[med-svn] [Git][med-team/kmer][master] 8 commits: Revert changes that do not fit latest upload which was not commited…
Andreas Tille
gitlab at salsa.debian.org
Mon Aug 27 13:49:00 BST 2018
Andreas Tille pushed to branch master at Debian Med / kmer
Commits:
9c4cb1d7 by Andreas Tille at 2018-08-27T12:32:39Z
Revert changes that do not fit latest upload which was not commited unfortunately. Changes will be restored after commits belonging to last upload
- - - - -
7a8fd1fb by Andreas Tille at 2018-08-27T12:34:07Z
Use the same compile flags in all Linux builds, and include -fPIC atac .so were built without -fPIC on !amd64/ia64.
- - - - -
5482cf20 by Andreas Tille at 2018-08-27T12:34:14Z
Standards-Version: 4.2.0
- - - - -
75e0c570 by Andreas Tille at 2018-08-27T12:34:21Z
Upload to unstable
- - - - -
12042d88 by Liubov Chuprikova at 2018-08-27T12:40:16Z
Add autopkgtest
- - - - -
07672db9 by Liubov Chuprikova at 2018-08-27T12:41:19Z
Standards-Version: 4.2.1
- - - - -
230aadef by Andreas Tille at 2018-08-27T12:47:09Z
Add a patch to fix wrong evaluation order of an expression
- - - - -
03eabbfb by Andreas Tille at 2018-08-27T12:48:13Z
Add Bug-Debian field
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_wrong_evaluation_order.patch
- + debian/patches/linux-cflags.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,27 @@
-kmer (0~20150903+r2013-5) UNRELEASED; urgency=medium
+kmer (0~20150903+r2013-6) UNRELEASED; urgency=medium
* Team upload.
* Add autopkgtest.
- * Standards-Version: 4.2.0
+ * Standards-Version: 4.2.1
* Add a patch to fix wrong evaluation order in an expression
Closes: #906980
-- Liubov Chuprikova <chuprikovalv at gmail.com> Mon, 27 Aug 2018 11:37:43 +0200
+kmer (0~20150903+r2013-5) unstable; urgency=medium
+
+ * Team upload
+
+ [ Adrian Bunk ]
+ * Use the same compile flags in all Linux builds, and include -fPIC
+ atac .so were built without -fPIC on !amd64/ia64.
+ Closes: #907007
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.2.0
+
+ -- Andreas Tille <tille at debian.org> Sun, 26 Aug 2018 16:58:23 +0200
+
kmer (0~20150903+r2013-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
# For ATAC
dh-python,
python-all-dev
-Standards-Version: 4.2.0
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/kmer
Vcs-Git: https://salsa.debian.org/med-team/kmer.git
Homepage: http://kmer.sourceforge.net
=====================================
debian/patches/fix_wrong_evaluation_order.patch
=====================================
@@ -1,7 +1,7 @@
Author: Liubov Chuprikova <chuprikovalv at gmail.com>
Last-Update: Mon, 27 August 2018 11:24:36 +0200
Description: Fix a piece of code that has unpredictable results
-
+Bug-Debian: https://bugs.debian.org/906980
--- a/atac-driver/libatac/atacMatchList.C
+++ b/atac-driver/libatac/atacMatchList.C
=====================================
debian/patches/linux-cflags.patch
=====================================
@@ -0,0 +1,50 @@
+Description: Use the same compile flags in all Linux builds, and include -fPIC
+ atac .so were built without -fPIC on !amd64/ia64.
+Author: Adrian Bunk <bunk at debian.org>
+Bug-Debian: https://bugs.debian.org/907007
+Last-Update: Thu, 23 Aug 2018 05:16:16 +0300
+
+--- kmer-0~20150903+r2013.orig/configure.sh
++++ kmer-0~20150903+r2013/configure.sh
+@@ -57,12 +57,12 @@ if [ "x$target" = "x" ] ; then
+ ;;
+ Linux)
+ target="Linux-i686$opts"
+- if [ `uname -m` = "x86_64" ] ; then
+- target="Linux-amd64$opts"
+- fi
+- if [ `uname -m` = "ia64" ] ; then
+- target="Linux-ia64$opts"
+- fi
++ #if [ `uname -m` = "x86_64" ] ; then
++ # target="Linux-amd64$opts"
++ #fi
++ #if [ `uname -m` = "ia64" ] ; then
++ # target="Linux-ia64$opts"
++ #fi
+ ;;
+ SunOS)
+ target="solaris$opts"
+@@ -221,11 +221,11 @@ EOF
+ # Linux, optimized
+ CC := $CC
+ SHLIB_FLAGS := -shared
+-CFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
++CFLAGS_COMPILE := -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+ CLDFLAGS := -L/usr/local/lib
+ CLIBS := -pthread -ldl
+ CXX := $CXX
+-CXXFLAGS_COMPILE := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
++CXXFLAGS_COMPILE := -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
+ CXXLDFLAGS := -L/usr/local/lib
+ CXXLIBS := -pthread -ldl
+ ARFLAGS := ruvs
+@@ -350,7 +350,7 @@ EOF
+ echo " tru64, compaq Tru64, optimized"
+ echo " tru64-debug, compaq-debug Tru64, debug, warnings, trapuv"
+ echo ""
+- echo " linux Linux, i686, optimized"
++ echo " linux Linux, optimized"
+ echo " linux64 Linux, Opteron, optimized"
+ echo ""
+ echo " solaris Solaris, gcc, optimized (STALE)"
=====================================
debian/patches/series
=====================================
@@ -2,4 +2,5 @@ allow-freebsd-build.patch
atac-helper-script-paths.patch
atac-readme.patch
spelling.patch
+linux-cflags.patch
fix_wrong_evaluation_order.patch
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/c3bcaa2895258123dbf29e90a231c33074c6a264...03eabbfba11ecf6eac8fccb28b581e2e9661ed71
--
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/c3bcaa2895258123dbf29e90a231c33074c6a264...03eabbfba11ecf6eac8fccb28b581e2e9661ed71
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