Attachment 194016 Details for Bug 228758 – svn diff

[patch] svn diff

tRNAscan-SE.diff (text/plain), 10.43 KB, created by Motomichi Matsuzaki on 2018-06-05 09:52:34 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Motomichi Matsuzaki

Created: 2018-06-05 09:52:34 UTC

Size: 10.43 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 471747)
>+++ Makefile	(working copy)
>@@ -2,19 +2,17 @@
> # $FreeBSD$
> 
> 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
>+LICENSE=	GPLv2+
> 
>-USES=		perl5 tar:Z
>+USES=		perl5
> MAKE_ARGS=	BINDIR="${PREFIX}/bin" \
> 		LIBDIR="${DATADIR}" \
> 		CC="${CC}" \
>@@ -25,6 +23,16 @@
> PORTDATA=	*
> PORTDOCS=	Manual.ps
> 
>+PERLMOD_DIR=	tRNAscanSE
>+PERLMOD_FILES=	CM.pm Constants.pm Eufind.pm GeneticCode.pm LogFile.pm \
>+		Options.pm ScanResult.pm Sequence.pm SS.pm Stats.pm Tscan.pm \
>+		Utils.pm
>+
>+PLIST_DIRS+=	${SITE_PERL_REL}/${PERLMOD_DIR}
>+.for f in ${PERLMOD_FILES}
>+PLIST_FILES+=	${SITE_PERL_REL}/${PERLMOD_DIR}/${f}
>+.endfor
>+
> OPTIONS_DEFINE=	DOCS
> 
> post-patch:
>@@ -41,6 +49,10 @@
> .for f in TPCsignal Dsignal *.cm gcode.*
> 	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}
> .endfor
>+	${MKDIR} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
>+.for f in ${PERLMOD_FILES}
>+	${INSTALL_DATA} ${WRKSRC}/${PERLMOD_DIR}/${f} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
>+.endfor
> 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR}
> 
>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/

Actions: View | Diff

Attachments on bug 228758: 194013 | 194016 | 194046