[med-svn] r9752 - trunk/packages/hhsuite/trunk/debian/patches

Laszlo Kajan lkajan-guest at alioth.debian.org
Wed Feb 22 13:27:26 UTC 2012 

Author: lkajan-guest
Date: 2012-02-22 13:27:26 +0000 (Wed, 22 Feb 2012)
New Revision: 9752

Modified:
   trunk/packages/hhsuite/trunk/debian/patches/Makefile
   trunk/packages/hhsuite/trunk/debian/patches/default_path
Log:
added back -lz to HHALIGN_LIBS

Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile	2012-02-22 11:53:20 UTC (rev 9751)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile	2012-02-22 13:27:26 UTC (rev 9752)
@@ -1,7 +1,7 @@
 Index: hhsuite-2.0.12/Makefile
 ===================================================================
 --- hhsuite-2.0.12.orig/Makefile	2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/Makefile	2012-02-22 10:19:29.386857448 +0100
++++ hhsuite-2.0.12/Makefile	2012-02-22 13:37:06.000000000 +0100
 @@ -1,5 +1,5 @@
  # This can be overridden e.g.: make install INSTALL_DIR=...
 -INSTALL_DIR?=$(PWD)
@@ -110,7 +110,7 @@
 Index: hhsuite-2.0.12/scripts/HHPaths.pm
 ===================================================================
 --- hhsuite-2.0.12.orig/scripts/HHPaths.pm	2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/scripts/HHPaths.pm	2012-02-22 10:09:29.891044474 +0100
++++ hhsuite-2.0.12/scripts/HHPaths.pm	2012-02-22 14:15:28.118982064 +0100
 @@ -38,7 +38,7 @@
  # The lines below probably do not need to be changed
  
@@ -123,7 +123,7 @@
 Index: hhsuite-2.0.12/src/hhdecl.C
 ===================================================================
 --- hhsuite-2.0.12.orig/src/hhdecl.C	2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/src/hhdecl.C	2012-02-22 10:24:33.614919605 +0100
++++ hhsuite-2.0.12/src/hhdecl.C	2012-02-22 13:37:06.000000000 +0100
 @@ -278,7 +278,7 @@
    if(getenv("HHLIB"))
      strcpy(hhlib, getenv("HHLIB"));
@@ -154,7 +154,7 @@
 Index: hhsuite-2.0.12/lib/ffindex/Makefile
 ===================================================================
 --- hhsuite-2.0.12.orig/lib/ffindex/Makefile	2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.12/lib/ffindex/Makefile	2012-02-22 10:09:29.907007650 +0100
++++ hhsuite-2.0.12/lib/ffindex/Makefile	2012-02-22 13:37:06.000000000 +0100
 @@ -7,13 +7,7 @@
  endif
  
@@ -175,7 +175,7 @@
 Index: hhsuite-2.0.12/lib/ffindex/src/Makefile
 ===================================================================
 --- hhsuite-2.0.12.orig/lib/ffindex/src/Makefile	2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/Makefile	2012-02-22 10:09:29.919044543 +0100
++++ hhsuite-2.0.12/lib/ffindex/src/Makefile	2012-02-22 13:37:06.000000000 +0100
 @@ -1,12 +1,14 @@
  INSTALL_DIR?=..
 -libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
@@ -241,16 +241,3 @@
  	rmdir $(INSTALL_DIR)/bin || true
  	rmdir $(INSTALL_DIR)/$(libdir) || true
  	rmdir $(INSTALL_DIR)/include || true
-Index: hhsuite-2.0.12/src/Makefile
-===================================================================
---- hhsuite-2.0.12.orig/src/Makefile	2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/src/Makefile	2012-02-22 10:24:47.806919585 +0100
-@@ -46,7 +46,7 @@
-   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

Modified: trunk/packages/hhsuite/trunk/debian/patches/default_path
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/default_path	2012-02-22 11:53:20 UTC (rev 9751)
+++ trunk/packages/hhsuite/trunk/debian/patches/default_path	2012-02-22 13:27:26 UTC (rev 9752)
@@ -1,7 +1,7 @@
 Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c
 ===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_build.c	2012-02-22 10:33:59.075044452 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c	2012-02-22 10:34:01.415044434 +0100
+--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_build.c	2012-02-22 14:15:27.966982036 +0100
++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c	2012-02-22 14:15:57.550982145 +0100
 @@ -31,7 +31,7 @@
  
  void usage(char *program_name)
@@ -22,8 +22,8 @@
  int main(int argn, char **argv)
 Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c
 ===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_get.c	2012-02-22 10:33:59.099044560 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c	2012-02-22 10:34:01.419044624 +0100
+--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_get.c	2012-02-22 14:15:27.990982045 +0100
++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c	2012-02-22 14:15:57.554982179 +0100
 @@ -26,9 +26,8 @@
  {
    if(argn < 3)
@@ -38,8 +38,8 @@
    char *data_filename  = argv[1];
 Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c
 ===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_modify.c	2012-02-22 10:33:59.131044487 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c	2012-02-22 10:34:01.431044580 +0100
+--- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_modify.c	2012-02-22 14:15:28.022982106 +0100
++++ hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c	2012-02-22 14:15:57.562982390 +0100
 @@ -30,7 +30,7 @@
  
  void usage(char *program_name)
@@ -60,8 +60,8 @@
  int main(int argn, char **argv)
 Index: hhsuite-2.0.12/src/hhblits.C
 ===================================================================
---- hhsuite-2.0.12.orig/src/hhblits.C	2012-02-22 10:33:59.155044512 +0100
-+++ hhsuite-2.0.12/src/hhblits.C	2012-02-22 10:34:01.443044553 +0100
+--- hhsuite-2.0.12.orig/src/hhblits.C	2012-02-22 14:15:28.046982074 +0100
++++ hhsuite-2.0.12/src/hhblits.C	2012-02-22 14:15:57.578982148 +0100
 @@ -295,8 +295,8 @@
    printf(" -M [0,100]     use FASTA: columns with fewer than X%% gaps are match states   \n");
    if (all) { 
@@ -89,8 +89,8 @@
  
 Index: hhsuite-2.0.12/src/hhsearch.C
 ===================================================================
---- hhsuite-2.0.12.orig/src/hhsearch.C	2012-02-22 10:33:59.178967644 +0100
-+++ hhsuite-2.0.12/src/hhsearch.C	2012-02-22 10:34:01.451044569 +0100
+--- hhsuite-2.0.12.orig/src/hhsearch.C	2012-02-22 14:15:28.066982015 +0100
++++ hhsuite-2.0.12/src/hhsearch.C	2012-02-22 14:15:57.586982154 +0100
 @@ -326,7 +326,7 @@
    printf(" -pcc  [0,3]    extinction exponent for tau(Neff)  (def=%-.1f)     \n",par.pcc);
    printf(" -pcw  [0,3]    weight of pos-specificity for pcs  (def=%-.1f)      \n",par.pcw);
@@ -102,8 +102,8 @@
  }
 Index: hhsuite-2.0.12/scripts/HHPaths.pm
 ===================================================================
---- hhsuite-2.0.12.orig/scripts/HHPaths.pm	2012-02-22 10:33:59.227044558 +0100
-+++ hhsuite-2.0.12/scripts/HHPaths.pm	2012-02-22 10:34:01.459044633 +0100
+--- hhsuite-2.0.12.orig/scripts/HHPaths.pm	2012-02-22 14:15:28.118982064 +0100
++++ hhsuite-2.0.12/scripts/HHPaths.pm	2012-02-22 14:15:57.590982410 +0100
 @@ -38,7 +38,7 @@
  # The lines below probably do not need to be changed
  
@@ -115,8 +115,8 @@
  our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
 Index: hhsuite-2.0.12/src/Makefile
 ===================================================================
---- hhsuite-2.0.12.orig/src/Makefile	2012-02-22 10:33:59.203044519 +0100
-+++ hhsuite-2.0.12/src/Makefile	2012-02-22 10:34:01.467044453 +0100
+--- hhsuite-2.0.12.orig/src/Makefile	2012-02-22 14:15:50.830982145 +0100
++++ hhsuite-2.0.12/src/Makefile	2012-02-22 14:15:57.602982363 +0100
 @@ -92,7 +92,7 @@
  	  $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
  
@@ -128,8 +128,8 @@
  	 $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
 Index: hhsuite-2.0.12/scripts/addss.pl
 ===================================================================
---- hhsuite-2.0.12.orig/scripts/addss.pl	2012-02-22 10:33:59.247044552 +0100
-+++ hhsuite-2.0.12/scripts/addss.pl	2012-02-22 10:34:01.471044421 +0100
+--- hhsuite-2.0.12.orig/scripts/addss.pl	2012-02-22 14:15:28.138982026 +0100
++++ hhsuite-2.0.12/scripts/addss.pl	2012-02-22 14:15:57.606982395 +0100
 @@ -28,7 +28,7 @@
  
  #     We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
@@ -141,8 +141,8 @@
  use File::Temp qw/ tempfile tempdir /;
 Index: hhsuite-2.0.12/scripts/hhblitsdb.pl
 ===================================================================
---- hhsuite-2.0.12.orig/scripts/hhblitsdb.pl	2012-02-22 10:33:59.271044501 +0100
-+++ hhsuite-2.0.12/scripts/hhblitsdb.pl	2012-02-22 10:34:01.479044570 +0100
+--- hhsuite-2.0.12.orig/scripts/hhblitsdb.pl	2012-02-22 14:15:28.162982056 +0100
++++ hhsuite-2.0.12/scripts/hhblitsdb.pl	2012-02-22 14:15:57.618982227 +0100
 @@ -28,7 +28,7 @@
  
  #     We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
@@ -154,8 +154,8 @@
  
 Index: hhsuite-2.0.12/scripts/hhmakemodel.pl
 ===================================================================
---- hhsuite-2.0.12.orig/scripts/hhmakemodel.pl	2012-02-22 10:33:59.299044594 +0100
-+++ hhsuite-2.0.12/scripts/hhmakemodel.pl	2012-02-22 10:34:01.487044455 +0100
+--- hhsuite-2.0.12.orig/scripts/hhmakemodel.pl	2012-02-22 14:15:28.190982103 +0100
++++ hhsuite-2.0.12/scripts/hhmakemodel.pl	2012-02-22 14:15:57.626982140 +0100
 @@ -28,7 +28,7 @@
  
  #     We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de

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