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)

3 files changed, 342 insertions, 5 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 27aa3d0d500a..a84f1757b684 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/vienna-rna
-# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.19 2008/10/09 13:03:30 markusle Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.20 2009/07/30 08:31:01 ssuominen Exp $
+
+  30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org>
+  vienna-rna-1.7.2.ebuild, +files/vienna-rna-1.7.2-gcc4.4.patch:
+  Fix building with GCC 4.4 and GLIBC 2.10+ wrt #274044. Rename getline to
+  v_getline. Missing include.
 
   09 Oct 2008; Markus Dittrich <markusle@gentoo.org>
   vienna-rna-1.7.2.ebuild:
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
new file mode 100644
index 000000000000..3ba7e636ccfa
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.4.patch
@@ -0,0 +1,331 @@
+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>
diff --git a/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
index 8a7d435c3882..42da1126e2a2 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.3 2008/10/09 13:03:30 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.4 2009/07/30 08:31:01 ssuominen Exp $
 
 inherit toolchain-funcs multilib eutils versionator autotools perl-module
 
@@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86 ~ppc"
 DEPEND="dev-lang/perl
 	media-libs/gd"
 
-S="${WORKDIR}/ViennaRNA-${PV}"
+S=${WORKDIR}/ViennaRNA-${PV}
 
 src_unpack() {
 	unpack ${A}
@@ -25,6 +25,7 @@ src_unpack() {
 	epatch "${FILESDIR}"/${P}-gcc4.3.patch
 	epatch "${FILESDIR}"/${P}-LDFLAGS.patch
 	epatch "${FILESDIR}"/${P}-disable-gd.patch
+	epatch "${FILESDIR}"/${P}-gcc4.4.patch
 	eautoreconf
 
 	# we need a separate eautoreconf in RNAforester