Imported Debian patch 0.1.5c-2

diff --git a/debian/README.Debian b/debian/README.Debian
index f85211831e5bf66c517c7465e58ad2f84729d1d6..431ec29d995d392e3e5d3660de6cae5644b5b3b5 100644 (file)
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -5,6 +5,9 @@ The extra utilities found in the ‘misc’ directory of the upstream archive ar
 placed in ‘/usr/share/samtools’ and ‘/usr/lib/samtools’ for Perl scripts and
 binary executables respectively.
 
 placed in ‘/usr/share/samtools’ and ‘/usr/lib/samtools’ for Perl scripts and
 binary executables respectively.
 

-Currently, the BAM library only exists in static version.
+Currently, the BAM library only exists in static version. It (actually the
+whole package) is built with the -fPIC option, to allow the compilation of the
+Bio::SamTools Perl module on the amd64 platform (Debian package
+libbio-samtools-perl).

 
 

- -- Charles Plessy <plessy@debian.org>  Sat, 08 Aug 2009 11:50:09 +0900
+ -- Charles Plessy <plessy@debian.org>  Thu, 03 Sep 2009 19:24:02 +0900

diff --git a/debian/changelog b/debian/changelog
index c858785f937b4f0ad1ee8aee486ce0e6e44a4118..9aebad2cf61c967e728129bec59a6ba7b70e5e37 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+samtools (0.1.5c-2) unstable; urgency=low
+
+  * Rebuilt with -fPIC (debian/rules, README.Debian).
+  * Small corrections to the description from upstream (debian/changelog).
+  * Incremented Standards-Version to reflect conformance with Policy 3.8.3
+    (no changes needed).
+
+ -- Charles Plessy <plessy@debian.org>  Thu, 03 Sep 2009 19:29:40 +0900
+

 samtools (0.1.5c-1) unstable; urgency=low
 
   * Initial release (Closes: #540453)
 samtools (0.1.5c-1) unstable; urgency=low
 
   * Initial release (Closes: #540453)

diff --git a/debian/control b/debian/control
index 0020fc580ef91623c1afcb0f78e961b35e8e933f..acaa75cc26a34b5da6a827ef31ee365361200422 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy@debian.org>
 Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy@debian.org>
 Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev

-Standards-Version: 3.8.2
+Standards-Version: 3.8.3

 Homepage: http://samtools.sourceforge.net
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
 Homepage: http://samtools.sourceforge.net
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/


@@ -15,10 +15,10 @@ Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: processing sequence alignments in SAM and BAM formats
  Samtools is a set of utilities that manipulate nucleotide sequence alignments
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: processing sequence alignments in SAM and BAM formats
  Samtools is a set of utilities that manipulate nucleotide sequence alignments

- in the BAM format. It imports from and exports to the SAM (Sequence
- Alignment/Map) format, does sorting, merging and indexing, and allows to
- retrieve reads in any regions swiftly. It is designed to work on a stream, and
- is able to open a BAM (not SAM) file on a remote FTP server.
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP server.

 
 Package: libbam-dev
 Architecture: any
 
 Package: libbam-dev
 Architecture: any


@@ -27,6 +27,6 @@ Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: manipulates nucleotide sequence alignments in BAM or SAM format 
  The BAM library provides I/O and various operations on manipulating nucleotide
  sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
 Description: manipulates nucleotide sequence alignments in BAM or SAM format 
  The BAM library provides I/O and various operations on manipulating nucleotide
  sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence

- Alignment/Map) format. It now supports importing from or exporting to TAM,
+ Alignment/Map) format. It now supports importing from or exporting to SAM,

  sorting, merging, generating pileup, and quickly retrieval of reads overlapped
  with a specified region. 
  sorting, merging, generating pileup, and quickly retrieval of reads overlapped
  with a specified region. 

diff --git a/debian/rules b/debian/rules
index 451ca815bffaafd7ad0ecbfb11dedde97a500fd4..ee5c351837f5e41fbfb82fd3c62be5d5d0d7fb61 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -3,5 +3,7 @@
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
 

+CFLAGS += -fPIC
+

 DEB_MAKE_BUILD_TARGET = all all-recur razip lib
 DEB_MAKE_CHECK_TARGET = -C examples all
 DEB_MAKE_BUILD_TARGET = all all-recur razip lib
 DEB_MAKE_CHECK_TARGET = -C examples all