Your message dated Tue, 20 Aug 2019 17:21:16 +0000
with message-id <[email protected]>
and subject line Bug#925737: fixed in libbpp-seq-omics 2.4.1-4
has caused the Debian Bug report #925737,
regarding libbpp-seq-omics: 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.)
--
925737: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925737
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libbpp-seq-omics
Version: 2.4.1-3
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-seq-omics_2.4.1-3_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.
[...]
@@ -476,7 +480,7 @@
_ZNK3bpp8SeqRange5cloneEv@Base 2.4.1
_ZNK3bpp8SeqRange9getStrandEv@Base 2.4.1
_ZNK3bpp9BppDouble5cloneEv@Base 2.4.1
- _ZNKSt15_Deque_iteratorISt6vectorIbSaIbEERS2_PS2_EplEl@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNKSt15_Deque_iteratorISt6vectorIbSaIbEERS2_PS2_EplEl@Base
2.4.1
_ZNKSt5ctypeIcE8do_widenEc@Base 2.4.1
_ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED1Ev@Base 2.4.1
_ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED2Ev@Base 2.4.1
@@ -486,9 +490,9 @@
_ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 2.4.1
_ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base
2.4.1
_ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base
2.4.1
-
_ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_@Base
2.4.1
+#MISSING: 2.4.1-3#
_ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_@Base
2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_@Base
2.4.1
-
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_@Base
2.4.1
+#MISSING: 2.4.1-3#
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_@Base
2.4.1
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base
2.4.1
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2.4.1
_ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base
2.4.1
@@ -497,6 +501,7 @@
_ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base
2.4.1
_ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE19_M_destroy_data_auxESt15_Deque_iteratorIS2_RS2_PS2_ES8_@Base
2.4.1
_ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_@Base 2.4.1
+ _ZNSt5dequeImSaImEE17_M_push_front_auxIJmEEEvDpOT_@Base 2.4.1-3
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
2.4.1
@@ -507,7 +512,7 @@
_ZNSt6vectorIPKN3bpp11MafSequenceESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base
2.4.1
_ZNSt6vectorIPN3bpp13AlphabetStateESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
_ZNSt6vectorIPN3bpp13SiteContainerESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
-
_ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_@Base
2.4.1
+#MISSING: 2.4.1-3#
_ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_@Base
2.4.1
_ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
_ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
_ZNSt6vectorIPN3bpp18SymbolListListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base
2.4.1
@@ -523,21 +528,21 @@
_ZNSt6vectorIS_IiSaIiEESaIS1_EED2Ev@Base 2.4.1
_ZNSt6vectorIS_ImSaImEESaIS1_EED1Ev@Base 2.4.1
_ZNSt6vectorIS_ImSaImEESaIS1_EED2Ev@Base 2.4.1
- _ZNSt6vectorIbSaIbEEC1ERKS1_@Base 2.4.1
- _ZNSt6vectorIbSaIbEEC2ERKS1_@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIbSaIbEEC1ERKS1_@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIbSaIbEEC2ERKS1_@Base 2.4.1
_ZNSt6vectorIiSaIiEE17_M_default_appendEm@Base 2.4.1
_ZNSt6vectorIiSaIiEE17_M_realloc_insertIJRKiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_@Base
2.4.1
- _ZNSt6vectorIiSaIiEEC1ERKS1_@Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ERKS1_@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC1ERKS1_@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC2ERKS1_@Base 2.4.1
_ZNSt6vectorIiSaIiEEaSERKS1_@Base 2.4.1
_ZNSt6vectorIjSaIjEE14_M_fill_assignEmRKj@Base 2.4.1
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base
2.4.1
_ZNSt6vectorImSaImEE12emplace_backIJmEEEvDpOT_@Base 2.4.1
_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
- _ZNSt6vectorImSaImEE9push_backERKm@Base 2.4.1
- _ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@Base 2.4.1
- _ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorImSaImEE9push_backERKm@Base 2.4.1
+#MISSING: 2.4.1-3#
_ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@Base 2.4.1
+#MISSING: 2.4.1-3#
_ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@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
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
--- End Message ---
--- Begin Message ---
Source: libbpp-seq-omics
Source-Version: 2.4.1-4
We believe that the bug you reported is fixed in the latest version of
libbpp-seq-omics, 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-seq-omics 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: SHA512
Format: 1.8
Date: Tue, 20 Aug 2019 18:20:38 +0200
Source: libbpp-seq-omics
Architecture: source
Version: 2.4.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 925737
Changes:
libbpp-seq-omics (2.4.1-4) unstable; urgency=medium
.
* Rebuild for new version of gcc to fix symbols
Closes: #925737
* debhelper-compat 12
* Standards-Version: 4.4.0
* Trim trailing whitespace.
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