Your message dated Sun, 26 Jul 2020 20:56:03 +0000 with message-id <e1jzngh-0006nf...@fasolo.debian.org> and subject line Bug#957793: fixed in sigma-align 1.1.3-7 has caused the Debian Bug report #957793, regarding sigma-align: ftbfs with GCC-10 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.) -- 957793: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957793 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:sigma-align Version: 1.1.3-6 Severity: normal Tags: sid bullseye User: debian-...@lists.debian.org Usertags: ftbfs-gcc-10 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-10/g++-10, but succeeds to build with gcc-9/g++-9. 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/gcc10-20200225/sigma-align_1.1.3-6_unstable_gcc10.log The last lines of the build log are at the end of this report. To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html [...] checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking glib.h usability... yes checking glib.h presence... yes checking for glib.h... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether time.h and sys/time.h may both be included... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for gettimeofday... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j4 make[1]: Entering directory '/<<PKGBUILDDIR>>' make all-recursive make[2]: Entering directory '/<<PKGBUILDDIR>>' Making all in src make[3]: Entering directory '/<<PKGBUILDDIR>>/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parseopts.o parseopts.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readfasta.o readfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getbgprobs.o getbgprobs.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o setbgprobs.o setbgprobs.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o initseqfrags.o initseqfrags.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o commonroutines.o commonroutines.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o setbgw.o setbgw.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o printhelp.o printhelp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blockseq.o blockseq.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble_frags_to_seqs.o assemble_frags_to_seqs.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_routines.o print_routines.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getopt_long.o getopt_long.c getopt_long.c: In function ‘getopt_internal’: getopt_long.c:295:4: warning: implicit declaration of function ‘warnx’ [-Wimplicit-function-declaration] 295 | warnx(illoptchar, optchar); | ^~~~~ gcc -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o sigma main.o parseopts.o readfasta.o getbgprobs.o setbgprobs.o initseqfrags.o commonroutines.o setbgw.o printhelp.o blockseq.o assemble_frags_to_seqs.o print_routines.o getopt_long.o -lglib-2.0 -lm /usr/bin/ld: parseopts.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: getbgprobs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: setbgprobs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: initseqfrags.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: commonroutines.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: setbgw.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: blockseq.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: assemble_frags_to_seqs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here /usr/bin/ld: print_routines.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here collect2: error: ld returned 1 exit status make[3]: *** [Makefile:359: sigma] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: *** [Makefile:435: all-recursive] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>' make[1]: *** [Makefile:333: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j4 returned exit code 2 make: *** [debian/rules:4: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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--- Begin Message ---Source: sigma-align Source-Version: 1.1.3-7 Done: Shayan Doust <he...@shayandoust.me> We believe that the bug you reported is fixed in the latest version of sigma-align, 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 957...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Shayan Doust <he...@shayandoust.me> (supplier of updated sigma-align 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: Sun, 26 Jul 2020 18:19:50 +0100 Source: sigma-align Architecture: source Version: 1.1.3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Shayan Doust <he...@shayandoust.me> Closes: 957793 Changes: sigma-align (1.1.3-7) unstable; urgency=medium . * Team upload. . [ Shayan Doust ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Use versioned copyright format URI. * Use secure URI in Homepage field. * Set fields Upstream-Name, Upstream-Contact in debian/copyright. * Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright). * gcc-10 patch (Closes: #957793) . [ Steffen Möller ] * Updated RRIDs in d/u/metadata * Updated bio.tools Checksums-Sha1: 308322b694ce99909befad0b1439bba0873aafba 2024 sigma-align_1.1.3-7.dsc 631d930755a25db54f0c367d0858ba326f289c7f 3908 sigma-align_1.1.3-7.debian.tar.xz 45103ab31b7de1e54e61d72add4a38bf050a99ee 6757 sigma-align_1.1.3-7_amd64.buildinfo Checksums-Sha256: 577668177d7fdcacb88fc4168716733d5df54a1ecd7856ba17ba72a5d61205bb 2024 sigma-align_1.1.3-7.dsc 094ea66a6498396e009e226847628cc341c86240cc83224398c2f83bc9fd286a 3908 sigma-align_1.1.3-7.debian.tar.xz 0c5917a2f028484ffe1169a6711241141210256416dbe6c02b859e25b1aaa619 6757 sigma-align_1.1.3-7_amd64.buildinfo Files: 6098c014b9f3fe686408fe01d6d64422 2024 science optional sigma-align_1.1.3-7.dsc 9144f52bf153d4f129e01e711a6cff7a 3908 science optional sigma-align_1.1.3-7.debian.tar.xz a32444690c20d8dadd95391efed7c452 6757 science optional sigma-align_1.1.3-7_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8d3GoRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFF5w/8CfuvXbvWCJyl5gcfq9gSXsnKwSB1U1NT clC+Qd8OBFJM8k5dSs5sGTOOFnN9LgcziY7en6eRdGIrKZMJR9mYD4AD+Xj20F8w fA1ALpikUAPyiykW9eUHKyg9Eel0jInbSXp0zqLcKjW7ujkDM2/dHXEYVRG3Cvv9 uGCYgT265cUfwRlWWH95uzGkKGMBA44B5oU4QlfrlE1F7tb2tHdysgb5t8aDWxDO qlIRUX26MVKB67cNIlLUQs0HP0A25j7YCYrN3WpR2tn7gp11QhwJpWaySDPXcUdm waygMUgwt7/Mym/kyXanyvsaB4PIf4GwdMlgX6jfNaduIVoEXBnD8OT8RN6O9niJ h21kISEvHPmEomvzJzKTLISAZFxMV2TBJbGmpiPG7QOK9+6In5tZyPOSl7qYE5oB VV8wXqBKUupcCV09DLOFvjXK0exslBsZrEij5u+37S+yi+iY0O+37eEW+rNCa96O JnOOSE9kl6dSW8Gpp0M2vzBhWQnUguRyr196QKLc4qEXtyIxDHUJbaQjYSUwlJfN 8u1xRXroMQSDJmFEKOnfKt0THGrEtpeYiIM98fho8gZGExm2bJVFoM69u06NA3ZZ KlPhAfYpVc0HLnUeiPGU/yF7r+S3ZHEjsb97Vk/Y5HqE3m1JOSwCEh3fiCax/DfY xA/k6icLg0U= =S6IP -----END PGP SIGNATURE-----
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