Étienne Mollier pushed to branch master at Debian Med / maq
Commits: e78f2463 by Étienne Mollier at 2024-08-05T22:44:23+02:00 gcc-14.patch: new: fix improper uses of gzFile pointers. Closes: #1075253 - - - - - b3377254 by Étienne Mollier at 2024-08-05T22:46:44+02:00 d/*lintian-overrides: update mismatched overrides. - - - - - 7f7a686e by Étienne Mollier at 2024-08-05T22:47:20+02:00 d/control: declare compliance to standards version 4.7.0. - - - - - 5d319057 by Étienne Mollier at 2024-08-05T22:48:04+02:00 d/control: add myself to uploaders. - - - - - 1e9734ce by Étienne Mollier at 2024-08-05T22:50:33+02:00 ready to upload to unstable. - - - - - 5 changed files: - debian/changelog - debian/control - debian/maq.lintian-overrides - + debian/patches/gcc-14.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +maq (0.7.1-10) unstable; urgency=medium + + * gcc-14.patch: new: fix improper uses of gzFile pointers. (Closes: #1075253) + * d/*lintian-overrides: update mismatched overrides. + * d/control: declare compliance to standards version 4.7.0. + * d/control: add myself to uploaders. + + -- Étienne Mollier <[email protected]> Mon, 05 Aug 2024 22:48:54 +0200 + maq (0.7.1-9) unstable; urgency=medium * Standards-Version: 4.5.0 (routine-update) ===================================== debian/control ===================================== @@ -1,12 +1,13 @@ Source: maq Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Andreas Tille <[email protected]>, - Charles Plessy <[email protected]> + Charles Plessy <[email protected]>, + Étienne Mollier <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 13), zlib1g-dev -Standards-Version: 4.5.0 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/maq Vcs-Git: https://salsa.debian.org/med-team/maq.git Homepage: http://maq.sourceforge.net/ ===================================== debian/maq.lintian-overrides ===================================== @@ -1,4 +1,3 @@ # Maq ships `maq' and `maq.pl', it is therefore not possible to rename `maq.pl'. -maq: script-with-language-extension usr/bin/maq.pl -# see https://lists.debian.org/debian-med/2018/06/msg00043.html -maq: script-with-language-extension usr/bin/*.* +# also see https://lists.debian.org/debian-med/2018/06/msg00043.html +maq: script-with-language-extension [usr/bin/*.pl] ===================================== debian/patches/gcc-14.patch ===================================== @@ -0,0 +1,45 @@ +Description: fix improper variable declaration as a pointer. + On two occasions, a gzFile is declared as a pointer, except the type + mismatches with the expected type by the gz API, resulting in errors + like: + . + fastq2bfq.c:30:12: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] + 30 | fp = gzopen(str, "w"); + | ^ + fastq2bfq.c:36:28: error: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types] + 36 | fp = gzopen(str, "w"); + | ^ + fastq2bfq.c:47:25: error: passing argument 1 of ‘gzwrite’ from incompatible pointer type [-Wincompatible-pointer-types] + 47 | gzwrite(fp, &i, sizeof(int)); + | ^~ + | | + | struct gzFile_s ** + +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075253 +Forwarded: no +Last-Update: 2024-08-05 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- maq.orig/fastq2bfq.c ++++ maq/fastq2bfq.c +@@ -15,7 +15,7 @@ + char name[256], str[1024]; + int l, is_new = 0, l_prefix = 0; + bit64_t n; +- gzFile *fp = 0; ++ gzFile fp = 0; + INIT_SEQ(seq); INIT_SEQ(qual); + seq_set_block_size(256); + n = 0; +--- maq.orig/simulate.c ++++ maq/simulate.c +@@ -74,7 +74,7 @@ + { + fqc_t *fqc; + FILE *fp; +- gzFile *fpout; ++ gzFile fpout; + if (argc < 3) { + fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n"); + return 1; ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ 10_prevent_-64_option.patch gcc-4.7.patch mayhem.patch +gcc-14.patch View it on GitLab: https://salsa.debian.org/med-team/maq/-/compare/b733545b3b5057e04f7a8297f53de090508cf52c...1e9734ce968e57bcf92985f7496fe090bedf8de8 -- View it on GitLab: https://salsa.debian.org/med-team/maq/-/compare/b733545b3b5057e04f7a8297f53de090508cf52c...1e9734ce968e57bcf92985f7496fe090bedf8de8 You're receiving this email because of your account on salsa.debian.org.
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