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authorV3n3RiX <venerix@redcorelinux.org>2017-10-29 11:22:34 +0000
committerV3n3RiX <venerix@redcorelinux.org>2017-10-29 11:22:34 +0000
commitbd7908c6630f38067350d396ac5d18c3cc2434a0 (patch)
tree3559b3e11424f5529527f2474d8a977a91ee3389 /sci-biology/trnascan-se
parent8b2628ad8526c806375e7b157889e4274b70248b (diff)
gentoo resync : 29.10.2017
Diffstat (limited to 'sci-biology/trnascan-se')
-rw-r--r--sci-biology/trnascan-se/Manifest2
-rw-r--r--sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch292
-rw-r--r--sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch26
3 files changed, 0 insertions, 320 deletions
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