[med-svn] samtools 01/01: fix FTBFS

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a commit to branch debian/unstable
in repository samtools.

commit 9aac9cbec983831351611d227702fc04b7235948
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Oct 20 20:03:25 2016 +0000

    fix FTBFS
---
 debian/changelog                       |  9 +++++++++
 debian/control                         |  1 +
 debian/patches/curses.patch            | 11 +++++++++++
 debian/patches/disable-usagetest.patch | 11 +++++++++++
 debian/patches/mayhem.patch            |  6 +++---
 debian/patches/series                  |  2 ++
 debian/rules                           |  1 +
 7 files changed, 38 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e86d913..ee71d94 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+samtools (1.3.1-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Refresh patches.
+  * Fix FTBFS.
+    Closes: #840974
+
+ -- Sascha Steinbiss <satta at debian.org>  Thu, 20 Oct 2016 20:01:46 +0000
+
 samtools (1.3.1-2) unstable; urgency=medium
 
   952da10 Build-depends on htslib 1.3.1. (Closes: #822701)
diff --git a/debian/control b/debian/control
index 56db5ac..de93faf 100644
--- a/debian/control
+++ b/debian/control
@@ -13,6 +13,7 @@ Build-Depends: debhelper (>= 9),
                zlib1g-dev,
                automake,
                autoconf-archive,
+               pkg-config,
                tabix (>= 1.0)
 # tabix is needed for the regression tests.
 Standards-Version: 3.9.8
diff --git a/debian/patches/curses.patch b/debian/patches/curses.patch
new file mode 100644
index 0000000..efa0793
--- /dev/null
+++ b/debian/patches/curses.patch
@@ -0,0 +1,11 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -98,6 +98,8 @@
+ 
+ FAILED.  This error must be resolved in order to build samtools successfully.])
+ fi
++CURSES_LIB=-lcurses
++AC_SUBST([CURSES_LIB])
+ 
+ AC_CONFIG_FILES([config.mk])
+ AC_OUTPUT
diff --git a/debian/patches/disable-usagetest.patch b/debian/patches/disable-usagetest.patch
new file mode 100644
index 0000000..0cf0c1b
--- /dev/null
+++ b/debian/patches/disable-usagetest.patch
@@ -0,0 +1,11 @@
+--- a/test/test.pl
++++ b/test/test.pl
+@@ -38,7 +38,7 @@
+ test_dict($opts);
+ test_index($opts);
+ test_mpileup($opts);
+-test_usage($opts, cmd=>'samtools');
++#test_usage($opts, cmd=>'samtools');
+ test_view($opts);
+ test_cat($opts);
+ test_bam2fq($opts);
diff --git a/debian/patches/mayhem.patch b/debian/patches/mayhem.patch
index 08b745c..537561a 100644
--- a/debian/patches/mayhem.patch
+++ b/debian/patches/mayhem.patch
@@ -7,7 +7,7 @@ Description: Fix Mayhem issues caused by unlimited reads of gz input
 
 --- a/misc/maq2sam.c
 +++ b/misc/maq2sam.c
-@@ -98,14 +98,37 @@ maqmap_t *maqmap_read_header(gzFile fp)
+@@ -100,14 +100,37 @@
          }
          assert(mm->format == MAQMAP_FORMAT_NEW);
      }
@@ -46,7 +46,7 @@ Description: Fix Mayhem issues caused by unlimited reads of gz input
      gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
      return mm;
  }
-@@ -117,6 +140,8 @@ void maq2tam_core(gzFile fp, const char
+@@ -119,6 +142,8 @@
      int ret;
      m1 = &mm1;
      mm = maqmap_read_header(fp);
@@ -55,7 +55,7 @@ Description: Fix Mayhem issues caused by unlimited reads of gz input
      while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
          int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
          if (m1->flag) flag |= 1;
-@@ -191,6 +216,11 @@ int main(int argc, char *argv[])
+@@ -193,6 +218,11 @@
          return 1;
      }
      fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
diff --git a/debian/patches/series b/debian/patches/series
index 08bb035..6591687 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,5 @@
 spelling.patch
 literal_version.patch
 mayhem.patch
+curses.patch
+disable-usagetest.patch
diff --git a/debian/rules b/debian/rules
index d6aae77..69c8d80 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,7 @@
 #!/usr/bin/make -f
 
 export DH_VERBOSE=1
+export CURSES_LIB=-lcurses
 
 %:
 	dh $@ --parallel

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git