[med-svn] r14238 - in trunk/packages/hhsuite/trunk/debian: . patches

Steffen Möller moeller at alioth.debian.org
Thu Jul 25 14:11:24 UTC 2013 

Author: moeller
Date: 2013-07-25 14:11:24 +0000 (Thu, 25 Jul 2013)
New Revision: 14238

Added:
   trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base
   trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs
   trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch
Removed:
   trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base
   trunk/packages/hhsuite/trunk/debian/patches/hardening
Modified:
   trunk/packages/hhsuite/trunk/debian/changelog
   trunk/packages/hhsuite/trunk/debian/control
   trunk/packages/hhsuite/trunk/debian/hhsuite-data.install
   trunk/packages/hhsuite/trunk/debian/hhsuite-data.links
   trunk/packages/hhsuite/trunk/debian/hhsuite.docs
   trunk/packages/hhsuite/trunk/debian/hhsuite.install
   trunk/packages/hhsuite/trunk/debian/hhsuite.links
   trunk/packages/hhsuite/trunk/debian/patches/rest1
   trunk/packages/hhsuite/trunk/debian/patches/series
Log:
Merged own attempt to package hhsuite 2.0.16 with
the one of Laszlo ... sorry, I did not look right.

A noticable change may be the scripts directory,
which moved from the hhuite-data directory
hhsuite itself. Laslo - is that fine with you?
Also, a new hhsuite-doc package now separates the
user guide from the binaries.



Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/changelog	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,13 +1,20 @@
 hhsuite (2.0.16-2) UNRELEASED; urgency=low
 
-  * NOT RELEASED YET
+  [Steffen Moeller]
+  * Bumped standard to 3.9.4.
+  * Removed DMUA flag.
+  * Created new -doc package and moved user guide to it
+  * Moved scripts directory from hhsuite-data to hhsuite
+  * Added CHANGES file to .docs
+  * joined hardening patch with rest1
 
- -- Laszlo Kajan <lkajan at rostlab.org>  Tue, 28 May 2013 10:01:03 +0200
+ -- Steffen Moeller <moeller at debian.org>  Thu, 25 Jul 2013 16:05:49 +0200
 
 hhsuite (2.0.16-1) unstable; urgency=low
 
+  [Laszlo Kajan]
   * New upstream release.
-  * Updated d/watch file.
+  * Updated debian/watch file.
 
  -- Laszlo Kajan <lkajan at rostlab.org>  Mon, 24 Sep 2012 09:32:14 +0200
 

Modified: trunk/packages/hhsuite/trunk/debian/control
===================================================================
--- trunk/packages/hhsuite/trunk/debian/control	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/control	2013-07-25 14:11:24 UTC (rev 14238)
@@ -4,11 +4,10 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>
 Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Homepage: http://toolkit.genzentrum.lmu.de/sections/search
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
-DM-Upload-Allowed: yes
 
 Package: hhsuite
 Architecture: amd64
@@ -33,6 +32,13 @@
  HHblits is faster, up to twice as sensitive and produces more accurate
  alignments.
 
+Package: hhsuite-doc
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: hhsuite
+Description: documentation for HHsuite for HMM-HMM comparisons
+ This package provides a PDF with the user guide for the HH-suite.
+
 Package: hhsuite-data
 Architecture: all
 Depends: ${misc:Depends}

Modified: trunk/packages/hhsuite/trunk/debian/hhsuite-data.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-data.install	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.install	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,2 +1 @@
 usr/share/hhsuite/data
-usr/share/hhsuite/scripts

Modified: trunk/packages/hhsuite/trunk/debian/hhsuite-data.links
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-data.links	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.links	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,3 +1,2 @@
-usr/share/hhsuite/scripts usr/lib/hhsuite/scripts
 usr/share/hhsuite/data/context_data.lib usr/lib/hhsuite/data/context_data.lib
 usr/share/hhsuite/data/cs219.lib usr/lib/hhsuite/data/cs219.lib

Copied: trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base (from rev 13047, trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base)
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base	2013-07-25 14:11:24 UTC (rev 14238)
@@ -0,0 +1,8 @@
+Document: hhsuite
+Title: HH-suite User Guide
+Author: Johannes Söding, Michael Remmert, Andreas Hauser
+Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz

Added: trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-doc.docs	2013-07-25 14:11:24 UTC (rev 14238)
@@ -0,0 +1 @@
+hhsuite-userguide.pdf

Deleted: trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.doc-base	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,8 +0,0 @@
-Document: hhsuite
-Title: HH-suite User Guide
-Author: Johannes Söding, Michael Remmert, Andreas Hauser
-Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment.
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz

Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.docs	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.docs	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,2 +1,2 @@
-hhsuite-userguide.pdf
 README
+CHANGES

Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.install	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.install	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,3 +1,4 @@
 usr/bin/hh*
 usr/lib/hhsuite/bin
 usr/lib/hhsuite/data
+usr/share/hhsuite/scripts

Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.links
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.links	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.links	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1 +1,2 @@
-/usr/lib/hhsuite usr/lib/hh
+usr/share/hhsuite/scripts usr/lib/hhsuite/scripts
+usr/lib/hhsuite usr/lib/hh

Added: trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch	2013-07-25 14:11:24 UTC (rev 14238)
@@ -0,0 +1,16 @@
+Index: hhsuite-2.0.16/data/Makefile
+===================================================================
+--- /dev/null
++++ hhsuite-2.0.16/data/Makefile
+@@ -0,0 +1,11 @@
++#!/usr/bin/make -f
++
++DUMMYDB:=do_not_delete.phr do_not_delete.pin do_not_delete.psq
++
++all: $(DUMMYDB)
++
++%.phr %.pin %.psq : %
++	formatdb -i '$<' && rm -f formatdb.log
++
++clean:
++	rm -f $(DUMMYDB) formatdb.log

Deleted: trunk/packages/hhsuite/trunk/debian/patches/hardening
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/hardening	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/patches/hardening	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,22 +0,0 @@
-Description: Hardening patch.
-Author: Laszlo Kajan <lkajan at rostlab.org>
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -20,7 +20,7 @@
-   OBJECT_LIBS = -openmp
- else # ifndef ICC
-   CXX = g++
--  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp
-+  CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp
-   HHSEARCH_LIBS = -lpthread
-   HHBLITS_LIBS = -lpthread -fopenmp
-   HHALIGN_LIBS = 
-@@ -51,7 +51,7 @@
-   endif
- endif # ifndef ICC
- 
--CPP = $(CXX) $(CXXFLAGS)
-+CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)
- CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)
- 
- 

Modified: trunk/packages/hhsuite/trunk/debian/patches/rest1
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/rest1	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/patches/rest1	2013-07-25 14:11:24 UTC (rev 14238)
@@ -1,24 +1,36 @@
 Description: Assorted patches
+  * Set paths to hhsuite components for Perl scripts.
   * Add a Makefile to generate data/do_not_delete.phr,do_not_delete.pin,do_not_delete.psq .
 Author: Laszlo Kajan <lkajan at rostlab.org>
---- a/src/Makefile
-+++ b/src/Makefile
+Index: hhsuite-2.0.16/src/Makefile
+===================================================================
+--- hhsuite-2.0.16.orig/src/Makefile
++++ hhsuite-2.0.16/src/Makefile
 @@ -14,13 +14,13 @@
  
  ifdef ICC
    CXX = env LANG=C icc
 -  CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) -I$(FFINDEX_DIR)
-+  CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR)
++  CXXFLAGS += -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR)
    HHSEARCH_LIBS = -lpthread -lrt
    HHBLITS_LIBS = -lpthread -lrt -openmp
    OBJECT_LIBS = -openmp
  else # ifndef ICC
    CXX = g++
 -  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR) -fopenmp
-+  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp
++  CXXFLAGS += -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -fopenmp
    HHSEARCH_LIBS = -lpthread
    HHBLITS_LIBS = -lpthread -fopenmp
    HHALIGN_LIBS = 
+@@ -51,7 +51,7 @@
+   endif
+ endif # ifndef ICC
+ 
+-CPP = $(CXX) $(CXXFLAGS)
++CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)
+ CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)
+ 
+ 
 @@ -92,7 +92,7 @@
  	  $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
  
@@ -28,17 +40,3 @@
  
  hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
  	 $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
---- /dev/null
-+++ b/data/Makefile
-@@ -0,0 +1,11 @@
-+#!/usr/bin/make -f
-+
-+DUMMYDB:=do_not_delete.phr do_not_delete.pin do_not_delete.psq
-+
-+all: $(DUMMYDB)
-+
-+%.phr %.pin %.psq : %
-+	formatdb -i '$<' && rm -f formatdb.log
-+
-+clean:
-+	rm -f $(DUMMYDB) formatdb.log

Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series	2013-07-25 14:10:10 UTC (rev 14237)
+++ trunk/packages/hhsuite/trunk/debian/patches/series	2013-07-25 14:11:24 UTC (rev 14238)
@@ -3,8 +3,8 @@
 help
 rest1
 perlscript_uselib
-hardening
 unused_variables_warning
 unnecessary_libz
 perl_interpreter
 version_bump
+add_Makefile_in_data.patch

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