01/01: gnu: bcftools: Fix building on aarch64.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 3837108e403d385cd0b616fb601b9942c8bb213f
Author: Efraim Flashner <address@hidden>
Date:   Tue Aug 15 10:30:33 2017 +0300

    gnu: bcftools: Fix building on aarch64.
    
    * gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file.
    * gnu/packages/bioinformatics.scm (bcftools)[source]: Use it.
    * gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                             |  1 +
 gnu/packages/bioinformatics.scm                          |  1 +
 gnu/packages/patches/bcftools-regidx-unsigned-char.patch | 16 ++++++++++++++++
 3 files changed, 18 insertions(+)

diff --git a/gnu/local.mk b/gnu/local.mk
index b15a16b..2ab6901 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -527,6 +527,7 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/awesome-reproducible-png.patch          \
   %D%/packages/patches/azr3.patch                              \
   %D%/packages/patches/bash-completion-directories.patch       \
+  %D%/packages/patches/bcftools-regidx-unsigned-char.patch     \
   %D%/packages/patches/binutils-ld-new-dtags.patch             \
   %D%/packages/patches/binutils-loongson-workaround.patch      \
   %D%/packages/patches/binutils-mips-bash-bug.patch            \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d64294..17cd214 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -311,6 +311,7 @@ BAM files.")
               (sha256
                (base32
                 "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
+              (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled htslib.
diff --git a/gnu/packages/patches/bcftools-regidx-unsigned-char.patch 
b/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
new file mode 100644
index 0000000..af5bc16
--- /dev/null
+++ b/gnu/packages/patches/bcftools-regidx-unsigned-char.patch
@@ -0,0 +1,16 @@
+Description: Fix test-regidx argument parsing on archs with unsigned char
+ On architectures where char is unsigned "c >= 0" was always true.
+Author: Adrian Bunk <address@hidden>
+Bug-Debian: https://bugs.debian.org/865060
+
+--- a/test/test-regidx.c
++++ b/test/test-regidx.c
+@@ -336,7 +336,7 @@
+         {"seed",1,0,'s'},
+         {0,0,0,0}
+     };
+-    char c;
++    int c;
+     int seed = (int)time(NULL);
+     while ((c = getopt_long(argc, argv, "hvs:",loptions,NULL)) >= 0) 
+     {