diff options
Diffstat (limited to 'sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch')
| -rw-r--r-- | sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch | 331 |
1 files changed, 0 insertions, 331 deletions
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch deleted file mode 100644 index 3ba7e636ccfa..000000000000 --- a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch +++ /dev/null @@ -1,331 +0,0 @@ -diff -ur ViennaRNA-1.7.2.orig/Kinfold/main.c ViennaRNA-1.7.2/Kinfold/main.c ---- ViennaRNA-1.7.2.orig/Kinfold/main.c 2006-11-24 10:13:55.000000000 +0200 -+++ ViennaRNA-1.7.2/Kinfold/main.c 2009-07-30 11:27:39.000000000 +0300 -@@ -27,7 +27,7 @@ - /* PRIVAT FUNCTIONS */ - static void ini_energy_model(void); - static void read_data(void); --static char *getline(FILE *fp); -+static char *v_getline(FILE *fp); - static void clean_up(void); - - /**/ -@@ -133,7 +133,7 @@ - /* - read sequence - */ -- ctmp = getline(stdin); -+ ctmp = v_getline(stdin); - len = strlen(ctmp); - GAV.farbe = (char *)calloc(len+1, sizeof(char)); - assert(GAV.farbe != NULL); -@@ -153,7 +153,7 @@ - read start structure - */ - if (GTV.start) { -- ctmp = getline(stdin); -+ ctmp = v_getline(stdin); - len = strlen(ctmp); - sscanf(ctmp, "%s", GAV.startform); - -@@ -174,7 +174,7 @@ - */ - if (GTV.stop) { - s = GAV.stopform; -- while (( ctmp = getline(stdin))) { -+ while (( ctmp = v_getline(stdin))) { - *s = (char *)calloc(GSV.len+1, sizeof(char)); - sscanf(ctmp, "%s", *s); - -@@ -207,7 +207,7 @@ - } - - /**/ --static char *getline(FILE *fp) { -+static char *v_getline(FILE *fp) { - char s[512], *line, *cp; - - line = NULL; -diff -ur ViennaRNA-1.7.2.orig/Readseq/ureadseq.c ViennaRNA-1.7.2/Readseq/ureadseq.c ---- ViennaRNA-1.7.2.orig/Readseq/ureadseq.c 2002-11-27 13:23:56.000000000 +0200 -+++ ViennaRNA-1.7.2/Readseq/ureadseq.c 2009-07-30 11:29:35.000000000 +0300 -@@ -136,12 +136,12 @@ - } - } - --Local void getline(struct ReadSeqVars *V) -+Local void v_getline(struct ReadSeqVars *V) - { - readline(V->f, V->s, &V->linestart); - } - --Local void ungetline(struct ReadSeqVars *V) -+Local void unv_getline(struct ReadSeqVars *V) - { - fseek(V->f, V->linestart, 0); - } -@@ -215,7 +215,7 @@ - - if (addfirst) addseq(V->s, V); - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - V->done |= (*endTest)( &addend, &ungetend, V); - if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) { -@@ -226,7 +226,7 @@ - if (V->choice == kListSequences) addinfo(V->seqid, V); - else { - V->allDone = (V->nseq >= V->choice); -- if (V->allDone && ungetend) ungetline(V); -+ if (V->allDone && ungetend) unv_getline(V); - } - } - -@@ -246,7 +246,7 @@ - - while (!V->allDone) { - do { -- getline(V); -+ v_getline(V); - for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */ - if (*si == 0) *V->s= 0; /* chop line to empty */ - } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) )); -@@ -272,13 +272,13 @@ - { /* ? only 1 seq/file ? */ - - while (!V->allDone) { -- getline(V); -+ v_getline(V); - if (strstr(V->s,"; DNA sequence ") == V->s) - strcpy(V->seqid, (V->s)+16); - else - strcpy(V->seqid, (V->s)+1); - while ((!feof(V->f)) && (*V->s == ';')) { -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - else readLoop(0, true, endStrider, V); -@@ -298,16 +298,16 @@ - - while (!V->allDone) { - while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) ) -- getline(V); -+ v_getline(V); - strcpy(V->seqid, (V->s)+16); - while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s)) -- getline(V); -+ v_getline(V); - readLoop(0, false, endPIR, V); - - if (!V->allDone) { - while (! (feof(V->f) || ((*V->s != 0) - && (strstr( V->s,"ENTRY") == V->s)))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -327,13 +327,13 @@ - while (!V->allDone) { - strcpy(V->seqid, (V->s)+12); - while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s)) -- getline(V); -+ v_getline(V); - readLoop(0, false, endGB, V); - - if (!V->allDone) { - while (! (feof(V->f) || ((*V->s != 0) - && (strstr( V->s,"LOCUS") == V->s)))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -364,11 +364,11 @@ - { - while (!V->allDone) { - strcpy(V->seqid, (V->s)+4); -- getline(V); /*skip title-junk line*/ -+ v_getline(V); /*skip title-junk line*/ - readLoop(0, false, endNBRF, V); - if (!V->allDone) { - while (!(feof(V->f) || (*V->s != 0 && *V->s == '>'))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -390,7 +390,7 @@ - readLoop(0, false, endPearson, V); - if (!V->allDone) { - while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>')))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -410,14 +410,14 @@ - while (!V->allDone) { - strcpy(V->seqid, (V->s)+5); - do { -- getline(V); -+ v_getline(V); - } while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s))); - - readLoop(0, false, endEMBL, V); - if (!V->allDone) { - while (!(feof(V->f) | - ((*V->s != '\0') & (strstr(V->s,"ID ") == V->s)))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -437,13 +437,13 @@ - /*! 1st string is Zuker's Fortran format */ - - while (!V->allDone) { -- getline(V); /*s == "seqLen seqid string..."*/ -+ v_getline(V); /*s == "seqLen seqid string..."*/ - strcpy(V->seqid, (V->s)+6); - readLoop(0, false, endZuker, V); - if (!V->allDone) { - while (!(feof(V->f) | - ((*V->s != '\0') & (*V->s == '(')))) -- getline(V); -+ v_getline(V); - } - if (feof(V->f)) V->allDone = true; - } -@@ -486,7 +486,7 @@ - do { - addseq(V->s, V); - V->done = feof(V->f); -- getline(V); -+ v_getline(V); - } while (!V->done); - if (V->choice == kListSequences) addinfo(V->seqid, V); - V->allDone = true; -@@ -498,7 +498,7 @@ - /* - 10nov91: Reading GCG files casued duplication of last line when - EOF followed that line !!! -- fix: getline now sets *V->s = 0 -+ fix: v_getline now sets *V->s = 0 - */ - char *si; - -@@ -512,7 +512,7 @@ - else if (si = strstr(V->seqid,"..")) *si = 0; - do { - V->done = feof(V->f); -- getline(V); -+ v_getline(V); - if (!V->done) addseq((V->s), V); - } while (!V->done); - if (V->choice == kListSequences) addinfo(V->seqid, V); -@@ -531,7 +531,7 @@ - if (V->addit) V->seqlen = 0; - rewind(V->f); V->nseq= 0; - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - - if (V->done && !(*V->s)) break; -@@ -614,7 +614,7 @@ - if (V->addit) V->seqlen = 0; - rewind(V->f); V->nseq= 0; - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - - if (V->done && !(*V->s)) break; -@@ -685,7 +685,7 @@ - domatch= (V->matchchar > 0); - - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - - if (V->done && !(*V->s)) break; -@@ -766,7 +766,7 @@ - /* rewind(V->f); V->nseq= 0; << do in caller !*/ - indata= true; /* call here after we find "matrix" */ - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - - if (V->done && !(*V->s)) break; -@@ -851,7 +851,7 @@ - /* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */ - - do { -- getline(V); -+ v_getline(V); - V->done = feof(V->f); - - if (V->done && !(*V->s)) break; -@@ -904,7 +904,7 @@ - while (isdigit(*si)) si++; - skipwhitespace(si); - V->topseqlen= atol(si); -- getline(V); -+ v_getline(V); - while (!V->allDone) { - V->seqlencount= 0; - strncpy(V->seqid, (V->s), 10); -@@ -935,10 +935,10 @@ - V->err = eFileNotFound; - else { - -- for (l = skiplines_; l > 0; l--) getline( V); -+ for (l = skiplines_; l > 0; l--) v_getline( V); - - do { -- getline( V); -+ v_getline( V); - for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ; - } while ((l == 0) && !feof(V->f)); - -@@ -963,7 +963,7 @@ - char *cp; - /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */ - while (!done) { -- getline( V); -+ v_getline( V); - tolowerstr( V->s); - if (strstr( V->s, "matrix")) done= true; - if (strstr( V->s, "interleav")) interleaved= true; -@@ -995,7 +995,7 @@ - break; - - case kFitch : -- strcpy(V->seqid, V->s); getline(V); -+ strcpy(V->seqid, V->s); v_getline(V); - readFitch(V); - break; - -@@ -1003,7 +1003,7 @@ - do { - gotuw = (strstr(V->s,"..") != NULL); - if (gotuw) readUWGCG(V); -- getline(V); -+ v_getline(V); - } while (!(feof(V->f) || V->allDone)); - break; - } -diff -ur ViennaRNA-1.7.2.orig/RNAforester/src/rnafuncs.cpp ViennaRNA-1.7.2/RNAforester/src/rnafuncs.cpp ---- ViennaRNA-1.7.2.orig/RNAforester/src/rnafuncs.cpp 2005-08-05 13:52:50.000000000 +0300 -+++ ViennaRNA-1.7.2/RNAforester/src/rnafuncs.cpp 2009-07-30 11:26:47.000000000 +0300 -@@ -1,3 +1,5 @@ -+#include <cstdio> -+ - #include <algorithm> - #include <cctype> - #include <iomanip> |