[med-svn] [sra-sdk] 01/01: renamed function to resolve name clash with gnutards to avoid FTBFS with glibc 2.25

[Andreas Tille]

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tille pushed a commit to branch master
in repository sra-sdk.

commit 926a355b399ebe135bf1db48ccea6748e95fed1d
Author: Andreas Tille <tille at debian.org>
Date:   Mon Dec 4 08:10:56 2017 +0100

    renamed function to resolve name clash with gnutards to avoid FTBFS with glibc 2.25
---
 debian/changelog                                   |  3 +++
 .../e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch | 31 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 35 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 1cabeed..f3a2304 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -10,6 +10,9 @@ sra-sdk (2.8.2-3+dfsg-1) UNRELEASED; urgency=medium
   * cme fix dpkg-control
   * Standards-Version: 4.1.1
   * debhelper 10
+  * renamed function to resolve name clash with gnutards to avoid
+    FTBFS with glibc 2.25
+    Closes: #882349
 
  -- Andreas Tille <tille at debian.org>  Thu, 19 Oct 2017 23:58:30 +0200
 
diff --git a/debian/patches/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch b/debian/patches/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch
new file mode 100644
index 0000000..f41d299
--- /dev/null
+++ b/debian/patches/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch
@@ -0,0 +1,31 @@
+From: "durbrowk at ncbi.nlm.nih.gov" <kmdurbrow at me.com>
+Date: Wed, 5 Apr 2017 12:50:07 -0400
+Subject: [PATCH] renamed function to resolve name clash with gnutards
+Bugs-Debian: https://bugs.debian.org/882349
+Origin: Upstream
+        https://github.com/ncbi/sra-tools/commit/e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab
+
+---
+ tools/bam-loader/bam.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+--- a/tools/bam-loader/bam.c
++++ b/tools/bam-loader/bam.c
+@@ -3997,7 +3997,7 @@ static unsigned insert_B(unsigned const
+     return n;
+ }
+ 
+-static unsigned canonicalize(uint32_t cigar[], unsigned n)
++static unsigned canonicalizeCIGAR(uint32_t cigar[], unsigned n)
+ {
+     unsigned i;
+     
+@@ -4042,7 +4042,7 @@ static unsigned GetCGCigar(BAM_Alignment
+     memmove(cigar, getCigarBase(self), n * 4);
+ 
+     if (n > 1)
+-        n = canonicalize(cigar, n); /* just in case */
++        n = canonicalizeCIGAR(cigar, n); /* just in case */
+     
+     for (i = 0, S = 0; i < gaps; ++i) {
+         unsigned const s = seg[2 * i + 0];
diff --git a/debian/patches/series b/debian/patches/series
index 29093bc..25c825e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -14,3 +14,4 @@ do_not_link_statically.patch
 link_debian_packaged_libmbed.patch
 seek_dynamic_libs.patch
 certs.kfg.patch
+e285ecd3fcd39eac2051ea7bccd5257c6dfb72ab.patch

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