[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna/files: vienna-rna-1.7.2-gcc4.4.patch

[Samuli Suominen (ssuominen)]

ssuominen    09/07/30 08:31:01

  Added:                vienna-rna-1.7.2-gcc4.4.patch
  Log:
  Fix building with GCC 4.4 and GLIBC 2.10+ wrt #274044. Rename getline to v_getline. Missing include.
  (Portage version: 2.2_rc33/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch?rev=1.1&content-type=text/plain

Index: vienna-rna-1.7.2-gcc4.4.patch
===================================================================
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>