sci-biology/wise: remove unused patch

Closes: https://github.com/gentoo/gentoo/pull/3708

diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
deleted file mode 100644 (file)
index 1ec433f..0000000
--- a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
+++ /dev/null
@@ -1,301 +0,0 @@
-diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
---- wise2.2.0.orig/src/HMMer2/sqio.c   2001-06-18 16:59:51.000000000 +0300
-+++ wise2.2.0/src/HMMer2/sqio.c        2009-08-05 22:39:04.000000000 +0300
-@@ -213,7 +213,7 @@
-     }
- }
- 
--/* 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 @@
-  * Returns:  (void)
-  */
- static void 
--getline(struct ReadSeqVars *V)
-+get_line(struct ReadSeqVars *V)
- {
-   char *cp;
-   
-@@ -299,7 +299,7 @@
-   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 @@
-   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 @@
-       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 @@
-         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 @@
-   /* get next line
-    */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -377,7 +377,7 @@
-   char *nm;
-                               /* position past ';' comments */
-   do {
--    getline(V);
-+    get_line(V);
-   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
- 
-   if (!feof(V->f))
-@@ -389,7 +389,7 @@
-     }
-   
-   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
--    getline(V);
-+    get_line(V);
- }
- 
- static int 
-@@ -411,7 +411,7 @@
-         if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
-           SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
-       }
--      getline(V);
-+      get_line(V);
-     }
- 
-   if (! feof(V->f))
-@@ -420,7 +420,7 @@
-   /* load next line
-    */
-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -438,7 +438,7 @@
-   int   in_definition;
- 
-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
-     {
-@@ -449,7 +449,7 @@
-   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)
-@@ -482,11 +482,11 @@
- 
- 
-   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
-@@ -515,7 +515,7 @@
-     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 @@
-   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 @@
-   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 @@
- 
-                               /* 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 @@
-     }
- 
-   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 @@
- 
-                               /* 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 @@
- {
-   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 @@
-   readLoop(0, endZuker, V);
- 
-   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
--    getline(V);
-+    get_line(V);
- }
- 
- static void 
-@@ -669,7 +669,7 @@
- 
-   do {
-     done = feof(V->f);
--    getline(V);
-+    get_line(V);
-     if (! done) addseq(V->sbuffer, V);
-   } while (!done);
- }
-@@ -681,7 +681,7 @@
-   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);
-@@ -689,7 +689,7 @@
-   /*CONSTCOND*/
-   while (1)
-     {
--      getline(V);
-+      get_line(V);
-       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
- 
-       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
-@@ -721,14 +721,14 @@
-   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);
-       }
-@@ -736,7 +736,7 @@
- 
- 
-   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -816,7 +816,7 @@
- 
-   /* Load the first line.
-    */
--  getline(dbfp);
-+  get_line(dbfp);
- 
-   return dbfp;
- }
-@@ -833,7 +833,7 @@
-     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 @@
-   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
-   else {
-     rewind(sqfp->f);
--    getline(sqfp);
-+    get_line(sqfp);
-   }
- }
- 
-@@ -949,7 +949,7 @@
-       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;
-