From: Olivier Sallou Date: Wed, 7 Mar 2012 11:02:16 +0000 (+0000) Subject: update for new upstream release X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~305 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=95f2065e81e1d6de16982f10d6dbfa3390fedb33;p=ncbi-blast%2B.git update for new upstream release --- diff --git a/debian/changelog b/debian/changelog index 9c8b7d62..cb7563ff 100644 --- a/debian/changelog +++ b/debian/changelog @@ -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 Thu, 22 Dec 2011 17:41:16 +0100 + -- Olivier Sallou Wed, 07 Mar 2012 09:37:10 +0100 ncbi-blast+ (2.2.25-7) unstable; urgency=low diff --git a/debian/patches/fix_checks b/debian/patches/fix_checks index ae0b435d..f64ede60 100644 --- a/debian/patches/fix_checks +++ b/debian/patches/fix_checks @@ -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 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 @@ diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 87b20928..217071b3 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -34,19 +34,6 @@ Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib + 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 =================================================================== @@ -61,19 +48,6 @@ Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib + 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 @@ Index: b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib =================================================================== --- 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 @@ -738,17 +710,4 @@ Index: b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app + xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS) 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) diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes index 4c5d18b0..c41b84bb 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -2,18 +2,14 @@ Subject: fix portability issues that led to Hurd build failures * 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 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 @@ Index: b/c++/src/build-system/configure CONF_f_runpath="-Wl,-rpath," ;; linux*:ICC ) -@@ -11416,7 +11416,7 @@ - #ifdef HAVE_UNISTD_H - # include - #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 @@ Index: b/c++/src/build-system/configure.ac CONF_f_runpath="-Wl,-rpath," ;; linux*:ICC ) -@@ -2811,7 +2811,7 @@ - #ifdef HAVE_UNISTD_H - # include - #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 #include @@ -66,10 +40,8 @@ Index: b/c++/src/connect/ncbi_socket_cxx.cpp # 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) diff --git a/debian/patches/series b/debian/patches/series index 6028e8dd..8eda07f4 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -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