From: Graham Inggs <ginggs@debian.org>
Date: Mon, 31 Jul 2017 11:35:34 +0000 (+0200)
Subject: Drop pysam_stdout_linkage.patch, not needed since compat symlinks were added
X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~183
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=ee30ec94215abf29e7dd1c8730dec8369c9c2b29;p=python-pysam.git

Drop pysam_stdout_linkage.patch, not needed since compat symlinks were added
---

diff --git a/debian/changelog b/debian/changelog
index e4c4dfe..412e553 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,8 @@ python-pysam (0.11.2.2+ds-2) UNRELEASED; urgency=medium
   * Mark debian/python-pysam.links executable for dh-exec
   * Drop exclude_test_tyring_to_access_remote_ftpserver.patch,
     fixed upstream
+  * Drop pysam_stdout_linkage.patch, not needed since
+    compatibility symlinks were added
 
  -- Graham Inggs <ginggs@debian.org>  Mon, 31 Jul 2017 12:37:39 +0200
 
diff --git a/debian/patches/pysam_stdout_linkage.patch b/debian/patches/pysam_stdout_linkage.patch
deleted file mode 100644
index 9e9b54e..0000000
--- a/debian/patches/pysam_stdout_linkage.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Description: fix missing symbols in libcsamtools and libcbcftools libraries
- Building on Ubuntu fails because a couple of the .sos wind up with
- unresolved references to symbols found elsewhere in the tree.  Fix their
- linkage so that they load cleanly.
-Author: Steve Langasek <steve.langasek@canonical.com>
-Last-Update: Fri, 28 Jul 2017 10:45:42 -0700
-Bug-Debian: https://bugs.debian.org/867017
-
---- a/setup.py
-+++ b/setup.py
-@@ -463,6 +463,7 @@ cutils = Extension(
- csamtools = Extension(
-     "pysam.libcsamtools",
-     [source_pattern % "samtools"] +
-+    ["pysam/pysam_util.c"] +
-     glob.glob(os.path.join("samtools", "*.pysam.c")) +
-     htslib_sources +
-     os_c_files,
-@@ -484,7 +485,8 @@ cbcftools = Extension(
-     library_dirs=["pysam"] + htslib_library_dirs,
-     include_dirs=["bcftools", "pysam", "."] +
-     include_os + htslib_include_dirs,
--    libraries=external_htslib_libraries + internal_htslib_libraries,
-+    libraries=external_htslib_libraries + internal_htslib_libraries + \
-+    [os.path.splitext("csamtools{}".format(suffix))[0]],
-     language="c",
-     extra_compile_args=extra_compile_args,
-     define_macros=define_macros
diff --git a/debian/patches/series b/debian/patches/series
index 0aa298f..27db99f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
-pysam_stdout_linkage.patch
 no-usage-test-without-tty.patch