.1
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_@Base
2.4.1
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base
2.4.1
_ZTIN3bpp10AlleleInfoE@Base 2.4.1
@@ -1287,7 +1295,7 @@
_ZTv0_n24_N3bpp11PopgenlibIOD0Ev@Base 2.4.1
_ZTv0_n24_N3bpp11PopgenlibIOD1Ev@Base 2.4.1
_ZTv0_n24_N3bpp13BasicSequenceD0Ev@Base 2.4.1
- _ZTv0_n24_N3bpp13BasicSequenceD1Ev@Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n24_N3bpp13BasicSequenceD1Ev@Base 2.4.1
_ZTv0_n24_N3bpp14DistanceMatrixD0Ev@Base 2.4.1
_ZTv0_n24_N3bpp14DistanceMatrixD1Ev@Base 2.4.1
_ZTv0_n24_N3bpp15BasicAlleleInfoD0Ev@Base 2.4.1
@@ -1341,6 +1349,7 @@
_ZTv0_n48_NK3bpp15DarwinVarSingle20getFormatDescriptionB5cxx11Ev@Base 2.4.1
_ZTv0_n48_NK3bpp16AbstractCoreSite11getPositionEv@Base 2.4.1
_ZTv0_n48_NK3bpp19GeneMapperCsvExport20getFormatDescriptionB5cxx11Ev@Base
2.4.1
+ _ZTv0_n48_NK3bpp20AbstractCoreSequence7getNameB5cxx11Ev@Base 2.4.1-1
_ZTv0_n48_NK3bpp25AbstractSequenceContainer11getAlphabetEv@Base 2.4.1
_ZTv0_n48_NK3bpp4Site11getPositionEv@Base 2.4.1
_ZTv0_n48_NK3bpp7Genepop20getFormatDescriptionB5cxx11Ev@Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:13: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned
exit status 2
--- End Message ---
--- Begin Message ---
Source: libbpp-popgen
Source-Version: 2.4.1-2
We believe that the bug you reported is fixed in the latest version of
libbpp-popgen, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated libbpp-popgen package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 21 Aug 2019 08:20:43 +0200
Source: libbpp-popgen
Binary: libbpp-popgen-dev libbpp-popgen8
Architecture: source
Version: 2.4.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
libbpp-popgen-dev - Bio++ Population Genetics library development files
libbpp-popgen8 - Bio++ Population Genetics library
Closes: 925733
Changes:
libbpp-popgen (2.4.1-2) unstable; urgency=medium
.
[ Jelmer Vernooij]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
.
[ Julien Dutheil ]
* d-shlibs (>= 0.82)
* Easier amd64 symbol file management
.
[ Andreas Tille ]
* Rebuild for new version of gcc to fix symbols
Closes: #925733
* debhelper-compat 12
* Standards-Version: 4.4.0
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
* Set upstream metadata fields: Contact, Name.
Checksums-Sha1:
4da38dc49eb11b455ef2023933ba8f5fd8de7f36 2210 libbpp-popgen_2.4.1-2.dsc
7fadb636be1f0f46ad431e97ebf4f9eb92db89ca 18500
libbpp-popgen_2.4.1-2.debian.tar.xz
Checksums-Sha256:
57bf5f6a5a852a573bdfd23b39b0b0a769745642d0381a740d8f284f38d6c57f 2210
libbpp-popgen_2.4.1-2.dsc
f30f558cb05ee1aba2bb0f5ec0e37ec1fda1a88ab02c1b69fa5091865c63bc16 18500
libbpp-popgen_2.4.1-2.debian.tar.xz
Files:
d6fbdd03d9e84c324c9418c33ef00a58 2210 science optional
libbpp-popgen_2.4.1-2.dsc
40fe4b0f2eaf63f890e816a5d132d2d9 18500 science optional
libbpp-popgen_2.4.1-2.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=e/K2
-----END PGP SIGNATURE-----
--- End Message ---
