[med-svn] r6889 - in trunk/packages/ncbi-blast-plus/trunk/debian: . patches
Aaron M. Ucko
ucko at alioth.debian.org
Sun May 29 15:42:19 UTC 2011
Author: ucko
Date: 2011-05-29 15:42:19 +0000 (Sun, 29 May 2011)
New Revision: 6889
Added:
trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_errors
trunk/packages/ncbi-blast-plus/trunk/debian/patches/legacy_rename_rpsblast
Removed:
trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error
trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast
Modified:
trunk/packages/ncbi-blast-plus/trunk/debian/control
trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
trunk/packages/ncbi-blast-plus/trunk/debian/rules
Log:
Formal cosmetic cleanups.
* debian/control: Drop leading "The" from ncbi-blast+'s short
description; use appropriate amounts of whitespace throughout.
* debian/patches: Rename lecagy_rename_rpsblast (sic) to legacy_* and
fix_gcc46_include_error to fix_gcc46_errors; update series accordingly.
* debian/rules: retire long-winded $(SOURCEDIR) and simply pass -Dc++ to dh;
drop boilerplate "Sample debian/rules" comment and an extra blank line.
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-05-29 15:35:21 UTC (rev 6888)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/control 2011-05-29 15:42:19 UTC (rev 6889)
@@ -10,11 +10,10 @@
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast-plus/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-blast-plus/?rev=0
-
Package: ncbi-blast+
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, ${python:Depends}, ncbi-data
-Description: The next generation suite of BLAST sequence search tools
+Description: next generation suite of BLAST sequence search tools
The Basic Local Alignment Search Tool (BLAST) is the most widely
used sequence similarity tool. There are versions of BLAST that
compare protein queries to protein databases, nucleotide queries
@@ -30,7 +29,7 @@
Package: ncbi-blast+-legacy
Architecture: all
-Depends: ncbi-blast+,${misc:Depends}
+Depends: ncbi-blast+, ${misc:Depends}
Description: NCBI Blast legacy call script
This package adds some fake scripts to call NCBI+ programs
with the NCBI blast command line. It makes use of the
Copied: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_errors (from rev 6885, trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error)
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_errors (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_errors 2011-05-29 15:42:19 UTC (rev 6889)
@@ -0,0 +1,28 @@
+Subject: GCC 4.6 compilation error due to missing def
+
+ * include/corelib/ncbistre.hpp: Add stddef definition required by gcc4.6
+ * src/objtools/blast/seqdb_reader/seqdbimpl.hpp: remove mutable reference
+
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+Last-Update: 2011-05-03
+--- a/c++/include/corelib/ncbistre.hpp
++++ b/c++/include/corelib/ncbistre.hpp
+@@ -116,6 +116,7 @@
+ #define SEEKOFF PUBSEEKOFF
+
+ #include <string>
++#include <stddef.h>
+
+
+ // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file)
+--- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
++++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
+@@ -1245,7 +1245,7 @@
+ CSeqDBAtlasHolder m_AtlasHolder;
+
+ /// Reference to memory management layer.
+- mutable CSeqDBAtlas & m_Atlas;
++ CSeqDBAtlas & m_Atlas;
+
+ /// The list of database names provided to the constructor.
+ string m_DBNames;
Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error 2011-05-29 15:35:21 UTC (rev 6888)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_gcc46_include_error 2011-05-29 15:42:19 UTC (rev 6889)
@@ -1,28 +0,0 @@
-Subject: GCC 4.6 compilation error due to missing def
-
- * include/corelib/ncbistre.hpp: Add stddef definition required by gcc4.6
- * src/objtools/blast/seqdb_reader/seqdbimpl.hpp: remove mutable reference
-
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-Last-Update: 2011-05-03
---- a/c++/include/corelib/ncbistre.hpp
-+++ b/c++/include/corelib/ncbistre.hpp
-@@ -116,6 +116,7 @@
- #define SEEKOFF PUBSEEKOFF
-
- #include <string>
-+#include <stddef.h>
-
-
- // (BEGIN_NCBI_SCOPE must be followed by END_NCBI_SCOPE later in this file)
---- a/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-+++ b/c++/src/objtools/blast/seqdb_reader/seqdbimpl.hpp
-@@ -1245,7 +1245,7 @@
- CSeqDBAtlasHolder m_AtlasHolder;
-
- /// Reference to memory management layer.
-- mutable CSeqDBAtlas & m_Atlas;
-+ CSeqDBAtlas & m_Atlas;
-
- /// The list of database names provided to the constructor.
- string m_DBNames;
Deleted: trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast 2011-05-29 15:35:21 UTC (rev 6888)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast 2011-05-29 15:42:19 UTC (rev 6889)
@@ -1,11 +0,0 @@
---- a/c++/src/app/blast/legacy_blast.pl
-+++ b/c++/src/app/blast/legacy_blast.pl
-@@ -1064,7 +1064,7 @@
- if (defined $opt_p and $opt_p =~ /f/i) {
- $retval .= "/rpstblastn";
- } else {
-- $retval .= "/rpsblast";
-+ $retval .= "/rpsblast+";
- }
- $retval .= &add_exe_extension();
-
Copied: trunk/packages/ncbi-blast-plus/trunk/debian/patches/legacy_rename_rpsblast (from rev 6885, trunk/packages/ncbi-blast-plus/trunk/debian/patches/lecagy_rename_rpsblast)
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/legacy_rename_rpsblast (rev 0)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/legacy_rename_rpsblast 2011-05-29 15:42:19 UTC (rev 6889)
@@ -0,0 +1,11 @@
+--- a/c++/src/app/blast/legacy_blast.pl
++++ b/c++/src/app/blast/legacy_blast.pl
+@@ -1064,7 +1064,7 @@
+ if (defined $opt_p and $opt_p =~ /f/i) {
+ $retval .= "/rpstblastn";
+ } else {
+- $retval .= "/rpsblast";
++ $retval .= "/rpsblast+";
+ }
+ $retval .= &add_exe_extension();
+
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/series 2011-05-29 15:35:21 UTC (rev 6888)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/series 2011-05-29 15:42:19 UTC (rev 6889)
@@ -1,3 +1,3 @@
-lecagy_rename_rpsblast
+legacy_rename_rpsblast
fix_checks
-fix_gcc46_include_error
+fix_gcc46_errors
Modified: trunk/packages/ncbi-blast-plus/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-05-29 15:35:21 UTC (rev 6888)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/rules 2011-05-29 15:42:19 UTC (rev 6889)
@@ -1,15 +1,9 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
-SOURCEDIR=${CURDIR}/c++
DEB_CONFIGURE_EXTRA_FLAGS=--with-dll --with-mt --without-autodep \
--without-makefile-auto-update --with-flat-makefile --without-dbapi \
--without-lzo --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD
@@ -22,7 +16,6 @@
DEB_CONFIGURE_EXTRA_FLAGS += --with-optimization
endif
-
override_dh_auto_configure:
cd c++ && LD_LIBRARY_PATH=$(CURDIR)/c++/BUILD/lib \
./configure $(DEB_CONFIGURE_EXTRA_FLAGS)
@@ -67,7 +60,7 @@
rm -f c++/src/objects/blastxml/blastxml.module
%:
- dh $@ --with autotools_dev --with quilt --sourcedir=$(SOURCEDIR)
+ dh $@ -Dc++ --with autotools_dev --with quilt
get-orig-source:
. debian/get-orig-source
More information about the debian-med-commit
mailing list