[med-svn] r9921 - in trunk/packages/ncbi-blast+/trunk/debian: . patches

Olivier Sallou osallou at alioth.debian.org
Wed Mar 7 11:02:17 UTC 2012 

Author: osallou
Date: 2012-03-07 11:02:16 +0000 (Wed, 07 Mar 2012)
New Revision: 9921

Modified:
   trunk/packages/ncbi-blast+/trunk/debian/changelog
   trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks
   trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
   trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
   trunk/packages/ncbi-blast+/trunk/debian/patches/series
Log:
update for new upstream release

Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2012-03-07 09:55:53 UTC (rev 9920)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog	2012-03-07 11:02:16 UTC (rev 9921)
@@ -1,8 +1,13 @@
-ncbi-blast+ (2.2.25-8) UNRELEASED; urgency=low
+ncbi-blast+ (2.2.26-1) unstable; urgency=low
 
+  [ Olivier Sallou ]
+  * New upstream release 
+  * Remove some patches, applied upstream
+
+  [ Andreas Tille]
   * debian/copyright: Added Upstream-Contact
 
- -- Andreas Tille <tille at debian.org>  Thu, 22 Dec 2011 17:41:16 +0100
+ -- Olivier Sallou <osallou at debian.org>  Wed, 07 Mar 2012 09:37:10 +0100
 
 ncbi-blast+ (2.2.25-7) unstable; urgency=low
 

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks	2012-03-07 09:55:53 UTC (rev 9920)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks	2012-03-07 11:02:16 UTC (rev 9921)
@@ -1,37 +1,9 @@
 Subject:  checks misreported as absent when unpacked under /*/src/*
 
- * scripts/common/check/check_add.sh: accept the relative source directory
  * src/build-system/Makefile.meta.in: supply it to check_add.sh
 
 Author: Aaron M. Ucko <ucko at debian.org>
 Last-Update: 2011-05-23
---- a/c++/scripts/common/check/check_add.sh	2011-05-23 18:49:10.000000000 -0400
-+++ b/c++/scripts/common/check/check_add.sh	2011-05-23 18:50:40.000000000 -0400
-@@ -28,14 +28,12 @@
- x_srcdir=`(cd "$1"; pwd)`
- x_test=$2
- x_signature=$3
-+x_srcdir_rel=$4
- x_use_ignore_list=${CHECK_USE_IGNORE_LIST-Y}
- x_delim=" ____ "
- # Default timeout for check (in seconds)
- x_timeout_default=200
- 
--# Convert source dir to relative path
--x_srcdir_rel=`echo "$x_srcdir" | perl -ne 's|^.*?/src/||; print'`
--
- # Check to necessity make test for this application
- if test ! -f "$x_srcdir/Makefile.$x_test.app";  then
-    echo "Warning: File \"$x_srcdir/Makefile.$x_test.app\" not found."
-@@ -46,7 +44,7 @@
- x_app=`grep '^ *APP[ =]' "$x_srcdir/Makefile.$x_test.app"`
- x_app=`echo "$x_app" | sed -e 's/^.*=//' -e 's/^ *//'`
- 
--x_tpath=`echo "$x_srcdir/$x_test" | perl -ne 's|^.*?/src/||; print'`
-+x_tpath=$x_srcdir_rel/$x_test
- if grep -c '^ *CHECK_CMD' $x_srcdir/Makefile.$x_test.app > /dev/null ; then 
-    # Check ignore list
-    x_use_ignore_list=`echo $x_use_ignore_list | tr '[a-z]' '[A-Z]' | sed -e 's/^\(.\).*/\1/g'`
 --- a/c++/src/build-system/Makefile.meta.in	2011-05-23 18:48:59.000000000 -0400
 +++ b/c++/src/build-system/Makefile.meta.in	2011-05-23 18:49:20.000000000 -0400
 @@ -188,7 +188,7 @@

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps	2012-03-07 09:55:53 UTC (rev 9920)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps	2012-03-07 11:02:16 UTC (rev 9921)
@@ -35,19 +35,6 @@
  ASN_DEP = seqset
  
  WATCHERS = morgulis
-Index: b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
-===================================================================
---- a/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -7,6 +7,8 @@
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
-+DLL_LIB = xobjmgr xncbi
-+
- ASN_DEP = seqset
- 
- WATCHERS = morgulis
 Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
 ===================================================================
 --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib	2010-04-26 09:36:34.000000000 -0400
@@ -61,19 +48,6 @@
 +          seq general xser tables xncbi
  
  WATCHERS = blastsoft
-Index: b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
-===================================================================
---- a/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -5,6 +5,8 @@
-       njn_localmaxstat njn_localmaxstatutil njn_ioutil njn_matrix \
-       njn_stringutil njn_dynprogprob njn_dynprogproblim njn_dynprogprobproto
- 
-+DLL_LIB = tables xutil xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
- 
 Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
 ===================================================================
 --- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib	2011-02-10 12:14:32.000000000 -0500
@@ -136,14 +110,12 @@
 ===================================================================
 --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib	2010-05-04 11:42:43.000000000 -0400
 +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -10,6 +10,6 @@
-       alnsegments alnseq alnvec alnvec_iterator alnvecprint		\
-       pairwise_aln sparse_aln sparse_ci
+@@ -12,3 +12,5 @@
  
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
+ WATCHERS = todorov dicuccio grichenk
  
- WATCHERS = todorov
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
++
 Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
 ===================================================================
 --- a/c++/src/objtools/readers/Makefile.xobjread.lib	2011-02-02 10:48:12.000000000 -0500
@@ -739,16 +711,3 @@
  LIB = $(LIB_:%=%$(STATIC))
  
  CXXFLAGS = $(FAST_CXXFLAGS)
-Index: b/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app
-===================================================================
---- a/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app	2011-08-29 12:18:27.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app	2011-08-29 12:18:31.000000000 -0400
-@@ -2,7 +2,7 @@
- SRC = main srsearch_app
- 
- LIB_ = xalgoblastdbindex xalgoblastdbindex_search blast composition_adjustment seqdb blastdb \
--      xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
-+      xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
- 
- CXXFLAGS = $(FAST_CXXFLAGS)

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes	2012-03-07 09:55:53 UTC (rev 9920)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes	2012-03-07 11:02:16 UTC (rev 9921)
@@ -2,18 +2,14 @@
 
 * src/build-system/configure(.ac):
   - Reflect the Hurd's support for -Wl,rpath,... .
-  - When checking how select works, reset the alarm from the signal handler
-    to avoid spinning forever.
 * src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
   cope with missing PATH_MAX everywhere, not just under Windows.
 
 Author: Aaron M. Ucko <ucko at debian.org>
 Last-Update: 2011-06-10
-Index: b/c++/src/build-system/configure
-===================================================================
---- a/c++/src/build-system/configure	2011-03-16 14:40:24.000000000 -0400
-+++ b/c++/src/build-system/configure	2011-08-29 12:12:56.000000000 -0400
-@@ -5559,7 +5559,7 @@
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5688,7 +5688,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -22,20 +18,9 @@
        CONF_f_runpath="-Wl,-rpath,"
        ;;
      linux*:ICC )
-@@ -11416,7 +11416,7 @@
-          #ifdef HAVE_UNISTD_H
-          #  include <unistd.h>
-          #endif
--         RETSIGTYPE handler(int sig) { }
-+         RETSIGTYPE handler(int sig) { alarm(0); }
- int
- main ()
- {
-Index: b/c++/src/build-system/configure.ac
-===================================================================
---- a/c++/src/build-system/configure.ac	2011-03-16 14:40:24.000000000 -0400
-+++ b/c++/src/build-system/configure.ac	2011-08-29 12:12:41.000000000 -0400
-@@ -1441,7 +1441,7 @@
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1496,7 +1496,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -44,19 +29,8 @@
        CONF_f_runpath="-Wl,-rpath,"
        ;;
      linux*:ICC )
-@@ -2811,7 +2811,7 @@
-          #ifdef HAVE_UNISTD_H
-          #  include <unistd.h>
-          #endif
--         RETSIGTYPE handler(int sig) { }]],
-+         RETSIGTYPE handler(int sig) { alarm(0); }]],
-        [[struct timeval timeout = { 5, 0 };
-          signal(SIGALRM, &handler);
-          alarm(1);
-Index: b/c++/src/connect/ncbi_socket_cxx.cpp
-===================================================================
---- a/c++/src/connect/ncbi_socket_cxx.cpp	2011-03-16 10:54:49.000000000 -0400
-+++ b/c++/src/connect/ncbi_socket_cxx.cpp	2011-08-29 12:11:45.000000000 -0400
+--- a/c++/src/connect/ncbi_socket_cxx.cpp
++++ b/c++/src/connect/ncbi_socket_cxx.cpp
 @@ -34,7 +34,7 @@
  #include <ncbi_pch.hpp>
  #include <connect/ncbi_socket_unix.hpp>
@@ -66,10 +40,8 @@
  #  define PATH_MAX 512                  // will actually use less than 32 chars
  #endif
  
-Index: b/c++/src/connect/ext/ncbi_localnet.c
-===================================================================
---- a/c++/src/connect/ext/ncbi_localnet.c	2010-03-22 12:11:37.000000000 -0400
-+++ b/c++/src/connect/ext/ncbi_localnet.c	2011-08-29 12:11:45.000000000 -0400
+--- a/c++/src/connect/ext/ncbi_localnet.c
++++ b/c++/src/connect/ext/ncbi_localnet.c
 @@ -64,6 +64,8 @@
  
  #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series	2012-03-07 09:55:53 UTC (rev 9920)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series	2012-03-07 11:02:16 UTC (rev 9921)
@@ -1,8 +1,4 @@
 hurd_fixes
 legacy_rename_rpsblast
-fix_checks
-fix_gcc46_errors
-support_other_cpus
 fix_lib_deps
 no_multiarch_rpath
-do_not_output_everything_to_stderr.patch

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