This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository bcftools.
commit 45584799270dcf363a0c9cca10342618c4b94f89 Author: Afif Elghraoui <[email protected]> Date: Thu Mar 31 00:52:25 2016 -0700 Backport upstream patch to fix build on arm64, armel, and ppc64el Closes: #812268 --- debian/patches/getopt-return-types.patch | 98 ++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 99 insertions(+) diff --git a/debian/patches/getopt-return-types.patch b/debian/patches/getopt-return-types.patch new file mode 100644 index 0000000..9c1bcf6 --- /dev/null +++ b/debian/patches/getopt-return-types.patch @@ -0,0 +1,98 @@ +From afecb4e96c3abc188e7fc155e35720e01aa13a81 Mon Sep 17 00:00:00 2001 +From: John Marshall <[email protected]> +Date: Tue, 15 Mar 2016 16:15:48 +0000 +Subject: [PATCH] getopt_long() returns int, not char + +Much like fgetc() returning EOF, we need to store getopt_long()'s +result in an int so that we can reliably check the -1 return value. +Hat tip @daviesrob; fixes the usage errors part of #389. +--- + consensus.c | 2 +- + plugins/GTisec.c | 2 +- + plugins/color-chrs.c | 2 +- + plugins/fill-tags.c | 2 +- + plugins/mendelian.c | 2 +- + plugins/tag2tag.c | 2 +- + plugins/vcf2sex.c | 3 ++- + polysomy.c | 3 ++- + 8 files changed, 10 insertions(+), 8 deletions(-) + +--- bcftools.orig/consensus.c ++++ bcftools/consensus.c +@@ -623,7 +623,7 @@ + {"chain",1,0,'c'}, + {0,0,0,0} + }; +- char c; ++ int c; + while ((c = getopt_long(argc, argv, "h?s:1iH:f:o:m:c:",loptions,NULL)) >= 0) + { + switch (c) +--- bcftools.orig/plugins/color-chrs.c ++++ bcftools/plugins/color-chrs.c +@@ -159,7 +159,7 @@ + {"unrelated",1,0,'u'}, + {0,0,0,0} + }; +- char c; ++ int c; + while ((c = getopt_long(argc, argv, "?ht:u:p:",loptions,NULL)) >= 0) + { + switch (c) +--- bcftools.orig/plugins/fill-tags.c ++++ bcftools/plugins/fill-tags.c +@@ -112,7 +112,7 @@ + {"tags",1,0,'t'}, + {0,0,0,0} + }; +- char c; ++ int c; + while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0) + { + switch (c) +--- bcftools.orig/plugins/mendelian.c ++++ bcftools/plugins/mendelian.c +@@ -100,7 +100,7 @@ + {"count",0,0,'c'}, + {0,0,0,0} + }; +- char c; ++ int c; + while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0) + { + switch (c) +--- bcftools.orig/plugins/tag2tag.c ++++ bcftools/plugins/tag2tag.c +@@ -83,7 +83,7 @@ + {"gl-to-pl",0,0,2}, + {0,0,0,0} + }; +- char c; ++ int c; + while ((c = getopt_long(argc, argv, "?hr",loptions,NULL)) >= 0) + { + switch (c) +--- bcftools.orig/plugins/vcf2sex.c ++++ bcftools/plugins/vcf2sex.c +@@ -389,7 +389,8 @@ + {"background",1,0,'b'}, + {0,0,0,0} + }; +- char c, *tmp, *ploidy_fname = NULL; ++ char *tmp, *ploidy_fname = NULL; ++ int c; + while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0) + { + switch (c) { +--- bcftools.orig/polysomy.c ++++ bcftools/polysomy.c +@@ -675,7 +675,8 @@ + {"regions-file",1,0,'R'}, + {0,0,0,0} + }; +- char c, *tmp; ++ char *tmp; ++ int c; + while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0) + { + switch (c) diff --git a/debian/patches/series b/debian/patches/series index 96c8d42..b532fa2 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -4,3 +4,4 @@ destdir.patch tests-pluginpath.patch spelling.patch peakfit-gsl2.patch +getopt-return-types.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
