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 <[email protected]>. + + -- Laszlo Kajan <[email protected]> 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 <[email protected]> +--- 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 <[email protected]> +Author: Laszlo Kajan <[email protected]> +--- 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
