[med-svn] r18277 - trunk/packages/hhsuite/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Mon Oct 13 13:00:23 UTC 2014
Author: tille
Date: 2014-10-13 13:00:22 +0000 (Mon, 13 Oct 2014)
New Revision: 18277
Modified:
trunk/packages/hhsuite/trunk/debian/patches/Makefile
trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch
trunk/packages/hhsuite/trunk/debian/patches/help
trunk/packages/hhsuite/trunk/debian/patches/paths
trunk/packages/hhsuite/trunk/debian/patches/rest1
trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz
trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning
Log:
Refreshed quilt patches
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2014-10-13 13:00:22 UTC (rev 18277)
@@ -14,7 +14,7 @@
# Guess wether to use lib or lib64
#libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-@@ -8,19 +8,17 @@
+@@ -8,19 +8,17 @@ libdir=lib
# Overriding this is currently not fully supported as the code won't know
# to what this is set then. You can try setting HHLIB.
@@ -40,7 +40,7 @@
$(MAKE) -C src all
doc:
-@@ -40,35 +38,34 @@
+@@ -40,35 +38,34 @@ ffindex_static:
$(MAKE) -C lib/ffindex FFINDEX_STATIC=1
install:
@@ -104,7 +104,7 @@
deinstall:
$(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR)
-@@ -89,9 +86,11 @@
+@@ -89,9 +86,11 @@ deinstall:
.PHONY: clean
clean:
Modified: trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/add_Makefile_in_data.patch 2014-10-13 13:00:22 UTC (rev 18277)
@@ -1,7 +1,5 @@
-Index: hhsuite-2.0.16/data/Makefile
-===================================================================
--- /dev/null
-+++ hhsuite-2.0.16/data/Makefile
++++ b/data/Makefile
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
Modified: trunk/packages/hhsuite/trunk/debian/patches/help
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/help 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/help 2014-10-13 13:00:22 UTC (rev 18277)
@@ -4,7 +4,7 @@
Author: Laszlo Kajan <lkajan at rostlab.org>
--- a/src/hhblits.C
+++ b/src/hhblits.C
-@@ -411,7 +411,12 @@
+@@ -411,7 +411,12 @@ void help(char all=0)
printf("An extended list of options can be obtained by calling 'hhblits -help'\n");
}
printf("\n");
Modified: trunk/packages/hhsuite/trunk/debian/patches/paths
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/paths 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/paths 2014-10-13 13:00:22 UTC (rev 18277)
@@ -4,7 +4,7 @@
Author: Laszlo Kajan <lkajan at rostlab.org>
--- a/scripts/HHPaths.pm
+++ b/scripts/HHPaths.pm
-@@ -31,6 +31,7 @@
+@@ -31,6 +31,7 @@ use Exporter;
our $VERSION = "version 2.0.16 (January 2013)";
our @ISA = qw(Exporter);
our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v);
@@ -12,7 +12,7 @@
##############################################################################################
# PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED)
-@@ -54,11 +55,13 @@
+@@ -54,11 +55,13 @@ our $dssp = "/cluster/databases/dssp
# The lines below probably do not need to be changed
# Setting paths for hh-suite perl scripts
@@ -32,7 +32,7 @@
our $cs_lib = "$hhdata/cs219.lib";
--- a/src/hhdecl.C
+++ b/src/hhdecl.C
-@@ -285,7 +285,7 @@
+@@ -285,7 +285,7 @@ void Parameters::SetDefaultPaths(char *p
if(getenv("HHLIB"))
strcpy(hhlib, getenv("HHLIB"));
else
@@ -41,7 +41,7 @@
strcat(strcpy(hhdata, hhlib), "/data");
strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
-@@ -300,7 +300,7 @@
+@@ -300,7 +300,7 @@ void Parameters::SetDefaultPaths(char *p
/* we did not find HHLIB, if called with full path or in dist dir, we can try relative to program path */
if(program_path != NULL)
{
Modified: trunk/packages/hhsuite/trunk/debian/patches/rest1
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/rest1 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/rest1 2014-10-13 13:00:22 UTC (rev 18277)
@@ -2,11 +2,9 @@
* 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>
-Index: hhsuite-2.0.16/src/Makefile
-===================================================================
---- hhsuite-2.0.16.orig/src/Makefile
-+++ hhsuite-2.0.16/src/Makefile
-@@ -14,13 +14,13 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -14,13 +14,13 @@ endif
ifdef ICC
CXX = env LANG=C icc
@@ -22,7 +20,7 @@
HHSEARCH_LIBS = -lpthread
HHBLITS_LIBS = -lpthread -fopenmp
HHALIGN_LIBS =
-@@ -51,7 +51,7 @@
+@@ -51,7 +51,7 @@ else # ifndef ICC
endif
endif # ifndef ICC
@@ -31,7 +29,7 @@
CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)
-@@ -92,7 +92,7 @@
+@@ -92,7 +92,7 @@ hhsearch_valgrind: hhsearch.C $(SOURCES)
$(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
Modified: trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/unnecessary_libz 2014-10-13 13:00:22 UTC (rev 18277)
@@ -3,7 +3,7 @@
Author: Laszlo Kajan <lkajan at rostlab.org>
--- a/src/Makefile
+++ b/src/Makefile
-@@ -46,7 +46,7 @@
+@@ -46,7 +46,7 @@ else # ifndef ICC
HHSEARCH_LIBS = -lpthread -lrt
HHBLITS_LIBS+=-lrt
ifndef NO_PNG
Modified: trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning 2014-10-13 12:55:59 UTC (rev 18276)
+++ trunk/packages/hhsuite/trunk/debian/patches/unused_variables_warning 2014-10-13 13:00:22 UTC (rev 18277)
@@ -3,7 +3,7 @@
Author: Laszlo Kajan <lkajan at rostlab.org>
--- a/src/pngwriter.cc
+++ b/src/pngwriter.cc
-@@ -3343,13 +3343,13 @@
+@@ -3343,13 +3343,13 @@ void pngwriter::scale_wh(int finalwidth,
{
std::cerr << " PNGwriter::scale_wh - ERROR **: Negative or zero final width or height not allowed." << std::endl;
}
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