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 <[email protected]> - 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 $(MAN1) + # remove pre-compiled binaries from bin - thanks to Michael Bienia <[email protected]> + rm -f bin/choose_seqs_via_psiblastseedmedian + rm -f bin/clump_output_alignedseq + rm -f bin/consensus_to_seq + rm -f bin/fastaseqs + rm -f bin/info_on_seqs + rm -f bin/process_alignment + rm -f bin/psiblast_res_to_fasta_dbpairwise + rm -f bin/seqs_from_psiblast_res override_dh_auto_build: man make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
