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satta pushed a commit to branch update_1.4.1
in repository bcftools.
commit cba50cc48d0eaa0316b88e7ffd606f3907d90119
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Jul 29 10:39:21 2017 +0200
fix FTBFS on some 32-bit archs
---
debian/changelog | 7 +++++++
debian/patches/fix-bufffer-overflow.patch | 16 ++++++++++++++++
debian/patches/fix-test_vcf_query.patch | 18 ++++++++++++++++++
debian/patches/series | 2 ++
4 files changed, 43 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 980fe0f..4fc6550 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+bcftools (1.4.1-3) unstable; urgency=medium
+
+ * Team upload.
+ * Incorporate patches from Ubuntu to fix FTBFS on some 32-bit archs.
+
+ -- Sascha Steinbiss <satta at debian.org> Sat, 29 Jul 2017 10:38:27 +0200
+
bcftools (1.4.1-2) unstable; urgency=medium
* Team upload
diff --git a/debian/patches/fix-bufffer-overflow.patch b/debian/patches/fix-bufffer-overflow.patch
new file mode 100644
index 0000000..8137544
--- /dev/null
+++ b/debian/patches/fix-bufffer-overflow.patch
@@ -0,0 +1,16 @@
+Description: Fix buffer overflow
+Origin: upstream, https://github.com/samtools/bcftools/commit/8bfb9d5a94aaab4617bc38cfefa8332729dbd837
+Bug: https://github.com/samtools/bcftools/issues/607
+Bug-Debian: https://bugs.debian.org/868958
+Author: Petr Danecek <pd3 at sanger.ac.uk>
+Last-Update: 2017-05-10
+--- a/filter.c
++++ b/filter.c
+@@ -832,6 +832,7 @@
+ {
+ char *se = ss;
+ while ( *se && *se!=',' ) se++;
++ hts_expand(double, i+1, tok->mvalues, tok->values);
+ if ( !*se ) tok->values[i] = strlen(ss);
+ else
+ {
diff --git a/debian/patches/fix-test_vcf_query.patch b/debian/patches/fix-test_vcf_query.patch
new file mode 100644
index 0000000..c09242f
--- /dev/null
+++ b/debian/patches/fix-test_vcf_query.patch
@@ -0,0 +1,18 @@
+Description: Fix test_vcf_query on 32-bit architectures
+ Introduced by upstream commit:
+ https://github.com/samtools/bcftools/commit/25d042b833987d32e5de1fc3a109d357c4d0f738
+Forwarded: not-yet
+Bug-Debian: https://bugs.debian.org/868958
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update 2017-07-21
+--- a/vcfnorm.c
++++ b/vcfnorm.c
+@@ -94,7 +94,7 @@
+ }
+ static inline int has_non_acgtn(char *seq, int nseq)
+ {
+- char *end = nseq ? seq + nseq : seq + UINT32_MAX; // arbitrary large number
++ char *end = nseq ? seq + nseq : seq + (UINT32_MAX >> 2); // arbitrary large number
+ while ( *seq && seq<end )
+ {
+ char c = toupper(*seq);
diff --git a/debian/patches/series b/debian/patches/series
index f5e9bf3..134a5fe 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,5 @@ compiler-flags.patch
destdir.patch
tests-pluginpath.patch
test-regidx-unsigned-char.patch
+fix-bufffer-overflow.patch
+fix-test_vcf_query.patch
--
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