[med-svn] r10968 - in trunk/packages/sift/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed May 23 15:08:59 UTC 2012
Author: lkajan-guest
Date: 2012-05-23 15:08:59 +0000 (Wed, 23 May 2012)
New Revision: 10968
Added:
trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings
trunk/packages/sift/trunk/debian/patches/ld-as-needed
Modified:
trunk/packages/sift/trunk/debian/patches/series
trunk/packages/sift/trunk/debian/rules
Log:
added patches from Michael Bienia <geser at ubuntu.com> - to be reviewed
Added: trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings
===================================================================
--- trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings (rev 0)
+++ trunk/packages/sift/trunk/debian/patches/fix_gcc_warnings 2012-05-23 15:08:59 UTC (rev 10968)
@@ -0,0 +1,96 @@
+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
+@@ -766,7 +766,7 @@
+ void
+ read_psiblast_header_until_first_alignment (FILE* fp)
+ {
+- char line[LARGE_BUFF_LENGTH];
++ char line[LINE_LEN];
+
+ 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 )
+ {
+- char line[MAXLEN];
++ char line[LINE_LEN];
+
+ while (!feof (fp) && fgets (line, LINE_LEN, fp) != NULL &&
+ strstr (line, "Sequences producing significant alignments") == NULL)
+@@ -1694,7 +1694,7 @@
+ assert (fp != NULL);
+ 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");
+ 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
+@@ -2184,7 +2184,7 @@
+ else
+ {
+ fprintf (stderr, "Can't open file '%s': %s.\n", qijname, strerror(errno) );
+- fprintf (stderr, "Current dir:\n", qijname );
++ fprintf (stderr, "Current dir: %s\n", qijname );
+ 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
+@@ -77,14 +77,14 @@
+
+ buff = strstr(Buffer, "Score=");
+ if (buff != NULL) {
+- sscanf (buff, "Score = %d", alignment->score);
++ sscanf (buff, "Score = %d", &alignment->score);
+ } else {
+ fprintf (errorfp, "Unable to read Score, parsing incorrect");
+ exit (-1);
+ }
+ buff = strstr (Buffer, "Expect = ");
+ if (buff != NULL) {
+- sscanf (buff, "Expect = %lf", alignment->evalue);
++ sscanf (buff, "Expect = %lf", &alignment->evalue);
+ } else {
+ fprintf (errorfp, "Unable to read e-value, parsing incorrect");
+ exit (-1);
+@@ -274,7 +274,7 @@
+ FILE* psiblastfp;
+ char name[KEY_WIDTH];
+ char *strptr;
+- char line[LARGE_BUFF_LENGTH];
++ char line[LINE_LEN];
+
+
+ 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
+@@ -137,7 +137,7 @@
+ char queryfilename[LARGE_BUFF_LENGTH];
+
+ if (argc < 4) {
+- printf ("clump.c : Clusters sequences into % clus");
++ printf ("clump.c : Clusters sequences into %% clus");
+ }
+
+ if (argc > 1 ) strcpy (seqfilename, argv[1]);
Added: trunk/packages/sift/trunk/debian/patches/ld-as-needed
===================================================================
--- trunk/packages/sift/trunk/debian/patches/ld-as-needed (rev 0)
+++ trunk/packages/sift/trunk/debian/patches/ld-as-needed 2012-05-23 15:08:59 UTC (rev 10968)
@@ -0,0 +1,24 @@
+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 @@
+ 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)\"
++LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) -L$(lib-prefix)/lib
++LIBS := -lblimps -lm
+
+ all: bin
+
+ bin: $(BIN)
+
++$(BIN): %: %.o
++ $(CC) $(LDFLAGS) -o $@ $< $(LIBS)
++
+ clean:
+ rm -f *.o $(BIN)
+
Modified: trunk/packages/sift/trunk/debian/patches/series
===================================================================
--- trunk/packages/sift/trunk/debian/patches/series 2012-05-23 14:37:06 UTC (rev 10967)
+++ trunk/packages/sift/trunk/debian/patches/series 2012-05-23 15:08:59 UTC (rev 10968)
@@ -1 +1,3 @@
fix_perl_interpreter_and_lib_path
+ld-as-needed
+fix_gcc_warnings
Modified: trunk/packages/sift/trunk/debian/rules
===================================================================
--- trunk/packages/sift/trunk/debian/rules 2012-05-23 14:37:06 UTC (rev 10967)
+++ trunk/packages/sift/trunk/debian/rules 2012-05-23 15:08:59 UTC (rev 10968)
@@ -27,6 +27,15 @@
override_dh_auto_clean:
if [ -e src/Makefile ]; then make -j$(parallel) -C src prefix=$(prefix) distclean; fi
rm -f $(MAN1)
+ # remove pre-compiled binaries from bin - thanks to Michael Bienia <geser at ubuntu.com>
+ rm -f bin/choose_seqs_via_psiblastseedmedian
+ rm -f bin/clump_output_alignedseq
+ rm -f bin/consensus_to_seq
+ rm -f bin/fastaseqs
+ rm -f bin/info_on_seqs
+ rm -f bin/process_alignment
+ rm -f bin/psiblast_res_to_fasta_dbpairwise
+ rm -f bin/seqs_from_psiblast_res
override_dh_auto_build: man
make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \
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