From: Aaron M. Ucko Date: Sun, 29 May 2011 15:42:19 +0000 (+0000) Subject: Formal cosmetic cleanups. X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~342 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=2b8ecea6be77e26ad52a47db602767a62ef80409;p=ncbi-blast%2B.git 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 7dccdf5a..954fb1df 100644 --- 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 index 00000000..a28de4ea --- /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 +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 ++#include + + + // (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 index a28de4ea..00000000 --- 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 -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 -+#include - - - // (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 index c2ff0664..00000000 --- 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 index 00000000..c2ff0664 --- /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+"; + } + $retval .= &add_exe_extension(); + diff --git a/debian/patches/series b/debian/patches/series index d9fc96d2..81229f6f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,3 @@ -lecagy_rename_rpsblast +legacy_rename_rpsblast fix_checks -fix_gcc46_include_error +fix_gcc46_errors diff --git a/debian/rules b/debian/rules index d608415b..e1ba35bb 100755 --- a/debian/rules +++ b/debian/rules @@ -1,15 +1,9 @@ #!/usr/bin/make -f # -*- makefile -*- -# Sample debian/rules that uses debhelper. -# This file was originally written by Joey Hess and Craig Small. -# As a special exception, when this file is copied by dh-make into a -# dh-make output file, you may use that output file without restriction. -# This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 -SOURCEDIR=${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