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.

diff --git a/debian/control b/debian/control
index 7dccdf5ab2df90a4bcace29139513f52ee69c74e..954fb1df785be0299917170c1ca14bae9fb62115 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -10,11 +10,10 @@ Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
 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 @@ Description: The next generation suite of BLAST sequence search tools
 
 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

diff --git a/debian/patches/fix_gcc46_errors b/debian/patches/fix_gcc46_errors
new file mode 100644 (file)
index 0000000..a28de4e
--- /dev/null
+++ b/debian/patches/fix_gcc46_errors
@@ -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@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;

diff --git a/debian/patches/fix_gcc46_include_error b/debian/patches/fix_gcc46_include_error
deleted file mode 100644 (file)
index a28de4e..0000000
--- a/debian/patches/fix_gcc46_include_error
+++ /dev/null
@@ -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@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;

diff --git a/debian/patches/lecagy_rename_rpsblast b/debian/patches/lecagy_rename_rpsblast
deleted file mode 100644 (file)
index c2ff066..0000000
--- a/debian/patches/lecagy_rename_rpsblast
+++ /dev/null
@@ -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();
- 

diff --git a/debian/patches/legacy_rename_rpsblast b/debian/patches/legacy_rename_rpsblast
new file mode 100644 (file)
index 0000000..c2ff066
--- /dev/null
+++ b/debian/patches/legacy_rename_rpsblast
@@ -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();
+ 

diff --git a/debian/patches/series b/debian/patches/series
index d9fc96d2e72a9a37181234cf64c02076a5e09ac5..81229f6f4cdcf912039d58ce0939cedf938514aa 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-lecagy_rename_rpsblast
+legacy_rename_rpsblast
 fix_checks
-fix_gcc46_include_error
+fix_gcc46_errors

diff --git a/debian/rules b/debian/rules
index d608415b7c1219e80e177212a0e7b73699002396..e1ba35bb7c1c00572300da0f7d4fac22d01d0c8a 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -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 @@ else
 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 @@ override_dh_clean:
        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