Bug#930368: gatb-core: FTBFS due to inaccurate symbols file

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Bug#930368: gatb-core: FTBFS due to inaccurate symbols file

Gilles Filippini-2
Source: gatb-core
Version: 1.4.1+git20181225.44d5a44+dfsg-2
Severity: serious
Justification: FTBFS

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Hi,

During a rebuild of gatb-core for unstable on amd64 I experienced a FTBFS at the
dh_makeshlibs step:

   dh_makeshlibs -O--sourcedirectory=gatb-core
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libgatbcore2/DEBIAN/symbols doesn't match completely debian/libgatbcore2.symbols.amd64
- --- debian/libgatbcore2.symbols.amd64 (libgatbcore2_1.4.1+git20181225.44d5a44+dfsg-2_amd64)
+++ dpkg-gensymbolsErQvax       2019-06-11 09:56:28.965481025 +0000
@@ -8997,7 +8997,7 @@
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1
- - _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
+#MISSING: 1.4.1+git20181225.44d5a44+dfsg-2# _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi3EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
@@ -9007,7 +9007,7 @@
  _ZNSt6vectorISt5tupleIJmiEESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJmiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt6threadSaIS0_EE17_M_realloc_insertIJZN10ThreadPoolC4EmEUlvE_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base 1.4.1
- - _ZNSt6vectorIbSaIbEE13_M_initializeEm@Base 1.4.1+git20181225.44d5a44+dfsg
+#MISSING: 1.4.1+git20181225.44d5a44+dfsg-2# _ZNSt6vectorIbSaIbEE13_M_initializeEm@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb@Base 1.4.1
  _ZNSt6vectorIbSaIbEE13_M_reallocateEm@Base 1.4.1
  _ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb@Base 1.4.1
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

Thanks,

_g.

- -- System Information:
Debian Release: buster/sid
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-5-amd64 (SMP w/4 CPU cores)
Kernel taint flags: TAINT_WARN
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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Bug#930368: marked as done (gatb-core: FTBFS due to inaccurate symbols file)

Debian Bug Tracking System
Your message dated Wed, 19 Jun 2019 11:18:31 +0000
with message-id <[hidden email]>
and subject line Bug#930368: fixed in gatb-core 1.4.1+git20181225.44d5a44+dfsg-3
has caused the Debian Bug report #930368,
regarding gatb-core: FTBFS due to inaccurate symbols file
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 [hidden email]
immediately.)


--
930368: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=930368
Debian Bug Tracking System
Contact [hidden email] with problems

Source: gatb-core
Version: 1.4.1+git20181225.44d5a44+dfsg-2
Severity: serious
Justification: FTBFS

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Hi,

During a rebuild of gatb-core for unstable on amd64 I experienced a FTBFS at the
dh_makeshlibs step:

   dh_makeshlibs -O--sourcedirectory=gatb-core
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libgatbcore2/DEBIAN/symbols doesn't match completely debian/libgatbcore2.symbols.amd64
- --- debian/libgatbcore2.symbols.amd64 (libgatbcore2_1.4.1+git20181225.44d5a44+dfsg-2_amd64)
+++ dpkg-gensymbolsErQvax       2019-06-11 09:56:28.965481025 +0000
@@ -8997,7 +8997,7 @@
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi1EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1
- - _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
+#MISSING: 1.4.1+git20181225.44d5a44+dfsg-2# _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE12emplace_backIJS7_EEEvDpOT_@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi2EEEjjjEESaIS7_EE7reserveEm@Base 1.4.1
  _ZNSt6vectorISt5tupleIJjN4gatb4core5tools4math8LargeIntILi3EEEjjjEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
@@ -9007,7 +9007,7 @@
  _ZNSt6vectorISt5tupleIJmiEESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt5tupleIJmiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_@Base 1.4.1
  _ZNSt6vectorISt6threadSaIS0_EE17_M_realloc_insertIJZN10ThreadPoolC4EmEUlvE_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_@Base 1.4.1
- - _ZNSt6vectorIbSaIbEE13_M_initializeEm@Base 1.4.1+git20181225.44d5a44+dfsg
+#MISSING: 1.4.1+git20181225.44d5a44+dfsg-2# _ZNSt6vectorIbSaIbEE13_M_initializeEm@Base 1.4.1+git20181225.44d5a44+dfsg
  _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb@Base 1.4.1
  _ZNSt6vectorIbSaIbEE13_M_reallocateEm@Base 1.4.1
  _ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb@Base 1.4.1
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

Thanks,

_g.

- -- System Information:
Debian Release: buster/sid
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-5-amd64 (SMP w/4 CPU cores)
Kernel taint flags: TAINT_WARN
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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Source: gatb-core
Source-Version: 1.4.1+git20181225.44d5a44+dfsg-3

We believe that the bug you reported is fixed in the latest version of
gatb-core, 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 [hidden email],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <[hidden email]> (supplier of updated gatb-core 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 [hidden email])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Wed, 19 Jun 2019 12:25:30 +0200
Source: gatb-core
Binary: gatb-core libgatbcore2 libgatbcore-dev gatb-core-testdata
Architecture: source
Version: 1.4.1+git20181225.44d5a44+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[hidden email]>
Changed-By: Andreas Tille <[hidden email]>
Description:
 gatb-core  - Genome Analysis Toolbox with de-Bruijn graph
 gatb-core-testdata - Genome Analysis Toolbox with de-Bruijn graph (test data)
 libgatbcore-dev - development library of the Genome Analysis Toolbox
 libgatbcore2 - dynamic library of the Genome Analysis Toolbox
Closes: 930368
Changes:
 gatb-core (1.4.1+git20181225.44d5a44+dfsg-3) unstable; urgency=medium
 .
   * Fix symbols
     Closes: #930368
Checksums-Sha1:
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Files:
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