[med-svn] [Git][med-team/htslib][master] 4 commits: Add missing Depends: libcurl4-gnutls-dev, libdeflate-dev

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / htslib


Commits:
a1dcd61d by Andreas Tille at 2020-10-05T08:23:17+02:00
Add missing Depends: libcurl4-gnutls-dev, libdeflate-dev

- - - - -
9605bc10 by Andreas Tille at 2020-10-05T08:34:47+02:00
Fix run-unit-test script

- - - - -
7e0bf2de by Andreas Tille at 2020-10-05T08:35:06+02:00
Fix autopkgtest

- - - - -
d4320da3 by Andreas Tille at 2020-10-05T08:48:19+02:00
Debian has no libexecdir - plugins should go to libdir

- - - - -


6 changed files:

- debian/changelog
- debian/control
- + debian/patches/plugins_to_lib.patch
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -2,6 +2,9 @@ htslib (1.11-2) UNRELEASED; urgency=medium
 
   * Enable plugins
     Closes: #971542
+  * Add missing Depends: libcurl4-gnutls-dev, libdeflate-dev
+  * Fix run-unit-test script
+  * Fix autopkgtest
 
  -- Andreas Tille <tille at debian.org>  Fri, 02 Oct 2020 11:35:21 +0200
 


=====================================
debian/control
=====================================
@@ -46,6 +46,8 @@ Architecture: any
 Multi-Arch: same
 Section: libdevel
 Depends: libhts3 (= ${binary:Version}),
+         libcurl4-gnutls-dev,
+         libdeflate-dev,
          liblzma-dev,
          zlib1g-dev,
          ${misc:Depends}


=====================================
debian/patches/plugins_to_lib.patch
=====================================
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 02 Oct 2020 11:35:21 +0200
+Description: Debian has no libexecdir - plugins should go to libdir
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -115,11 +115,11 @@ AC_ARG_WITH([libdeflate],
+ 
+ AC_ARG_WITH([plugin-dir],
+   [AS_HELP_STRING([--with-plugin-dir=DIR],
+-                  [plugin installation location [LIBEXECDIR/htslib]])],
++                  [plugin installation location [LIBDIR/htslib]])],
+   [case $withval in
+      yes|no) MSG_ERROR([no directory specified for --with-plugin-dir]) ;;
+    esac],
+-   [with_plugin_dir='$(libexecdir)/htslib'])
++   [with_plugin_dir='$(libdir)/htslib'])
+ AC_SUBST([plugindir], $with_plugin_dir)
+ 
+ AC_ARG_WITH([plugin-path],


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ fix_float_precision
 # big-endian
 cram_to_bam_export.patch
 273c5e76a1694aa2a13fd51c133abed2ef8ab4d3.patch
+plugins_to_lib.patch


=====================================
debian/rules
=====================================
@@ -83,6 +83,7 @@ override_dh_install-indep:
 	dh_install --indep
 	sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk
 	sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk
+	sed -i 's#\.\./\.\./htslib/hfile.h#htslib/hfile.h#' `grep -Rl '../../htslib/hfile.h' debian/htslib-test/*`
 
 override_dh_installdocs:
 	dh_installdocs


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,10 +1,12 @@
 #!/bin/bash
 set -e
+set -x
 
 pkg="htslib"
 
 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
-	AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+    AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+    trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
 cp -aL /usr/share/${pkg}-test/* "$AUTOPKGTEST_TMP"
@@ -17,7 +19,7 @@ sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk
 CFLAGS="-O2 -fno-strict-aliasing -fno-code-hoisting"
 
 if grep sse /proc/cpuinfo > /dev/null; then
-	CFLAGS+=" -msse -mfpmath=sse"
+	CFLAGS="${CFLAGS} -msse -mfpmath=sse"
 fi
 export CFLAGS
 



View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0

-- 
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201005/d0e9a575/attachment-0001.html>