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Diffstat (limited to 'sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch')
-rw-r--r--sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch302
1 files changed, 0 insertions, 302 deletions
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
deleted file mode 100644
index 42af0c7e849..00000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
+++ /dev/null
@@ -1,302 +0,0 @@
-diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
-index 5889e7d..bc95629 100644
---- a/src/HMMer2/sqio.c
-+++ b/src/HMMer2/sqio.c
-@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
- }
- }
-
--/* Function: getline()
-+/* Function: get_line()
- * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
- *
- * Purpose: read a line from a sequence file into V->sbuffer.
-@@ -229,7 +229,7 @@ readline(FILE *f, char *s)
- * Returns: (void)
- */
- static void
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
- char *cp;
-
-@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
- V->seqlen = 0;
- if (addfirst) addseq(V->sbuffer, V);
- do {
-- getline(V);
-+ get_line(V);
- /* feof() alone is a bug; files not necessarily \n terminated */
- if (*(V->sbuffer) == '\0' && feof(V->f))
- done = TRUE;
-@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V)
- 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)
-@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V)
- 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)
-@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V)
- 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);
-
-@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
- /* get next line
- */
- while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V)
- char *nm;
- /* position past ';' comments */
- do {
-- getline(V);
-+ get_line(V);
- } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
-
- if (!feof(V->f))
-@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
- }
-
- while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
-- getline(V);
-+ get_line(V);
- }
-
- static int
-@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V)
- if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- }
-- getline(V);
-+ get_line(V);
- }
-
- if (! feof(V->f))
-@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
- /* load next line
- */
- while ((!feof(V->f)) && (*V->sbuffer != ';'))
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V)
- int in_definition;
-
- while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
-- getline(V);
-+ get_line(V);
-
- if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
- {
-@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V)
- 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)
-@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V)
-
-
- 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
-@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
- 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) {
-@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V)
- else readLoop(0, endGCGdata, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ get_line(V);
- }
-
- static int
-@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
- if ((sptr = strtok(NULL, "\n")) != NULL)
- SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
- /* workaround for long NCBI NR lines */
-- while (V->longline && ! feof(V->f)) getline(V);
-+ while (V->longline && ! feof(V->f)) get_line(V);
-
- readLoop(0, endPearson, V);
-
- while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V)
-
- /* 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)
- {
-@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V)
- }
-
- 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)
-@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V)
-
- /* load next record's ID line */
- while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V)
- {
- 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);
-@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
- readLoop(0, endZuker, V);
-
- while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
-- getline(V);
-+ get_line(V);
- }
-
- static void
-@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
-
- do {
- done = feof(V->f);
-- getline(V);
-+ get_line(V);
- if (! done) addseq(V->sbuffer, V);
- } while (!done);
- }
-@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V)
- 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);
-@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V)
- /*CONSTCOND*/
- while (1)
- {
-- getline(V);
-+ get_line(V);
- if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
-
- if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V)
- 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);
- }
-@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
-
-
- while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
-- getline(V);
-+ get_line(V);
- }
-
-
-@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
-
- /* Load the first line.
- */
-- getline(dbfp);
-+ get_line(dbfp);
-
- return dbfp;
- }
-@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
- Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
-
- fseek(sqfp->f, offset, SEEK_SET);
-- getline(sqfp);
-+ get_line(sqfp);
- }
-
-
-@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
- if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
- else {
- rewind(sqfp->f);
-- getline(sqfp);
-+ get_line(sqfp);
- }
- }
-
-@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
- 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;
-