debian/changelog

-hhsuite (3.0~beta3+dfsg-2) UNRELEASED; urgency=medium
-
-  * Fix Vcs-Browser
-
- -- Andreas Tille <tille@debian.org>  Tue, 07 Aug 2018 08:11:35 +0200
-
 hhsuite (3.0~beta3+dfsg-1) unstable; urgency=medium
 
-  * Team upload.
-
+  [ Steffen Moeller ]
   * New upstream version.
   * debian/upstream/metadata:
     - yamllint cleanliness
@@ -18,7 +11,11 @@ hhsuite (3.0~beta3+dfsg-1) unstable; urgency=medium
   * Caveat: Does not compile with openmpi libraries discovered.
     See README.source.
 
- -- Steffen Moeller <moeller@debian.org>  Thu, 02 Aug 2018 17:42:28 +0200
+  [ Andreas Tille ]
+  * Fix Vcs-Browser
+  * Do not parse d/changelog to obtain version
+
+ -- Andreas Tille <tille@debian.org>  Tue, 21 Aug 2018 21:09:09 +0200
 
 hhsuite (3.0~beta2+dfsg-3) unstable; urgency=medium
 

debian/patches/Makefile

-Description: Patch to top level Makefile
-  * Make Makefile DESTDIR-aware.
-  * Fix install mode of data files.
-Forwarded: upstream is aware of these patches
- Upstream is Andreas Hauser <hauser@genzentrum.lmu.de>.
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/Makefile
-+++ b/Makefile
-@@ -1,5 +1,5 @@
--# This can be overridden e.g.: make install INSTALL_DIR=...
--INSTALL_DIR?=$(PWD)
-+# This can be overridden e.g.: make install PREFIX=...
-+PREFIX:=/usr
- 
- # Guess wether to use lib or lib64
- #libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-@@ -8,19 +8,17 @@ libdir=lib
- 
- # Overriding this is currently not fully supported as the code won't know
- # to what this is set then. You can try setting HHLIB.
--INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hh
--INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts
--INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data
-+INSTALL_LIB_DIR?=$(PREFIX)/$(libdir)/hhsuite
-+INSTALL_SCRIPTS_DIR?=$(PREFIX)/share/hhsuite/scripts
-+INSTALL_DATA_DIR?=$(PREFIX)/share/hhsuite/data
-+INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data
- INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
- 
- dist_name=hhsuite-2.0.16
- 
--.PHONY: all_static
--all_static: ffindex_static
--	$(MAKE) -C src all_static
--
- .PHONY: all
--all: ffindex
-+all:
-+	$(MAKE) -C data all
- 	$(MAKE) -C src all
- 
- doc:
-@@ -40,35 +38,34 @@ ffindex_static:
- 	$(MAKE) -C lib/ffindex FFINDEX_STATIC=1
- 	
- install:
--	$(MAKE) -C lib/ffindex install INSTALL_DIR=$(INSTALL_DIR)
--	mkdir -p $(INSTALL_DIR)/bin
--	install src/hhblits     $(INSTALL_DIR)/bin/hhblits
--	install src/hhalign     $(INSTALL_DIR)/bin/hhalign
--	install src/hhconsensus $(INSTALL_DIR)/bin/hhconsensus
--	install src/hhfilter    $(INSTALL_DIR)/bin/hhfilter
--	install src/hhmake      $(INSTALL_DIR)/bin/hhmake
--	install src/hhsearch    $(INSTALL_DIR)/bin/hhsearch
--	mkdir -p $(INSTALL_LIB_DIR)
--	mkdir -p $(INSTALL_LIB_BIN_DIR)
--	install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate
--	mkdir -p $(INSTALL_DATA_DIR)
--	install -m 0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib
--	install -m 0644 data/cs219.lib        $(INSTALL_DATA_DIR)/cs219.lib
--	install -m 0644 data/do_not_delete    $(INSTALL_DATA_DIR)/do_not_delete
--	install -m 0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr
--	install -m 0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin
--	install -m 0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq
--	mkdir -p $(INSTALL_SCRIPTS_DIR)
--	install -m 0644 scripts/Align.pm        $(INSTALL_SCRIPTS_DIR)/Align.pm
--	install -m 0644 scripts/HHPaths.pm      $(INSTALL_SCRIPTS_DIR)/HHPaths.pm
--	install scripts/addss.pl        $(INSTALL_SCRIPTS_DIR)/addss.pl
--	install scripts/create_profile_from_hhm.pl   $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
--	install scripts/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
--	install scripts/hhmakemodel.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
--	install scripts/reformat.pl    $(INSTALL_SCRIPTS_DIR)/reformat.pl
--	install scripts/splitfasta.pl    $(INSTALL_SCRIPTS_DIR)/splitfasta.pl
--	install scripts/multithread.pl    $(INSTALL_SCRIPTS_DIR)/multithread.pl
--	install scripts/hhblitsdb.pl    $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
-+	mkdir -p $(DESTDIR)$(PREFIX)/bin
-+	install src/hhblits     $(DESTDIR)$(PREFIX)/bin/hhblits
-+	install src/hhalign     $(DESTDIR)$(PREFIX)/bin/hhalign
-+	install src/hhconsensus $(DESTDIR)$(PREFIX)/bin/hhconsensus
-+	install src/hhfilter    $(DESTDIR)$(PREFIX)/bin/hhfilter
-+	install src/hhmake      $(DESTDIR)$(PREFIX)/bin/hhmake
-+	install src/hhsearch    $(DESTDIR)$(PREFIX)/bin/hhsearch
-+	mkdir -p $(DESTDIR)$(INSTALL_LIB_DIR)
-+	mkdir -p $(DESTDIR)$(INSTALL_LIB_BIN_DIR)
-+	install src/cstranslate $(DESTDIR)$(INSTALL_LIB_BIN_DIR)/cstranslate
-+	mkdir -p $(DESTDIR)$(INSTALL_DATA_DIR) $(DESTDIR)$(INSTALL_BDATA_DIR)
-+	install --mode=0644 data/context_data.lib $(DESTDIR)$(INSTALL_DATA_DIR)/context_data.lib
-+	install --mode=0644 data/cs219.lib        $(DESTDIR)$(INSTALL_DATA_DIR)/cs219.lib
-+	install --mode=0644 data/do_not_delete    $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete
-+	install --mode=0644 data/do_not_delete.phr $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.phr
-+	install --mode=0644 data/do_not_delete.pin $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.pin
-+	install --mode=0644 data/do_not_delete.psq $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.psq
-+	mkdir -p $(DESTDIR)$(INSTALL_SCRIPTS_DIR)
-+	install --mode=0644 scripts/Align.pm        $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/Align.pm
-+	install --mode=0644 scripts/HHPaths.pm      $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/HHPaths.pm
-+	install scripts/addss.pl        $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/addss.pl
-+	install scripts/create_profile_from_hhm.pl   $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
-+	install scripts/create_profile_from_hmmer.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
-+	install scripts/hhmakemodel.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
-+	install scripts/reformat.pl    $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/reformat.pl
-+	install scripts/splitfasta.pl  $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/splitfasta.pl
-+	install scripts/multithread.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl
-+	install scripts/hhblitsdb.pl   $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
- 
- deinstall:
- 	$(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR)
-@@ -89,9 +86,11 @@ deinstall:
- 
- .PHONY: clean
- clean:
--	cd lib/ffindex && $(MAKE) clean
- 	$(MAKE) -C src clean
- 
-+.PHONY: distclean
-+distclean: clean
-+
- dist/$(dist_name).tar.gz:
- 	make clean
- 	mkdir -p dist

debian/patches/gcc-6.1.patch

-Description: Use system provided log2 and log10 of gcc-6.1
-Bug-Debian: https://bugs.debian.org/831115
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
-
---- a/src/util.C
-+++ b/src/util.C
-@@ -55,8 +55,8 @@ inline int iround(double x) {return int(
- inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}
- 
- // log base 2
--inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}
--inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}
-+//inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}
-+//inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}
- 
- 
- /////////////////////////////////////////////////////////////////////////////////////

debian/patches/gcc-6.1_use_inline.patch

-Description: Rename redefined log2 to enable build using gcc-6.1
- Note: May be its just better to use the system provided log2
-  ---> While this patch works syntactically the system provided
-       log2 and log10 are really used since this patch is
-       deactivated but left for discussion as alternative to
-       gcc-6.1
-Bug-Debian: https://bugs.debian.org/831115
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
-
---- a/src/util.C
-+++ b/src/util.C
-@@ -55,7 +55,7 @@ inline int iround(double x) {return int(
- inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}
- 
- // log base 2
--inline float log2(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}
-+inline float log2_i(float x)  {return (x<=0? (float)(-100000):1.442695041*log(x));}
- inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}
- 
- 
-@@ -63,29 +63,29 @@ inline float log10(float x) {return (x<=
- // fast log base 2
- /////////////////////////////////////////////////////////////////////////////////////
- 
--// Fast log2 
-+// Fast log2_i
- // ATTENTION: need to compile with g++ -fno-strict-aliasing when using -O2 or -O3!!! 
- // Maximum deviation: +/- 2.1E-5
--// Run time: ~1.2E-8s on Intel core2 2.13GHz, log2(): 5.4E-8s
-+// Run time: ~1.2E-8s on Intel core2 2.13GHz, log2_i(): 5.4E-8s
- // For a negative argument, -128 is returned.
- // The function makes use of the representation of 4-byte floating point numbers:
- // seee eeee emmm mmmm mmmm mmmm mmmm mmmm
- // s is the sign, eee eee e gives the exponent + 127 (in hex: 0x7f).
- // The following 23 bits give the mantisse, the binary digits after the decimal 
- // point:  x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeeee-127)
--// Therefore,  log2(x) = eeeeeeee-127 + log2(1.mmmmmm...) 
--//                     = eeeeeeee-127 + log2(1+y),  where y = 0.mmmmmm... 
--//                     ~ eeeeeeee-127 + ((a*y+b)*y+c)*y 
-+// Therefore,  log2_i(x) = eeeeeeee-127 + log2_(1.mmmmmm...) 
-+//                       = eeeeeeee-127 + log2_(1+y),  where y = 0.mmmmmm... 
-+//                       ~ eeeeeeee-127 + ((a*y+b)*y+c)*y 
- // The coefficients a, b  were determined by a least squares fit, and c=1-a-b to get 1 at y=1.
- // Lower/higher order polynomials may be used for faster or more precise calculation:
--// Order 1: log2(1+y) ~ y                 
--// Order 2: log2(1+y) = (a*y + 1-a)*y, a=-0.3427                                           
-+// Order 1: log2_i(1+y) ~ y                 
-+// Order 2: log2_i(1+y) = (a*y + 1-a)*y, a=-0.3427                                           
- //  => max dev = +/- 8E-3, run time ~ ?
--// Order 3: log2(1+y) = ((a*y+b)*y + 1-a-b)*y, a=0.1564, b=-0.5773   
-+// Order 3: log2_i(1+y) = ((a*y+b)*y + 1-a-b)*y, a=0.1564, b=-0.5773   
- //  => max dev = +/- 1E-3, run time ~ ?
--// Order 4: log2(1+y) = (((a*y+b)*y+c)*y + 1-a-b-c)*y, a=-0.0803 b=0.3170 c=-0.6748 
-+// Order 4: log2_i(1+y) = (((a*y+b)*y+c)*y + 1-a-b-c)*y, a=-0.0803 b=0.3170 c=-0.6748 
- //  => max dev = +/- 1.4E-4, run time ~ ?
--// Order 5: log2(1+y) = ((((a*y+b)*y+c)*y+d)*y + 1-a-b-c-d)*y, 
-+// Order 5: log2_i(1+y) = ((((a*y+b)*y+c)*y+d)*y + 1-a-b-c-d)*y, 
- //     a=0.0440047 b=-0.1903190 c=0.4123442 d=-0.7077702 1-a-b-c-d=1.441740
- //  => max dev = +/- 2.1E-5, run time ~ 1.2E-8s
- inline float flog2(float x)
-@@ -155,7 +155,7 @@ __m128 _mm_flog2_ps(__m128 X)
-   R = _mm_add_ps(R, CONST32_D);           // R = ((a*X+b)*X+c)*X+d
-   R = _mm_mul_ps(R, X);                   // R = (((a*X+b)*X+c)*X+d)*X
-   R = _mm_add_ps(R, CONST32_E);           // R = (((a*X+b)*X+c)*X+d)*X+e
--  R = _mm_mul_ps(R, X);                   // R = ((((a*X+b)*X+c)*X+d)*X+e)*X ~ log2(1+X) !! 
-+  R = _mm_mul_ps(R, X);                   // R = ((((a*X+b)*X+c)*X+d)*X+e)*X ~ log2_i(1+X) !! 
-   R = _mm_add_ps(R, _mm_cvtepi32_ps(E));  // convert integer exponent to float and add to mantisse
-   return R;
- }
-@@ -172,7 +172,7 @@ __m128 _mm_flog2_ps(__m128 X)
- // In the code, *(int *)&x is an integer which contains the bytes as the 
- // floating point variable x is represented in memory. The expression 
- //     (((*(int *)&x) & 0x7f800000 ) >>23 )-0x7f is the exponent eeeeeeee, 
--// i.e., the largest integer that is smaller than log2(x) (e.g. -1 for 0.9).
-+// i.e., the largest integer that is smaller than log2_i(x) (e.g. -1 for 0.9).
- inline float fast_log2(float x)
- {
-   static float lg2[1025];         // lg2[i] = log2[1+x/1024]

debian/patches/help

-Description: fix paths in help pages
- Fix issues where the path in help pages is taken from the build-time location of the executables.
-Forwarded: not-needed
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/src/hhblits.C
-+++ b/src/hhblits.C
-@@ -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");
--  printf("Example: %s -i query.fas -oa3m query.a3m -n 1  \n",program_name);
-+  printf("Examples:\n");
-+  printf("%s -i query.fas -o query.hhr -d ./uniprot20\n",program_name);
-+  printf("\n");
-+  printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d ./uniprot20\n",program_name);
-+  printf("\n");
-+  printf("Download databases from <ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/databases/>.\n");
-   cout<<endl;
- }
- 
---- a/src/hhsearch.C
-+++ b/src/hhsearch.C
-@@ -48,6 +48,7 @@
- #include <float.h>    // FLT_MIN
- #include <ctype.h>    // islower, isdigit etc
- #include <time.h>     // clock_gettime etc. (in realtime library (-lrt compiler option))
-+#include <unistd.h>
- #include <errno.h>    // perror()
- #include <cassert>
- #include <stdexcept>

debian/patches/paths

-Description: Set hhsuite paths.
- Set paths to hhsuite components - as installed on Debian - correctly in absence of the (now superflouos) HHLIB environment variable.
-Forwarded: not-needed
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/scripts/HHPaths.pm
-+++ b/scripts/HHPaths.pm
-@@ -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 $v);
-+push @EXPORT, qw($hhshare $hhbdata);
- 
- ##############################################################################################
- # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) 
-@@ -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
--our $hhlib    = $ENV{"HHLIB"};     # main hh-suite directory
--our $hhdata   = $hhlib."/data";    # path to data directory for hhblits, example files
-+our $hhlib    = $ENV{"HHLIB"} || "/usr/lib/hhsuite";     # main hh-suite directory
-+our $hhshare  = $ENV{"HHLIB"} || "/usr/share/hhsuite";   # main hh-suite directory
-+our $hhdata   = $hhshare."/data";  # path to arch indep data directory for hhblits, example files
-+our $hhbdata  = $hhlib."/data";    # path to arch dep data directory for hhblits, example files
- our $hhbin    = $hhlib."/bin";     # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH)
--our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
--our $dummydb  = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
-+our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
-+our $dummydb  = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
- 
- # HHblits data files
- our $cs_lib = "$hhdata/cs219.lib";
---- a/src/hhdecl.C
-+++ b/src/hhdecl.C
-@@ -285,7 +285,7 @@ void Parameters::SetDefaultPaths(char *p
-   if(getenv("HHLIB"))
-     strcpy(hhlib, getenv("HHLIB"));
-   else
--    strcpy(hhlib, "/usr/lib/hh");
-+    strcpy(hhlib, "/usr/lib/hhsuite");
- 
-   strcat(strcpy(hhdata, hhlib), "/data");
-   strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
-@@ -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)
- 	{
--	  strcat(strcpy(hhlib, program_path), "../lib/hh");
-+	  strcat(strcpy(hhlib, program_path), "../lib/hhsuite");
- 	  strcat(strcpy(hhdata, hhlib), "/data");
- 	  strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
- 	  strcat(strcpy(cs_library, hhdata), "/cs219.lib");

debian/patches/rest1

-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@rostlab.org>
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -14,13 +14,13 @@ endif
- 
- 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$(CS_DIR)
-   HHSEARCH_LIBS = -lpthread -lrt
-   HHBLITS_LIBS = -lpthread -lrt -openmp
-   OBJECT_LIBS = -openmp
- else # ifndef ICC
-   CXX = g++
--  CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(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
-   HHSEARCH_LIBS = -lpthread
-   HHBLITS_LIBS = -lpthread -fopenmp
-   HHALIGN_LIBS = 
-@@ -51,7 +51,7 @@ else # ifndef ICC
-   endif
- endif # ifndef ICC
- 
--CPP = $(CXX) $(CXXFLAGS)
-+CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS)
- CPP_VALGRIND = $(CXX) -g $(CXXFLAGS)
- 
- 
-@@ -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)
--	 $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
-+	 $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex
- 
- hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
- 	 $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a

debian/patches/unnecessary_libz

-Description: remove unnecessary libz link
-Forwarded: yes
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -46,7 +46,7 @@ else # ifndef ICC
-     HHSEARCH_LIBS = -lpthread -lrt
-     HHBLITS_LIBS+=-lrt
-     ifndef NO_PNG
--      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng -lz
-+      HHALIGN_LIBS = -DNO_FREETYPE -DHH_PNG -lpng
-     endif
-   endif
- endif # ifndef ICC

debian/patches/unused_variables_warning

-Description: fix unused variables warning
-Forwarded: yes
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/src/pngwriter.cc
-+++ b/src/pngwriter.cc
-@@ -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;
-      }
--
-+/*
-    double kx;
-    double ky;
- 
-    kx = ((double)finalwidth)/((double)width_);
-    ky = ((double)finalheight)/((double)height_);
--
-+*/
-    pngwriter temp(finalwidth, finalheight, 0, "temp");
- 
-    int red, green, blue;

debian/patches/version_bump

-Description: fix version where it is not up to date
-Author: Laszlo Kajan <lkajan@rostlab.org>
---- a/src/hhdecl.C
-+++ b/src/hhdecl.C
-@@ -10,7 +10,7 @@
- //// Constants
- /////////////////////////////////////////////////////////////////////////////////////
- 
--EXTERN const char VERSION_AND_DATE[]="version 2.0.15 (June 2012)";
-+EXTERN const char VERSION_AND_DATE[]="version 2.0.16 (January 2013)";
- EXTERN const char REFERENCE[]="Remmert M, Biegert A, Hauser A, and Soding J.\nHHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.\nNat. Methods 9:173-175 (2011).\n";
- EXTERN const char COPYRIGHT[]="(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser\n";
- EXTERN const int MAXSEQ=65535; //max number of sequences in input alignment (must be <~30000 on cluster nodes??)

debian/rules

@@ -5,7 +5,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-VERSION=$(shell dpkg-parsechangelog -SVersion | cut -f1 -d+)
+include /usr/share/dpkg/default.mk
+
 TIMESTAMP=$(shell dpkg-parsechangelog -STimestamp)
 DATE=$(shell date --date=@$(TIMESTAMP) '+%d %B %Y')
 
@@ -25,7 +26,7 @@ override_dh_installman: $(HHMANPAGES)
 	dh_installman
 
 $(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
-	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
+	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(DEB_VERSION_UPSTREAM) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
 
 override_dh_auto_clean:
 	dh_auto_clean