[med-svn] r10972 - in trunk/packages/sift/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed May 23 19:21:33 UTC 2012
Author: lkajan-guest
Date: 2012-05-23 19:21:33 +0000 (Wed, 23 May 2012)
New Revision: 10972
Modified:
trunk/packages/sift/trunk/debian/changelog
trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings
trunk/packages/sift/trunk/debian/patches/ld-as-needed
Log:
added patches from Michael Bienia - reviewed
Modified: trunk/packages/sift/trunk/debian/changelog
===================================================================
--- trunk/packages/sift/trunk/debian/changelog 2012-05-23 17:14:45 UTC (rev 10971)
+++ trunk/packages/sift/trunk/debian/changelog 2012-05-23 19:21:33 UTC (rev 10972)
@@ -1,3 +1,9 @@
+sift (4.0.3b-3) unstable; urgency=low
+
+ * Added patches from Michael Bienia <geser at ubuntu.com>.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 23 May 2012 18:46:18 +0200
+
sift (4.0.3b-2) unstable; urgency=low
* Missing dependency blimps-utils added.
Modified: trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings 2012-05-23 17:14:45 UTC (rev 10971)
+++ trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings 2012-05-23 19:21:33 UTC (rev 10972)
@@ -1,25 +1,16 @@
-Index: sift-4.0.3b/src/Alignment.c
-===================================================================
---- sift-4.0.3b.orig/src/Alignment.c 2012-05-17 11:54:41.000000000 +0200
-+++ sift-4.0.3b/src/Alignment.c 2012-05-17 13:05:29.000000000 +0200
+Description: Fix gcc warnings.
+Author: Michael Bienia <geser at ubuntu.com>
+--- a/src/Alignment.c
++++ b/src/Alignment.c
@@ -766,7 +766,7 @@
void
read_psiblast_header_until_first_alignment (FILE* fp)
{
- char line[LARGE_BUFF_LENGTH];
-+ char line[LINE_LEN];
++ char line[LINE_LEN > LARGE_BUFF_LENGTH ? LINE_LEN : LARGE_BUFF_LENGTH];
read_psiblast_header_until_first (fp);
-@@ -775,7 +775,7 @@
- /* keep reading in lines */
- }
- fgets (line, LINE_LEN, fp); /* read in newline */
-- fgets (line,LARGE_BUFF_LENGTH, fp);
-+ fgets (line, LINE_LEN, fp);
- /*should be start of first alignment */
- } /* end of read_psiblast_header_until_first_alingment */
-
@@ -783,7 +783,7 @@
int
read_psiblast_header_until_first_no_error (FILE* fp,int return_error )
@@ -34,14 +25,12 @@
fgets (line, LARGE_BUFF_LENGTH, fp);
if (strstr (line, "Query") == NULL) {
- fprintf (stderr,"%s line should have Query:\n");
-+ fprintf (stderr,"line should have Query:\n");
++ fprintf (stderr,"'%s' line should have 'Query'\n", line);
exit (-1);
}
strptr = strtok (line, " \t\r\n"); /* this should be Query */
-Index: sift-4.0.3b/src/PN_convert.c
-===================================================================
---- sift-4.0.3b.orig/src/PN_convert.c 2012-05-17 11:54:41.000000000 +0200
-+++ sift-4.0.3b/src/PN_convert.c 2012-05-17 12:34:54.000000000 +0200
+--- a/src/PN_convert.c
++++ b/src/PN_convert.c
@@ -2184,7 +2184,7 @@
else
{
@@ -51,10 +40,8 @@
system( "pwd" );
exit (-1);
}
-Index: sift-4.0.3b/src/Psiblast.c
-===================================================================
---- sift-4.0.3b.orig/src/Psiblast.c 2012-05-17 11:54:41.000000000 +0200
-+++ sift-4.0.3b/src/Psiblast.c 2012-05-17 12:57:07.000000000 +0200
+--- a/src/Psiblast.c
++++ b/src/Psiblast.c
@@ -77,14 +77,14 @@
buff = strstr(Buffer, "Score=");
@@ -72,6 +59,15 @@
} else {
fprintf (errorfp, "Unable to read e-value, parsing incorrect");
exit (-1);
+@@ -95,7 +95,7 @@
+ fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get blank line */
+ fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get first line */;
+ get_start_pos = TRUE;
+- while (Buffer != "\n") {
++ while ( strcmp( Buffer, "\n" ) != 0 ) {
+ read_4_alignment_lines (Buffer, alignment, fp, get_start_pos);
+ get_start_pos = FALSE; /* read 1rst 4 alignment lines*/
+ /* already got the starting pos*/
@@ -274,7 +274,7 @@
FILE* psiblastfp;
char name[KEY_WIDTH];
@@ -81,10 +77,8 @@
if ((psiblastfp = fopen (psiblastres_file, "r")) == NULL)
-Index: sift-4.0.3b/src/clump_output_alignedseq.c
-===================================================================
---- sift-4.0.3b.orig/src/clump_output_alignedseq.c 2012-05-17 11:54:41.000000000 +0200
-+++ sift-4.0.3b/src/clump_output_alignedseq.c 2012-05-17 13:00:41.000000000 +0200
+--- a/src/clump_output_alignedseq.c
++++ b/src/clump_output_alignedseq.c
@@ -137,7 +137,7 @@
char queryfilename[LARGE_BUFF_LENGTH];
@@ -94,3 +88,14 @@
}
if (argc > 1 ) strcpy (seqfilename, argv[1]);
+--- a/src/Matrix_Info.c
++++ b/src/Matrix_Info.c
+@@ -467,7 +467,7 @@
+ case 2: /* +- phenotype is - */
+ if ( matrix->weights[aa_atob[c]][l] >= 0) {
+ pos_error_fp++; error_fp++;
+- printf ("incorrect less severe %d %d %c\n", l, matrix->weights[aa_atob[c]][l], c);
++ printf ("incorrect less severe %d %g %c\n", l, matrix->weights[aa_atob[c]][l], c);
+ print_type = print_incorrect;
+ } else if (matrix->weights[aa_atob[c]][l] < 0){
+ pos_notobserved_intolerant++;
Modified: trunk/packages/sift/trunk/debian/patches/ld-as-needed
===================================================================
--- trunk/packages/sift/trunk/debian/patches/ld-as-needed 2012-05-23 17:14:45 UTC (rev 10971)
+++ trunk/packages/sift/trunk/debian/patches/ld-as-needed 2012-05-23 19:21:33 UTC (rev 10972)
@@ -1,14 +1,22 @@
-Index: sift-4.0.3b/src/Makefile
-===================================================================
---- sift-4.0.3b.orig/src/Makefile 2012-05-17 11:54:41.000000000 +0200
-+++ sift-4.0.3b/src/Makefile 2012-05-17 12:22:59.000000000 +0200
-@@ -9,13 +9,17 @@
+Description: src/Makefile patch
+ [Michael Bienia]
+ As sift fails to link with ld --as-needed, I had to patch src/Makefile
+ to fix it. While at it I've also added support for dpkg-buildflags to
+ use in CFLAGS and LDFLAGS.
+ [Laszlo Kajan]
+ Added dpkg-buildflags to CPPFLAGS.
+Author: Michael Bienia <geser at ubuntu.com>
+Author: Laszlo Kajan <lkajan at rostlab.org>
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -9,13 +9,18 @@
seqs_from_psiblast_res
CC := gcc
-CFLAGS := -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\" $(CFLAGS)
-LDFLAGS := -L$(lib-prefix)/lib -lblimps $(LDFLAGS)
-+CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\"
++CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS := $(shell dpkg-buildflags --get CFLAGS) -Wno-unused-result -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\"
+LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib
+LIBS := -lblimps -lm
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