commit: dbe543ddfbdf83402b14e5ddea2969cbd486a0fa
Author: Michael Mair-Keimberger <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Mon Sep 18 13:16:24 2017 +0000
Commit: Patrice Clement <monsieurp <AT> gentoo <DOT> org>
CommitDate: Fri Oct 27 21:50:46 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dbe543dd
sci-biology/trnascan-se: remove unused patches.
.../files/trnascan-se-1.23-glibc-2.10.patch | 292 ---------------------
.../files/trnascan-se-1.23-ldflags.patch | 26 --
2 files changed, 318 deletions(-)
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
deleted file mode 100644
index e21da6e58db..00000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
+++ /dev/null
@@ -1,292 +0,0 @@
-diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c
---- trnascan-se-1.23.orig/sqio.c 2002-04-12 23:12:04.000000000 +0300
-+++ trnascan-se-1.23/sqio.c 2009-08-05 21:45:53.000000000 +0300
-@@ -235,7 +235,7 @@
- }
-
- static void
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
- readline(V->f, V->sbuffer);
- }
-@@ -306,7 +306,7 @@
- V->seqlen = 0;
- if (addfirst) addseq(V->sbuffer, V);
- do {
-- getline(V);
-+ get_line(V);
- done = feof(V->f);
- done |= (*endTest)(V->sbuffer, &addend);
- if (addend || !done)
-@@ -332,7 +332,7 @@
- char *sptr;
- /* load first line of entry */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
-- getline(V);
-+ get_line(V);
- if (feof(V->f)) return;
-
- if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
-@@ -341,7 +341,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
- }
- do {
-- getline(V);
-+ get_line(V);
- if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
- SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
- else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
-@@ -350,7 +350,7 @@
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
- }
- } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
-- getline(V); /* skip next line, coords */
-+ get_line(V); /* skip next line, coords */
-
- readLoop(0, endPIR, V);
-
-@@ -364,7 +364,7 @@
- /* get next line
- */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -382,7 +382,7 @@
- char *nm;
- /* position past ';' comments */
- do {
-- getline(V);
-+ get_line(V);
- } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
-
- if (!feof(V->f))
-@@ -394,7 +394,7 @@
- }
-
- while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
-- getline(V);
-+ get_line(V);
- }
-
- static int
-@@ -416,7 +416,7 @@
- if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- }
-- getline(V);
-+ get_line(V);
- }
-
- if (! feof(V->f))
-@@ -425,7 +425,7 @@
- /* load next line
- */
- while ((!feof(V->f)) && (*V->sbuffer != ';'))
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -443,7 +443,7 @@
- int in_definition;
-
- while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
-- getline(V);
-+ get_line(V);
-
- if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
- {
-@@ -454,7 +454,7 @@
- in_definition = FALSE;
- while (! feof(V->f))
- {
-- getline(V);
-+ get_line(V);
- if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
- {
- if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
-@@ -487,11 +487,11 @@
-
-
- while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") ==
V->sbuffer))))
-- getline(V);
-+ get_line(V);
- /* SRE: V->s now holds "//", so sequential
- reads are wedged: fixed Tue Jul 13 1993 */
- while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
-- getline(V);
-+ get_line(V);
- }
-
- static int
-@@ -521,12 +521,12 @@
- if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-
-- getline(V); /*skip title-junk line*/
-+ get_line(V); /*skip title-junk line*/
-
- readLoop(0, endNBRF, V);
-
- while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -559,7 +559,7 @@
- } else Die("bogus GCGdata format? %s", V->sbuffer);
-
- /* second line contains free text description */
-- getline(V);
-+ get_line(V);
- SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
-
- if (binary) {
-@@ -579,7 +579,7 @@
- else readLoop(0, endGCGdata, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ get_line(V);
- }
-
- static int
-@@ -625,7 +625,7 @@
- readLoop(0, endPearson, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -652,7 +652,7 @@
-
- /* make sure we have first line */
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
-- getline(V);
-+ get_line(V);
-
- if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
- {
-@@ -661,7 +661,7 @@
- }
-
- do {
-- getline(V);
-+ get_line(V);
- if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
- {
- if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
-@@ -685,7 +685,7 @@
-
- /* load next record's ID line */
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -701,7 +701,7 @@
- {
- char *sptr;
-
-- getline(V); /*s == "seqLen seqid string..."*/
-+ get_line(V); /*s == "seqLen seqid string..."*/
-
- if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -712,7 +712,7 @@
- readLoop(0, endZuker, V);
-
- while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
-- getline(V);
-+ get_line(V);
- }
-
- static void
-@@ -734,7 +734,7 @@
-
- do {
- done = feof(V->f);
-- getline(V);
-+ get_line(V);
- if (! done) addseq(V->sbuffer, V);
- } while (!done);
- }
-@@ -746,7 +746,7 @@
- char *sptr;
- int dostruc = FALSE;
-
-- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
-+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
-
- if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
-@@ -754,7 +754,7 @@
- /*CONSTCOND*/
- while (1)
- {
-- getline(V);
-+ get_line(V);
- if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
-
- if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -786,14 +786,14 @@
- while (1)
- {
- /* sequence line */
-- getline(V);
-+ get_line(V);
- if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
- break;
- addseq(V->sbuffer, V);
- /* structure line */
- if (dostruc)
- {
-- getline(V);
-+ get_line(V);
- if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
- addstruc(V->sbuffer, V);
- }
-@@ -801,7 +801,7 @@
-
-
- while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -848,7 +848,7 @@
-
- /* Load the first line.
- */
-- getline(dbfp);
-+ get_line(dbfp);
-
- return dbfp;
- }
-@@ -862,7 +862,7 @@
- SeqfilePosition(SQFILE *sqfp, long offset)
- {
- fseek(sqfp->f, offset, SEEK_SET);
-- getline(sqfp);
-+ get_line(sqfp);
- }
-
-
-@@ -954,7 +954,7 @@
- do { /* skip leading comments on GCG file */
- gotuw = (strstr(V->sbuffer,"..") != NULL);
- if (gotuw) readUWGCG(V);
-- getline(V);
-+ get_line(V);
- } while (! feof(V->f));
- break;
-
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
deleted file mode 100644
index 783e4340823..00000000000
--- a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 53e5c5b..a2d3feb 100644
---- a/Makefile
-+++ b/Makefile
-@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
- all: $(PROGS) tRNAscanSE setpaths
-
- covels-SE: $(OBJ) scan_main.o
-- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
-+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ)
$(LIBS)
-
- coves-SE: $(OBJ) score_main.o
-- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
-+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ)
$(LIBS)
-
- eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
-- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \
- pavesi.o $(SQUIDOBJ) $(LIBS)
-
- trnascan-1.4: trnascan.o
-- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
-+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4
trnascan.c
-
- tRNAscanSE:
- $(PERLDIR)/$(PERLBIN) checkversion.pl
