debian/changelog

-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@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@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

 Author: Liubov Chuprikova <chuprikovalv@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

+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@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