Your message dated Sun, 29 Dec 2019 20:52:27 +0000
with message-id <[email protected]>
and subject line Bug#947717: fixed in pbcopper 1.3.0+dfsg-2
has caused the Debian Bug report #947717,
regarding pbcopper FTBFS on all architectures except x32
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
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--
947717: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947717
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pbcopper
Version: 1.3.0+dfsg-1
Severity: serious
Justification: ftbfs
Tags: ftbfs sid bullseye
Dear maintainer,
Your package fails to build from source on all buildds except x32. Your
package is involved in the pbbam and htslib transitions and blocking
progress. Please have a look.
Paul
https://buildd.debian.org/status/package.php?p=pbcopper
Tail of log for pbcopper on arm64:
cc -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include
-Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
-D_FILE_OFFSET_BITS=64 -std=c11 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
-MD -MQ 'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o' -MF
'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o.d' -o
'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o' -c ../src/align/cssw/ssw.c
../src/align/cssw/ssw.c:38:10: fatal error: emmintrin.h: No such file or
directory
38 | #include <emmintrin.h>
| ^~~~~~~~~~~~~
compilation terminated.
[9/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o' -c
../src/align/LinearAlignment.cpp
[10/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o' -c
../src/align/BandedChainAlignment.cpp
[11/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o' -c
../src/align/AffineAlignment.cpp
[12/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o' -c
../src/align/SparseAlignment.cpp
[13/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o' -c
../src/align/PairwiseAlignment.cpp
[14/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o' -c
../src/align/FindSeeds.cpp
[15/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude
-I../include -Isrc/utility -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 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
-Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o' -MF
'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o.d' -o
'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o' -c
../src/align/ChainSeeds.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit code 1
make: *** [debian/rules:10: build-arch] Error 255
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: pbcopper
Source-Version: 1.3.0+dfsg-2
We believe that the bug you reported is fixed in the latest version of
pbcopper, 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.
Michael R. Crusoe <[email protected]> (supplier of updated pbcopper
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: Sun, 29 Dec 2019 18:58:05 +0100
Source: pbcopper
Architecture: source
Version: 1.3.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 947717
Changes:
pbcopper (1.3.0+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Add the SIMD everywhere headers so we can build on all archs again
Closes: #947717
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pbcopper_1.3.0+dfsg-2.debian.tar.xz
ca90835fc0431b2f038e9850fe30f9556ede4238 7539
pbcopper_1.3.0+dfsg-2_amd64.buildinfo
Checksums-Sha256:
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Files:
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9c391d5d183840a41fc6b79da0c60091 41084 libs optional
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--- End Message ---
