[med-svn] r6273 - in trunk/packages/maqview/trunk/debian: . patches source
Andreas Tille
tille at alioth.debian.org
Wed Mar 16 14:22:04 UTC 2011
Author: tille
Date: 2011-03-16 14:21:56 +0000 (Wed, 16 Mar 2011)
New Revision: 6273
Added:
trunk/packages/maqview/trunk/debian/mail_from_author
trunk/packages/maqview/trunk/debian/patches/
trunk/packages/maqview/trunk/debian/patches/fix-gcc-4.5.patch
trunk/packages/maqview/trunk/debian/patches/series
trunk/packages/maqview/trunk/debian/source/
trunk/packages/maqview/trunk/debian/source/format
Removed:
trunk/packages/maqview/trunk/debian/install
Modified:
trunk/packages/maqview/trunk/debian/changelog
trunk/packages/maqview/trunk/debian/compat
trunk/packages/maqview/trunk/debian/control
trunk/packages/maqview/trunk/debian/get-orig-source
trunk/packages/maqview/trunk/debian/rules
Log:
Uploaded to unstable
Modified: trunk/packages/maqview/trunk/debian/changelog
===================================================================
--- trunk/packages/maqview/trunk/debian/changelog 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/changelog 2011-03-16 14:21:56 UTC (rev 6273)
@@ -1,4 +1,4 @@
-maqview (0.2.5~zlibcopy-1) unstable; urgency=low
+maqview (0.2.5-1) unstable; urgency=low
* Initial release
Closes: #604497
Modified: trunk/packages/maqview/trunk/debian/compat
===================================================================
--- trunk/packages/maqview/trunk/debian/compat 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/compat 2011-03-16 14:21:56 UTC (rev 6273)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/maqview/trunk/debian/control
===================================================================
--- trunk/packages/maqview/trunk/debian/control 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/control 2011-03-16 14:21:56 UTC (rev 6273)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7.1), autotools-dev, automake, freeglut3-dev
+Build-Depends: debhelper (>= 8), autotools-dev, automake, freeglut3-dev, quilt
Standards-Version: 3.9.1
Homepage: http://maq.sourceforge.net/maqview.shtml
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maqview/trunk/?rev=0&sc=0
Modified: trunk/packages/maqview/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/maqview/trunk/debian/get-orig-source 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/get-orig-source 2011-03-16 14:21:56 UTC (rev 6273)
@@ -26,7 +26,7 @@
rm -rf .svn
cd ..
-mv ${PKG} ${PKG}-${VERSION}~zlibcopy
+mv ${PKG} ${PKG}-${VERSION}
-GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION~zlibcopy".orig.tar.gz "${PKG}-${VERSION}~zlibcopy"
-rm -rf "${PKG}-${VERSION}~zlibcopy"
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${PKG}-${VERSION}"
+rm -rf "${PKG}-${VERSION}"
Deleted: trunk/packages/maqview/trunk/debian/install
===================================================================
--- trunk/packages/maqview/trunk/debian/install 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/install 2011-03-16 14:21:56 UTC (rev 6273)
@@ -1,4 +0,0 @@
-maqindex usr/bin
-maqindex_socks usr/bin
-maqview usr/bin
-zrio usr/bin
Added: trunk/packages/maqview/trunk/debian/mail_from_author
===================================================================
--- trunk/packages/maqview/trunk/debian/mail_from_author (rev 0)
+++ trunk/packages/maqview/trunk/debian/mail_from_author 2011-03-16 14:21:56 UTC (rev 6273)
@@ -0,0 +1,75 @@
+Date: Tue, 23 Nov 2010 10:20:46 -0500
+From: Heng Li <lh3 at sanger.ac.uk>
+To: Andreas Tille <andreas at an3as.eu>
+Cc: Jue Ruan <ruanjue at gmail.com>,
+ Debian Med Project List <debian-med at lists.debian.org>
+Subject: Re: Usage of zlib in MaqView
+
+Hello Andreas,
+
+Many thanks for considering to port maqview to Debian Med.
+Unfortunately, I am afraid that for maqview we have to include those
+private zlib headers because maqview must use very low-level zlib
+structs and functions in order to achieve random access in a generic
+gzip file.
+
+At the same time, although maqview still has a few features that even
+the most modern viewers are missing, it is not the best any more (for
+example, IGV, which has been ported to Debian Med, is more generic and
+better). If you have difficulty in porting maqview, you may consider not
+to include maqview in Debian Med. This would be unfortunate for us, but
+we are unable to drop the dependency. I am sorry.
+
+Best wishes,
+
+Heng
+
+
+On Nov 19, 2010, at 6:06 PM, Andreas Tille wrote:
+
+> Hello,
+>
+> I'm writing you on behalf of the Debian Med project that has the goal to
+> provide medical and bioinformatical software to all Debian users. I hope
+> you like the attempt to include MaqView into Debian amongst other packages
+> as they are listed here
+>
+> http://debian-med.alioth.debian.org/tasks/bio
+>
+> Because I had a request to package MaqView and have started inspecting
+> the code. When doing so I noticed that you are using inside zrio.h the
+> header files
+>
+> #include "zutil.h"
+> #include "inftrees.h"
+> #include "inflate.h"
+>
+> according to the top remark in these files
+>
+> this file should *not* be used by applications. It is
+> part of the implementation of the compression library and is
+> subject to change. Applications should only use zlib.h.
+>
+> this is not the purpose of these files. I'm asking because in Debian
+> the packaged zlib library should be used with applications. This is for
+> consistency and security reasons.
+>
+> My question is: Could you imagine to find a solution which properly uses
+> only zlib.h as it was intended by the zlib authors for future releases
+> of MaqView?
+>
+> Kind regards
+>
+> Andreas.
+>
+> --
+> http://fam-tille.de
+
+
+
+--
+ The Wellcome Trust Sanger Institute is operated by Genome Research
+ Limited, a charity registered in England with number 1021457 and a
+ company registered in England with number 2742969, whose registered
+ office is 215 Euston Road, London, NW1 2BE.
+
Added: trunk/packages/maqview/trunk/debian/patches/fix-gcc-4.5.patch
===================================================================
--- trunk/packages/maqview/trunk/debian/patches/fix-gcc-4.5.patch (rev 0)
+++ trunk/packages/maqview/trunk/debian/patches/fix-gcc-4.5.patch 2011-03-16 14:21:56 UTC (rev 6273)
@@ -0,0 +1,13 @@
+--- maqview-0.2.5.orig/configure.ac
++++ maqview-0.2.5/configure.ac
+@@ -33,8 +33,8 @@
+ AC_ARG_ENABLE(static, [ --enable-static statically link GLUT (Linux Only)],
+ [is_static=1])
+ case $is_static in
+- 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm";;
+- 0) GLLIBS="-lGL -lglut -lm";;
++ 1) GLLIBS="-Wl,-Bstatic -lglut -Wl,-Bdynamic -lGL -lGLU -lm -lX11";;
++ 0) GLLIBS="-lGL -lGLU -lglut -lm -lX11";;
+ esac
+ AC_SUBST([GLLIBS]);;
+ # *) AC_MSG_ERROR([OS is not supported]);;
Added: trunk/packages/maqview/trunk/debian/patches/series
===================================================================
--- trunk/packages/maqview/trunk/debian/patches/series (rev 0)
+++ trunk/packages/maqview/trunk/debian/patches/series 2011-03-16 14:21:56 UTC (rev 6273)
@@ -0,0 +1 @@
+fix-gcc-4.5.patch
Modified: trunk/packages/maqview/trunk/debian/rules
===================================================================
--- trunk/packages/maqview/trunk/debian/rules 2011-03-16 10:24:15 UTC (rev 6272)
+++ trunk/packages/maqview/trunk/debian/rules 2011-03-16 14:21:56 UTC (rev 6273)
@@ -8,7 +8,7 @@
override_dh_auto_configure:
./autogen.sh
- dh_auto_configure
+ ./configure
make -f Makefile.generic maqview.1
### The *.class files in the source package can be reproduced by simply running
# javac MaqDataClient.java
@@ -20,5 +20,9 @@
rm -f aclocal.m4 config.guess config.h.in config.sub configure depcomp install-sh Makefile.in missing
rm -f *.1
+override_dh_install:
+ mv $(CURDIR)/debian/`dh_listpackages`/usr/local/bin $(CURDIR)/debian/`dh_listpackages`/usr
+ rm -rf $(CURDIR)/debian/`dh_listpackages`/usr/local
+
get-orig-source:
. debian/get-orig-source
Added: trunk/packages/maqview/trunk/debian/source/format
===================================================================
--- trunk/packages/maqview/trunk/debian/source/format (rev 0)
+++ trunk/packages/maqview/trunk/debian/source/format 2011-03-16 14:21:56 UTC (rev 6273)
@@ -0,0 +1 @@
+3.0 (quilt)
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