Your message dated Fri, 11 Sep 2020 10:00:21 +0000
with message-id <e1kgfqv-0003uy...@fasolo.debian.org>
and subject line Bug#959643: fixed in pbbam 1.3.0+dfsg-1
has caused the Debian Bug report #959643,
regarding pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of
overloaded ‘CigarData(const char [1])’ is ambiguous
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 ow...@bugs.debian.org
immediately.)
--
959643: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959643
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: pbbam
Version: 1.0.6+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include
> -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o'
> -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c
> ../tests/src/test_BamWriter.cpp
> ../tests/src/test_BamWriter.cpp: In function ‘void
> BamWriterTests::checkSingleRecord(bool)’:
> ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded
> ‘CigarData(const char [1])’ is ambiguous
> 40 | bamRecord.Impl().CigarData("");
> | ^
> In file included from ../include/pbbam/BamRecord.h:24,
> from ../tests/src/test_BamWriter.cpp:11:
> ../include/pbbam/BamRecordImpl.h:251:20: note: candidate:
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const
> Cigar&)’
> 251 | BamRecordImpl& CigarData(const Cigar& cigar);
> | ^~~~~~~~~
> ../include/pbbam/BamRecordImpl.h:258:20: note: candidate:
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const
> string&)’
> 258 | BamRecordImpl& CigarData(const std::string& cigarString);
> | ^~~~~~~~~
> [129/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c
> ../tests/src/test_BamRecordMapping.cpp
> [130/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c
> ../tests/src/test_BamRecordClipping.cpp
> [131/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -c
> ../tests/src/test_BamRecordImplVariableData.cpp
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v
> returned exit code 1
> make: *** [debian/rules:13: build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2020/05/01/pbbam_1.0.6+dfsg-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: pbbam
Source-Version: 1.3.0+dfsg-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
pbbam, 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 959...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated pbbam 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 01 Sep 2020 15:37:58 +0200
Source: pbbam
Binary: libpbbam-dev libpbbam1.3.0 libpbbam1.3.0-dbgsym pbbamtools
pbbamtools-dbgsym
Architecture: source amd64
Version: 1.3.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers)
libpbbam1.3.0 - Pacific Biosciences binary alignment/map (BAM) library
pbbamtools - processing Pacific Biosciences binary alignment/map files
Closes: 959643
Changes:
pbbam (1.3.0+dfsg-1) unstable; urgency=medium
.
* Fix watch file
* New upstream version (+ bump soname)
Closes: #959643
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Repository, Repository-Browse.
* Fix d-shlibs override
* Silence dh_missing by removing unneeded *.la file
* New ABI version -> changed binary package name to libpbbam1.3.0
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pbbamtools-dbgsym_1.3.0+dfsg-1_amd64.deb
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pbbamtools_1.3.0+dfsg-1_amd64.deb
Checksums-Sha256:
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Files:
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pbbam_1.3.0+dfsg.orig.tar.xz
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pbbam_1.3.0+dfsg-1.debian.tar.xz
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libpbbam-dev_1.3.0+dfsg-1_amd64.deb
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pbbamtools-dbgsym_1.3.0+dfsg-1_amd64.deb
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pbbamtools_1.3.0+dfsg-1_amd64.deb
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--- End Message ---
