Your message dated Sun, 19 Feb 2023 13:34:33 +0000
with message-id <[email protected]>
and subject line Bug#1031473: fixed in libvcflib 1.0.9+dfsg-1
has caused the Debian Bug report #1031473,
regarding libvcflib-dev lacks dependency on libwfa2-dev
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.
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--
1031473: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1031473
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: freebayes
Version: 1.3.6-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: [email protected]
Usertags: ftbfs-20230216 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF
> libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o
> libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
> In file included from ../src/AlleleParser.h:32,
> from ../src/DataLikelihood.h:20,
> from ../src/DataLikelihood.cpp:1:
> /usr/include/vcflib/Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such
> file or directory
> 36 | #include "wavefront/wfa.hpp"
> | ^~~~~~~~~~~~~~~~~~~
> compilation terminated.
> [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF
> libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o
> libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp
> FAILED: libfreebayes_common.a.p/src_AlleleParser.cpp.o
> c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF
> libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o
> libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp
> In file included from ../src/AlleleParser.h:32,
> from ../src/AlleleParser.cpp:1:
> /usr/include/vcflib/Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such
> file or directory
> 36 | #include "wavefront/wfa.hpp"
> | ^~~~~~~~~~~~~~~~~~~
> compilation terminated.
> [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_Contamination.cpp.o -MF
> libfreebayes_common.a.p/src_Contamination.cpp.o.d -o
> libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp
> [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o
> -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o
> libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp
> [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF
> libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o
> libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp
> [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o
> -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o
> libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp
> [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ
> libfreebayes_common.a.p/src_BedReader.cpp.o -MF
> libfreebayes_common.a.p/src_BedReader.cpp.o.d -o
> libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp
> [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath
> -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack
> -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always
> -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable
> -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o
> -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o
> libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp
> ../src/Allele.cpp: In member function ‘const short int
> Allele::currentQuality() const’:
> ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not
> handled in switch [-Wswitch]
> 160 | switch (this->type) {
> | ^
> ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not
> handled in switch [-Wswitch]
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit
> code 1
> make: *** [debian/rules:6: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2023/02/16/freebayes_1.3.6-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230216;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230216&[email protected]&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: libvcflib
Source-Version: 1.0.9+dfsg-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libvcflib, 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 libvcflib 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: Sun, 19 Feb 2023 13:54:18 +0100
Source: libvcflib
Architecture: source
Version: 1.0.9+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1031473
Changes:
libvcflib (1.0.9+dfsg-1) unstable; urgency=medium
.
[ Étienne Mollier ]
* New upstream version 1.0.9+dfsg
* d/patches: refresh everything.
* wfa2_linking: add patch; fix linker errors.
.
[ Andreas Tille ]
* libvcflib-dev: Depends: libwfa2-dev
Closes: #1031473
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libvcflib_1.0.9+dfsg-1.debian.tar.xz
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Checksums-Sha256:
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Files:
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