gentoo resync : 29.10.2017

5 files changed, 0 insertions, 334 deletions

diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index d97ee24d63d1..7a0c8ba961b3 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -1,5 +1,4 @@
 AUX 3.1-Makefile.patch 1103 SHA256 de49b937edc714ba84ea2ae0900ea92b73c58048fafb8d616e8dfa44b548e927 SHA512 6e0daf4478b5b992ed1647bf653320b18cd2582ca69ebe761654bd4bd9c9c46b7de183ae84a28582cb5543603362eb7eb6c306ff562c3ec18c292d89480fd127 WHIRLPOOL 2d491dff1be16cf09413ff2f1087bc6888509a4db5dad56ec79422ed42e688855e1ff6f6d456257631b69ca3c185cba6143c1dcad353fef2b9af49ab9a2f5501
-AUX 3.1-fgets.patch 427 SHA256 a1f52692ad3593278718a8d2cc95d176e8bcd773305a6f6769a5c76106cd6423 SHA512 f6fbea6ff576482d394eeaa841db689d4f410ac29274f20713bfd6ad3ae4182dce1f7675be113a94d2b08dd3cc0c7a900bf23cfdd6a8d034622b8aa06194af90 WHIRLPOOL 01d246024996df3d78f0330b753d2457805c1561a8fa99a080400c0b34730db014d60e5147c6689aa489385bd313a7809b3b22c036cdd6ddd23cf326042cec1d
 AUX 3.1-path.patch 1128 SHA256 0b91a360760bd27f4ba43639d32e891d5576595451e1f7285632fc9ad38a80fa SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c WHIRLPOOL 33802ea504dea3445c8024b9c13eb351a009f13ee4b4a1d126392e5d807006d08dc0c582972eac2d13975d9acc9f6b5ccbf1bdc09115810abcc63dcae5e393cd
 AUX 3.2-fgets.patch 427 SHA256 95d68881c502c567025eb5e74fcd545bf012ded48ab2731aa70827f0ff449696 SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb WHIRLPOOL 92b0c8af14387db54eef5ea171ffd0c096658f6922729a6a1a1836eeb14b21b1feb3cd330dfb564eb3aaa8435d18b55f4559da96fb32f666f88349a1af3fb191
 DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34
diff --git a/sci-biology/psipred/files/3.1-fgets.patch b/sci-biology/psipred/files/3.1-fgets.patch
deleted file mode 100644
index e58d677258e0..000000000000
--- a/sci-biology/psipred/files/3.1-fgets.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
-index 4d8e5ff..0d82483 100644
---- a/src/sspred_avpred.c
-+++ b/src/sspred_avpred.c
-@@ -213,7 +213,7 @@ predict(int argc, char **argv)
- int             getmtx(FILE *lfil)
- {
-     int             aa, i, j, naa;
--    char            buf[256], *p;
-+    char            buf[65536], *p;
-     
-     if (fscanf(lfil, "%d", &naa) != 1)
- 	fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
index d5df13d2c367..718cc6e7c376 100644
--- a/sci-biology/trnascan-se/Manifest
+++ b/sci-biology/trnascan-se/Manifest
@@ -1,5 +1,3 @@
-AUX trnascan-se-1.23-glibc-2.10.patch 6702 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42 SHA512 2df0a5d6bf633b9b1c1ccce002c5a751a3f5c5eedf755b24a3af1a6d07a93816b6be4195aa3142ebcbd16ad9b373223f398fbac1d91769b26be1d295f080f181 WHIRLPOOL d8bc3d22d50446ffc628276261d091cb0552e564c0d80c9c6fe6e4108c3c036a11fadd48c45a115fef56ac01a49df0b7a0cebb026fcff05344822c29b074f971
-AUX trnascan-se-1.23-ldflags.patch 971 SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9 SHA512 bcfdc71dc8454e110d45f44bf9c4a0b4e77ca85bcf0b501dd2de60c47418bc5d442b1ac976c6a333eb4398a12e4478b8817436246a1f872df208d5eaf64c3ac2 WHIRLPOOL f1afc811efcc061a114ab6b14ac2ef4ce8c7091bdfa6a392ac55dd6f1e38f1d1ded94f218309e2e3abd515ef80bffbefd7e4ed30d993e16603c0477b988f48b3
 AUX trnascan-se-1.31-ldflags.patch 973 SHA256 e103841dfe3f289493c80fc938a3c9318a550e160b3269b9856405ee48dc648a SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df WHIRLPOOL 2ba11012cd414d2dc9a523109bfebe726a347558cf1098f52410fc88c652665e6babeaef5581dce12fdd1a83af8ed417d8040ef481d5036a9632838f997333c2
 DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665
 EBUILD trnascan-se-1.31.ebuild 1191 SHA256 f70623b4b41a9efe071bb98865a3eb1ecc67293f42371d32ed118c47c3fb6ebb SHA512 d79fa9d244d4f3ab98fff94aca074bd23cc953c0b812a270daca2e80c440fcdcfd38e92cba2eea6ccd2ad9873c8fb898f46b9f4356c638d01fa0f2b21e23c55b WHIRLPOOL 564cd24e354568dfcedf143fe6a60746ee282c334e6ee20fde196803cf57a237c52913be7be1ef559b0403bdb8676cc9bb3429e4f9f27dcd4b71b6c5c8f4527b
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 e21da6e58db0..000000000000
--- 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 783e4340823d..000000000000
--- 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