From owner-svn-ports-all@freebsd.org Fri May 13 18:38:35 2016 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id E890EB3A467; Fri, 13 May 2016 18:38:35 +0000 (UTC) (envelope-from bapt@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id A293510FD; Fri, 13 May 2016 18:38:35 +0000 (UTC) (envelope-from bapt@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u4DIcYLx052928; Fri, 13 May 2016 18:38:34 GMT (envelope-from bapt@FreeBSD.org) Received: (from bapt@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u4DIcYBP052927; Fri, 13 May 2016 18:38:34 GMT (envelope-from bapt@FreeBSD.org) Message-Id: <201605131838.u4DIcYBP052927@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: bapt set sender to bapt@FreeBSD.org using -f From: Baptiste Daroussin Date: Fri, 13 May 2016 18:38:34 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r415128 - head/biology/tRNAscan-SE/files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.22 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 May 2016 18:38:36 -0000 Author: bapt Date: Fri May 13 18:38:34 2016 New Revision: 415128 URL: https://svnweb.freebsd.org/changeset/ports/415128 Log: Prevent collision with getline(3) Added: head/biology/tRNAscan-SE/files/patch-sqio.c (contents, props changed) Added: head/biology/tRNAscan-SE/files/patch-sqio.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tRNAscan-SE/files/patch-sqio.c Fri May 13 18:38:34 2016 (r415128) @@ -0,0 +1,291 @@ +--- 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; +