Fix building with GLIBC 2.10+ wrt #278307.

Package-Manager: portage-2.2_rc36/cvs/Linux x86_64

4 files changed, 315 insertions, 7 deletions

diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
index 8b12e0883680..c6f4c2a0cfa0 100644
--- a/sci-biology/wise/ChangeLog
+++ b/sci-biology/wise/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/wise
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.13 2008/06/09 10:12:00 markusle Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.14 2009/08/05 19:42:00 ssuominen Exp $
+
+  05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> wise-2.2.0.ebuild,
+  +files/wise-2.2.0-glibc-2.10.patch:
+  Fix building with GLIBC 2.10+ wrt #278307.
 
   09 Jun 2008; Markus Dittrich <markusle@gentoo.org> wise-2.2.0.ebuild:
   Switched virtual/tetex -> virtual/latex-base and added amd64 
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index 3523024c7275..1c23935eedec 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1,6 +1,7 @@
+AUX wise-2.2.0-glibc-2.10.patch 7044 RMD160 bf7e9b784fee83bca6f532550a44911f65b83a44 SHA1 7b70e9734b18259c78e8ea4bb0362c4072a8afa5 SHA256 92086174f059ab9732cf502acd9619fc5c9e1c34c5018b6c493d5203ec629503
 AUX wise-api.tex.patch 2234 RMD160 c1780513680ad00562ba7589bd44ffa86ee996f4 SHA1 16c2b37efc603003448d37de2b67986b86020777 SHA256 31042f660669ea9df9bc608006cd40479e004f5cbb9aed055d3ec58a853c145d
 AUX wise-env 40 RMD160 2ac8408df8a36f789c28d8d55cf892dba78359c5 SHA1 76bce2a14ae2c2afa82e2c537383d4e730dfcb07 SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36
 DIST wise2.2.0.tar.gz 2108151 RMD160 a4292fbfb405d19b628fe5c829d746297e740862 SHA1 77cc08e9cda9416641370c9b45191192fc7cacd3 SHA256 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
-EBUILD wise-2.2.0.ebuild 2004 RMD160 052c6952e8b97808456e08b98dfc7bd1a9bbc1e6 SHA1 2088d7d0d7f99c3c88b9cdc328edd4412780aaf2 SHA256 1b3ee2b3b03a41ff58053f1eb43d0506399699c629b9822920bbff171d723dd0
-MISC ChangeLog 1845 RMD160 31aa2ba35d7b2769e5d223913c283728566997cb SHA1 ac468920e600aab160495c53bc820e572db7665a SHA256 26796b28dd7605b18577e011b352497a7c118e310c384385a5e3e0861c3cc1a8
+EBUILD wise-2.2.0.ebuild 2059 RMD160 d9b78053d4e682bd329305b384fa56618f293680 SHA1 19b2890f03ae0946d8c3d44b9d798496cce98ed6 SHA256 b149947b48b8ba989abf88a019b6b8c30562e90497c62a3c1e644fc8d264be01
+MISC ChangeLog 2003 RMD160 8882b890bf91663d54ba6e95b968d297827f2922 SHA1 b1cab908d796849e5a088c8f5c29f17ee9c8f49b SHA256 2b13ac8674e6d5774ea4e57f063466374f323ef6b6934a9efd3e05c8fb9c48e7
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
new file mode 100644
index 000000000000..1ec433f19227
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
@@ -0,0 +1,301 @@
+diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
+--- wise2.2.0.orig/src/HMMer2/sqio.c	2001-06-18 16:59:51.000000000 +0300
++++ wise2.2.0/src/HMMer2/sqio.c	2009-08-05 22:39:04.000000000 +0300
+@@ -213,7 +213,7 @@
+     }
+ }
+ 
+-/* Function: getline()
++/* Function: get_line()
+  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
+  *
+  * Purpose:  read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+  * Returns:  (void)
+  */
+ static void 
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+   char *cp;
+   
+@@ -299,7 +299,7 @@
+   V->seqlen = 0;
+   if (addfirst) addseq(V->sbuffer, V);
+   do {
+-    getline(V);
++    get_line(V);
+ 	/* feof() alone is a bug; files not necessarily \n terminated */
+     if (*(V->sbuffer) == '\0' && feof(V->f))
+       done = TRUE;
+@@ -327,7 +327,7 @@
+   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)
+@@ -336,7 +336,7 @@
+       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)
+@@ -345,7 +345,7 @@
+ 	  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);
+ 
+@@ -359,7 +359,7 @@
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -377,7 +377,7 @@
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    get_line(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -389,7 +389,7 @@
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int 
+@@ -411,7 +411,7 @@
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      get_line(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -420,7 +420,7 @@
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -438,7 +438,7 @@
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -449,7 +449,7 @@
+   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)
+@@ -482,11 +482,11 @@
+ 
+ 
+   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
+@@ -515,7 +515,7 @@
+     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) {
+@@ -535,7 +535,7 @@
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -555,12 +555,12 @@
+   if ((sptr = strtok(NULL, "\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ 				/* workaround for long NCBI NR lines */
+-  while (V->longline && ! feof(V->f)) getline(V);
++  while (V->longline && ! feof(V->f)) get_line(V);
+ 
+   readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -587,7 +587,7 @@
+ 
+ 				/* 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)
+     {
+@@ -596,7 +596,7 @@
+     }
+ 
+   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)
+@@ -620,7 +620,7 @@
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -636,7 +636,7 @@
+ {
+   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);
+@@ -647,7 +647,7 @@
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static void 
+@@ -669,7 +669,7 @@
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    get_line(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -681,7 +681,7 @@
+   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);
+@@ -689,7 +689,7 @@
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      get_line(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+   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);
+ 	}
+@@ -736,7 +736,7 @@
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -816,7 +816,7 @@
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  get_line(dbfp);
+ 
+   return dbfp;
+ }
+@@ -833,7 +833,7 @@
+     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+ 
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  get_line(sqfp);
+ }
+ 
+ 
+@@ -853,7 +853,7 @@
+   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+   else {
+     rewind(sqfp->f);
+-    getline(sqfp);
++    get_line(sqfp);
+   }
+ }
+ 
+@@ -949,7 +949,7 @@
+       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;
+ 
diff --git a/sci-biology/wise/wise-2.2.0.ebuild b/sci-biology/wise/wise-2.2.0.ebuild
index f59d09a928a9..da6d2419950e 100644
--- a/sci-biology/wise/wise-2.2.0.ebuild
+++ b/sci-biology/wise/wise-2.2.0.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/wise/wise-2.2.0.ebuild,v 1.9 2008/06/09 10:12:00 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.10 2009/08/05 19:42:00 ssuominen Exp $
 
 inherit eutils toolchain-funcs
 
@@ -20,10 +20,12 @@ DEPEND="${RDEPEND}
 	dev-lang/perl
 	virtual/latex-base"
 
-S="${WORKDIR}/${PN}${PV}"
+S=${WORKDIR}/${PN}${PV}
 
 src_unpack() {
 	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
 	cd "${S}"/src
 #	if use threads; then
 #		append-flags "-DPTHREAD"