Index: Makefile =================================================================== --- Makefile (revision 471747) +++ Makefile (working copy) @@ -2,19 +2,15 @@ # $FreeBSD$ PORTNAME= tRNAscan-SE -PORTVERSION= 1.23 -PORTREVISION= 1 +PORTVERSION= 1.3.1 +PORTEPOCH= 1 CATEGORIES= biology -MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/ +MASTER_SITES= http://lowelab.ucsc.edu/software/ MAINTAINER= ports@FreeBSD.org COMMENT= Improved tool for transfer RNA detection -BROKEN= No public distfiles -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2018-06-06 - -USES= perl5 tar:Z +USES= perl5 MAKE_ARGS= BINDIR="${PREFIX}/bin" \ LIBDIR="${DATADIR}" \ CC="${CC}" \ Index: distinfo =================================================================== --- distinfo (revision 471747) +++ distinfo (working copy) @@ -1,2 +1,3 @@ -SHA256 (tRNAscan-SE-1.23.tar.Z) = 843caf3e258a6293300513ddca7eb7dbbd2225e5baae1e5a7bcafd509f6dd550 -SIZE (tRNAscan-SE-1.23.tar.Z) = 846349 +TIMESTAMP = 1528187117 +SHA256 (tRNAscan-SE-1.3.1.tar.gz) = 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 +SIZE (tRNAscan-SE-1.3.1.tar.gz) = 740960 Index: files/patch-sqio.c =================================================================== --- files/patch-sqio.c (revision 471747) +++ files/patch-sqio.c (nonexistent) @@ -1,291 +0,0 @@ ---- sqio.c.orig 2002-04-12 20:12:04 UTC -+++ sqio.c -@@ -235,7 +235,7 @@ readline(FILE *f, char *s) - } - - static void --getline(struct ReadSeqVars *V) -+get_line(struct ReadSeqVars *V) - { - readline(V->f, V->sbuffer); - } -@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch - 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 @@ 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) -@@ -341,7 +341,7 @@ 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) -@@ -350,7 +350,7 @@ 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); - -@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V) - /* get next line - */ - while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) -- getline(V); -+ get_line(V); - } - - -@@ -382,7 +382,7 @@ 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)) -@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V) - } - - while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) -- getline(V); -+ get_line(V); - } - - static int -@@ -416,7 +416,7 @@ 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)) -@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V) - /* load next line - */ - while ((!feof(V->f)) && (*V->sbuffer != ';')) -- getline(V); -+ get_line(V); - } - - -@@ -443,7 +443,7 @@ 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) - { -@@ -454,7 +454,7 @@ 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) -@@ -487,11 +487,11 @@ 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 -@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V) - 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 @@ readGCGdata(struct ReadSeqVars *V) - } 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 @@ 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 -@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V) - readLoop(0, endPearson, V); - - while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) -- getline(V); -+ get_line(V); - } - - -@@ -652,7 +652,7 @@ 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) - { -@@ -661,7 +661,7 @@ 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) -@@ -685,7 +685,7 @@ 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); - } - - -@@ -701,7 +701,7 @@ 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); -@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V) - readLoop(0, endZuker, V); - - while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) -- getline(V); -+ get_line(V); - } - - static void -@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V) - - do { - done = feof(V->f); -- getline(V); -+ get_line(V); - if (! done) addseq(V->sbuffer, V); - } while (!done); - } -@@ -746,7 +746,7 @@ 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); -@@ -754,7 +754,7 @@ 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) -@@ -786,14 +786,14 @@ 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); - } -@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V) - - - while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) -- getline(V); -+ get_line(V); - } - - -@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format, - - /* Load the first line. - */ -- getline(dbfp); -+ get_line(dbfp); - - return dbfp; - } -@@ -862,7 +862,7 @@ void - SeqfilePosition(SQFILE *sqfp, long offset) - { - fseek(sqfp->f, offset, SEEK_SET); -- getline(sqfp); -+ get_line(sqfp); - } - - -@@ -954,7 +954,7 @@ ReadSeq(SQFILE *V, int format, char **re - 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; - Property changes on: files/patch-sqio.c ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: pkg-descr =================================================================== --- pkg-descr (revision 471747) +++ pkg-descr (working copy) @@ -7,4 +7,4 @@ post-processing, and outputting the results in one of several formats. -WWW: http://selab.janelia.org/software.html +WWW: http://lowelab.ucsc.edu/tRNAscan-SE/