Your message dated Mon, 01 Jul 2013 09:20:52 +0000 with message-id <e1utai1-0000vf...@franck.debian.org> and subject line Bug#701348: fixed in rnahybrid 2.1.1-2 has caused the Debian Bug report #701348, regarding rnahybrid: ftbfs with GCC-4.8 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.) -- 701348: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=701348 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:rnahybrid Version: 2.1.1-1 Severity: important Tags: sid jessie User: debian-...@lists.debian.org Usertags: ftbfs-gcc-4.8 The package fails to build in a test rebuild on at least amd64 with gcc-4.8/g++-4.8, but succeeds to build with gcc-4.7/g++-4.7. The severity of this report may be raised before the jessie release. XXX The full build log can be found at: http://people.debian.org/~doko/logs-20130217/gcc48/rnahybrid_2.1.1-1_unstable_gcc48.log The last lines of the build log are at the end of this report. To build with GCC 4.8, either set CC=gcc-4.8 CXX=g++-4.8 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t experimental install g++ g++-4.7 g++-4.8 libc6-dev The test rebuild was done with eglibc-2.17 and GCC-4.8, so some issues might be caused by the updated glibc. [...] rnaeffective.c:288:16: warning: incompatible implicit declaration of built-in function 'strlen' [enabled by default] seqlen = strlen(query_sq); ^ rnaeffective.c:299:20: warning: incompatible implicit declaration of built-in function 'strchr' [enabled by default] index_one = (int) strchr(alphabet,letter_one); ^ rnaeffective.c:299:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] index_one = (int) strchr(alphabet,letter_one); ^ rnaeffective.c:300:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] index_two = (int) strchr(alphabet,letter_two); ^ rnaeffective.c:303:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++; ^ rnaeffective.c:303:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++; ^ rnaeffective.c:346:15: warning: incompatible implicit declaration of built-in function 'strlen' [enabled by default] for (i=0; i<strlen(alphabet); i++) { ^ rnaeffective.c:436:6: warning: incompatible implicit declaration of built-in function 'strcpy' [enabled by default] strcpy(x, " "); ^ rnaeffective.c:437:6: warning: incompatible implicit declaration of built-in function 'strcat' [enabled by default] strcat(x, target_sq); ^ rnaeffective.c:565:6: warning: incompatible implicit declaration of built-in function 'strcpy' [enabled by default] strcpy(x, " "); ^ rnaeffective.c:566:6: warning: incompatible implicit declaration of built-in function 'strcat' [enabled by default] strcat(x, target_sq); ^ x86_64-linux-gnu-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,defs -o RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm make[3]: Leaving directory `/«PKGBUILDDIR»/src' Making all in man make[3]: Entering directory `/«PKGBUILDDIR»/man' make[3]: Nothing to be done for `all'. make[3]: Leaving directory `/«PKGBUILDDIR»/man' make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules override_dh_auto_test make[1]: Entering directory `/«PKGBUILDDIR»' src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta make[1]: *** [override_dh_auto_test] Segmentation fault make[1]: Leaving directory `/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
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--- Begin Message ---Source: rnahybrid Source-Version: 2.1.1-2 We believe that the bug you reported is fixed in the latest version of rnahybrid, 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 701...@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 rnahybrid 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: SHA1 Format: 1.8 Date: Mon, 01 Jul 2013 11:03:39 +0200 Source: rnahybrid Binary: rnahybrid Architecture: source amd64 Version: 2.1.1-2 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: rnahybrid - Fast and effective prediction of microRNA/target duplexes Closes: 701348 Changes: rnahybrid (2.1.1-2) unstable; urgency=low . * debian/upstream: Make author field BibTeX compliant * debian/control: - cme fix dpkg-control - use anonscm in VCS fields * debian/patches/gcc-4.8.patch: Fix build error with gcc-4.8 by adding string.h Closes: #701348 Checksums-Sha1: a8ef486015b437cb63bff4c407cd8747241381bd 1419 rnahybrid_2.1.1-2.dsc 53134330bec6bcce5631fd63303add1fbd7706f9 3648 rnahybrid_2.1.1-2.debian.tar.gz 019a939ffe77c008afe7d6d1582ec136aa3f159d 284830 rnahybrid_2.1.1-2_amd64.deb Checksums-Sha256: 489d77e3a341a2273905161c6d26725232f4cd223a94e7f53000b5f40389b864 1419 rnahybrid_2.1.1-2.dsc d00e899b35f29dcd7d330e7e10a16dd81056ba07c996b785e3c50d723d003cfc 3648 rnahybrid_2.1.1-2.debian.tar.gz f4a0b9fa0c9cdb258dc64e313f81dc164375609b2a37d1cea4ef958578399d44 284830 rnahybrid_2.1.1-2_amd64.deb Files: be0d22af44395e8381ea97fcc23f9fea 1419 science optional rnahybrid_2.1.1-2.dsc 409efd67be9dcac8346a3847ba2395cc 3648 science optional rnahybrid_2.1.1-2.debian.tar.gz cd36ef063dd52517edb388a5a44f9c4d 284830 science optional rnahybrid_2.1.1-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iEYEARECAAYFAlHRRyIACgkQYDBbMcCf01rhQwCgseKgi5l/9TJUXbp0pPR9azxF qe0AoMNoNO1Yl9qh6ZR/GU+GeHeD1eCN =QkSd -----END PGP SIGNATURE-----
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