[med-svn] r8823 - in trunk/packages/ensembl/ensembl/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-12-07 21:06:23 +0000 (Wed, 07 Dec 2011)
New Revision: 8823

Added:
   trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch
Modified:
   trunk/packages/ensembl/ensembl/trunk/debian/changelog
   trunk/packages/ensembl/ensembl/trunk/debian/control
   trunk/packages/ensembl/ensembl/trunk/debian/patches/series
   trunk/packages/ensembl/ensembl/trunk/debian/rules
Log:
Five lintian warnings and one warning at build time less ...


Modified: trunk/packages/ensembl/ensembl/trunk/debian/changelog
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-07 20:42:52 UTC (rev 8822)
+++ trunk/packages/ensembl/ensembl/trunk/debian/changelog	2011-12-07 21:06:23 UTC (rev 8823)
@@ -12,6 +12,7 @@
     - Internal dependencies always (= ${source:Version})
     - ensembl contains scripts explicitly requiring tcsh, so remove
       c-shell alternatives
+    - no need for ${shlibs:Depends} in ensembl (arch=all)
   * debian/prepare_ensembl_source_packages.sh:
     - Make sure the files that should be removed will be really removed
     - Make script way less noisy
@@ -37,8 +38,10 @@
   * debian/adjust_shebang_line.sh:
     - Be less verbose but provide an easy option to switch on verbosity
     - Fix another invalid shebang line ("#! perl")
+  * debian/patches/fix_usr_bin_env_typo.patch: Fix typo - should be
+    reported upstream
 
- -- Andreas Tille <tille at debian.org>  Wed, 30 Nov 2011 13:30:15 +0100
+ -- Andreas Tille <tille at debian.org>  Wed, 07 Dec 2011 21:58:31 +0100
 
 ensembl (63-1~lucid1) lucid; urgency=low
 

Modified: trunk/packages/ensembl/ensembl/trunk/debian/control
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-07 20:42:52 UTC (rev 8822)
+++ trunk/packages/ensembl/ensembl/trunk/debian/control	2011-12-07 21:06:23 UTC (rev 8823)
@@ -17,7 +17,7 @@
 Package: ensembl
 Architecture: all
 Pre-Depends: debconf
-Depends: ${shlibs:Depends}, ${misc:Depends}, apache2-mpm-prefork, tcsh, expat,
+Depends: ${misc:Depends}, apache2-mpm-prefork, tcsh, expat,
  libcgi-pm-perl, libcgi-session-perl, libdb-file-lock-perl, libdbd-mysql,
  perl-modules, ensembl-bin (>= ${source:Version}),
  libensembl-core-perl (= ${source:Version}),

Added: trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch	                        (rev 0)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch	2011-12-07 21:06:23 UTC (rev 8823)
@@ -0,0 +1,8 @@
+--- ensembl-65.orig/ensembl-variation/scripts/misc/generate_reg_file.pl
++++ ensembl-65/ensembl-variation/scripts/misc/generate_reg_file.pl
+@@ -1,4 +1,4 @@
+-#!/use/bin/env perl
++#!/usr/bin/env perl
+ 
+ use strict;
+ use warnings;

Modified: trunk/packages/ensembl/ensembl/trunk/debian/patches/series
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/patches/series	2011-12-07 20:42:52 UTC (rev 8822)
+++ trunk/packages/ensembl/ensembl/trunk/debian/patches/series	2011-12-07 21:06:23 UTC (rev 8823)
@@ -6,3 +6,4 @@
 sessiondbconn.patch
 httpd.patch
 SiteDefs_tmpdir.patch
+fix_usr_bin_env_typo.patch

Modified: trunk/packages/ensembl/ensembl/trunk/debian/rules
===================================================================
--- trunk/packages/ensembl/ensembl/trunk/debian/rules	2011-12-07 20:42:52 UTC (rev 8822)
+++ trunk/packages/ensembl/ensembl/trunk/debian/rules	2011-12-07 21:06:23 UTC (rev 8823)
@@ -30,10 +30,15 @@
 	# will be fixed there
 	mkdir -p $(TMPINSTDIR)
 	cp -a `find . -mindepth 1 -maxdepth 1 -type d | grep -v -e cbuild -e .pc -e debian` $(TMPINSTDIR)
+
+	# fix permissions
 	find $(TMPINSTDIR) -name "*.pm" -o -name "*.png" -o -name "*.gif" -o -name README \
-                -o -name "*.sql" -o -name "*.pdf" -o -name "*.html" \
+                -o -name "*.sql" -o -name "*.pdf" -o -name "*.html" -o -name "*.dump" \
 		-o -name "*.sxw" -o -name "*.conf.example" -o -name "*.txt" \
-				| xargs -r --max-args 10 chmod 644
+		-o -name "*.tcl" \
+				| xargs -r --max-args 10 chmod a-x
+	find $(TMPINSTDIR) -name pfetch2ensembl -o -name "*.registry" \
+				| xargs -r --max-args 10 chmod a+x
 
 	# FIXME: Since version 64 Ensembl contains a copy of doxygen as binary.
 	#        It needs checking in far this is needed at runtime.  Debian packaged version
@@ -84,8 +89,6 @@
 	# do not ship extra license files
 	rm -f debian/libensembl-core-perl/usr/share/ensembl/ensembl/misc-scripts/alternative_splicing/AltSplicingToolkit/COPYING
 	rm -f debian/libensembl-core-perl/usr/share/ensembl/ensembl/LICENSE
-	# fix permissions
-	chmod a+x debian/libensembl-core-perl/usr/share/ensembl/ensembl/misc-scripts/golden_path/pfetch2ensembl
 
 override_dh_auto_clean:
 	dh_auto_clean