Fix for glibc-2.11, fix for bug 315595

(Portage version: 2.2_rc67/cvs/Linux x86_64)

7 files changed, 297 insertions, 7 deletions

diff --git a/sci-chemistry/molden/ChangeLog b/sci-chemistry/molden/ChangeLog
index 9611cf06b4e4..5dfa153285bb 100644
--- a/sci-chemistry/molden/ChangeLog
+++ b/sci-chemistry/molden/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/molden
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/ChangeLog,v 1.32 2010/02/26 05:33:34 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/ChangeLog,v 1.33 2010/06/24 16:03:06 jlec Exp $
+
+*molden-4.8-r1 (24 Jun 2010)
+*molden-4.7-r1 (24 Jun 2010)
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> +molden-4.7-r1.ebuild,
+  +files/molden-4.7-glibc-2.11.patch, +files/molden-4.7-implicit-dec.patch,
+  +files/molden-4.7-ldflags.patch, +molden-4.8-r1.ebuild,
+  files/molden-4.8-ldflags.patch:
+  Fix for glibc-2.11, fix for bug #315595
 
 *molden-4.8 (26 Feb 2010)
 
diff --git a/sci-chemistry/molden/files/molden-4.7-glibc-2.11.patch b/sci-chemistry/molden/files/molden-4.7-glibc-2.11.patch
new file mode 100644
index 000000000000..70125518c330
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.7-glibc-2.11.patch
@@ -0,0 +1,116 @@
+diff --git a/xwin.c b/xwin.c
+index d38f87c..d328ee6 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -3776,7 +3776,7 @@ static int imoptm = 0;
+ static int ibopth = 0;
+ static int iboptl = 0;
+ static int iboptm = 0;
+-static int linkat = 0;
++static int lnkat = 0;
+ 
+ static QBOXSTRU IANZboxes[MAXAT];
+ static QBOXSTRU IZboxes[MAXAT][4];
+@@ -19234,7 +19234,7 @@ int i;
+ 		if (ioniom == 1) {
+ 		  int ism, isl;
+ 
+-		  linkat = 0;
++		  lnkat = 0;
+ 
+ 		  /* Counting the number of Link atoms between H and lower 
+ 		     levels*/
+@@ -19247,10 +19247,10 @@ int i;
+ 		     if (ionij != 0) continue;
+ 		     nconn = xyzp->iconn[j*(MXCON+1)];
+ 		     for (k=1;k<=nconn;k++) {
+-		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
++		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) lnkat++;
+ 		     }
+ 		  }
+-		  linkat += 20000;
++		  lnkat += 20000;
+ 		  jobcom->itotc = jobcom->icopth;
+ 		  jobcom->imult = jobcom->ispopth;
+ 		  if (CheckChargeMult()) {
+@@ -19271,7 +19271,7 @@ int i;
+ 
+ 		}  else if (ioniom == 2) {
+ 
+-	          linkat = 0;
++	          lnkat = 0;
+ 
+ 		  /* Counting the number of Link atoms between H and 
+ 		       lower levels*/
+@@ -19281,10 +19281,10 @@ int i;
+ 			 if(ionij != 0) continue;
+ 		         nconn = xyzp->iconn[j*(MXCON+1)];
+ 		         for (k=1;k<=nconn;k++) {
+-		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
++		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) lnkat++;
+ 		         }
+ 		  }
+-		  linkat += 20000;
++		  lnkat += 20000;
+ 		  jobcom->itotc = jobcom->icopth;
+ 		  jobcom->imult = jobcom->ispopth;
+ 		  if (CheckChargeMult()) {
+@@ -19296,7 +19296,7 @@ int i;
+ 	               break;
+ */
+ 		  }
+-	          linkat = 0;
++	          lnkat = 0;
+ 
+ 		  /* Counting the number of Link atoms between H+M and 
+ 		     lower levels*/
+@@ -19306,10 +19306,10 @@ int i;
+ 			if (ionij == 2) continue;
+ 			nconn = xyzp->iconn[j*(MXCON+1)];
+ 			for (k=1;k<=nconn;k++) {
+-			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
++			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) lnkat++;
+ 			}
+ 		  }
+-		  linkat += 20000;
++		  lnkat += 20000;
+ 		  jobcom->itotc = jobcom->icoptm;
+ 		  jobcom->imult = jobcom->ispoptm;
+ 		  if (CheckChargeMult()) {
+@@ -19324,7 +19324,7 @@ int i;
+ 		  icopt = jobcom->icoptl+3;
+ 		  ispopt = jobcom->ispoptl-1;
+ 		}
+-		linkat = 0;
++		lnkat = 0;
+ 		jobcom->itotc = icopt - 3;
+ 		jobcom->imult = ispopt + 1;
+ 		jobcom->ito = itopt[jmode] + 1;
+@@ -19576,10 +19576,10 @@ int CheckChargeMult()
+    ionil = 0;
+ 
+    if (ioniom) {
+-     ionil = 3 - (linkat / 10000);
+-     linkat -= (linkat / 10000) * 10000;
++     ionil = 3 - (lnkat / 10000);
++     lnkat -= (lnkat / 10000) * 10000;
+    } else {
+-     linkat = 0;
++     lnkat = 0;
+    }
+ 
+    if (*zmptrp->ihaszm) {
+@@ -19602,10 +19602,10 @@ int CheckChargeMult()
+       }
+    }
+ /*
+-   fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
+-                   ionil,ne,jobcom->itotc,linkat,jobcom->imult);
++   fprintf(stderr,"ionil %d ne %d itotc %d lnkat %d mult %d\n",
++                   ionil,ne,jobcom->itotc,lnkat,jobcom->imult);
+ */
+-   ne = ne - jobcom->itotc + linkat;
++   ne = ne - jobcom->itotc + lnkat;
+    if (ne % 2 == jobcom->imult % 2) return(1);
+    return(0);
+ }
diff --git a/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
new file mode 100644
index 000000000000..dd5aba4f17da
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
@@ -0,0 +1,12 @@
+diff --git a/silly.c b/silly.c
+index 57d07e8..102156a 100644
+--- a/silly.c
++++ b/silly.c
+@@ -13,6 +13,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <string.h>
+ 
+ #ifndef WIN32
+ #include <GL/gl.h>
diff --git a/sci-chemistry/molden/files/molden-4.7-ldflags.patch b/sci-chemistry/molden/files/molden-4.7-ldflags.patch
new file mode 100644
index 000000000000..2dc3f94c1b72
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.7-ldflags.patch
@@ -0,0 +1,13 @@
+diff --git a/makefile b/makefile
+index 410ca25..30dd5e1 100644
+--- a/makefile
++++ b/makefile
+@@ -265,7 +265,7 @@ short_wrl:	short_wrl.o
+ # Moldens OpenGL helper program
+ 
+ moldenogl:	oglmol.o silly.o
+-	$(CC) -o moldenogl oglmol.o silly.o $(LIBSOGL)
++	$(CC) $(LDFLAGS) -o moldenogl oglmol.o silly.o $(LIBSOGL)
+ 
+ # conversion of CADPAC output to molden format
+ 
diff --git a/sci-chemistry/molden/files/molden-4.8-ldflags.patch b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
index 3759f1406f00..92fa6c665f3f 100644
--- a/sci-chemistry/molden/files/molden-4.8-ldflags.patch
+++ b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
@@ -1,7 +1,8 @@
-diff -Naur molden4.8.old/makefile molden4.8/makefile
---- molden4.8.old/makefile	2009-09-21 12:01:33.000000000 -0400
-+++ molden4.8/makefile	2010-02-26 00:11:28.000000000 -0500
-@@ -224,7 +224,7 @@
+diff --git a/makefile b/makefile
+index 81147a3..9e2353e 100644
+--- a/makefile
++++ b/makefile
+@@ -224,10 +224,10 @@ all:	molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
  
  
  molden:	$(OBJS) mpdum.o xwin.o 
@@ -9,8 +10,12 @@ diff -Naur molden4.8.old/makefile molden4.8/makefile
 +	$(LDR) $(LDFLAGS) -o molden $(OBJS) mpdum.o xwin.o $(LIBS)
  
  gmolden:	$(OBJS) mpdum.o xwingl.o 
- 	$(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
-@@ -269,7 +269,7 @@
+-	$(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
++	$(LDR) $(LDFLAGS)  -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
+ 
+ ambfor/ambfor:	ambfor/*.f ambfor/*.c
+ 	$(MAKE) -C ambfor FC=${FC} FFLAGS="${FFLAGS}" LDR="${LDR}" CFLAGS="${CFLAGS}"
+@@ -269,7 +269,7 @@ short_wrl:	short_wrl.o
  # Moldens OpenGL helper program
  
  moldenogl:	oglmol.o silly.o
diff --git a/sci-chemistry/molden/molden-4.7-r1.ebuild b/sci-chemistry/molden/molden-4.7-r1.ebuild
new file mode 100644
index 000000000000..70362d28567e
--- /dev/null
+++ b/sci-chemistry/molden/molden-4.7-r1.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-4.7-r1.ebuild,v 1.1 2010/06/24 16:03:06 jlec Exp $
+
+EAPI="3"
+
+inherit eutils flag-o-matic fortran toolchain-funcs
+
+FORTRAN="g77 gfortran"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac."
+HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
+SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ia64 ~x86"
+IUSE="opengl"
+
+RDEPEND="
+	x11-libs/libXmu
+	opengl? (
+		virtual/glut
+		virtual/opengl )"
+DEPEND="${RDEPEND}
+	app-editors/vim"
+	# vim provides ex, which the build system uses (surf/Makefile, at least)
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-glibc-2.11.patch
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+	epatch "${FILESDIR}"/${P}-implicit-dec.patch
+	sed 's:makedepend:gccmakedep:g' -i surf/Makefile
+}
+
+src_compile() {
+	# Use -mieee on alpha, according to the Makefile
+	use alpha && append-flags -mieee
+
+	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
+	# unfortunately a bash bug prevents us from doing typeset and
+	# assignment on the same line.
+	typeset -a args
+	args=( CC="$(tc-getCC) ${CFLAGS}" \
+		FC="${FORTRANC}" LDR="${FORTRANC} ${LDFLAGS}" FFLAGS="${FFLAGS}" )
+
+	einfo "Building Molden..."
+	emake -j1 "${args[@]}" || die "molden emake failed"
+	if use opengl ; then
+		einfo "Building Molden OpenGL helper..."
+		emake -j1 "${args[@]}" moldenogl || die "moldenogl emake failed"
+	fi
+}
+
+src_install() {
+	dobin ${PN} g${PN} || die "failed to install molden executable."
+	if use opengl ; then
+		dobin ${PN}ogl || die "failed to install moldenogl."
+	fi
+
+	dodoc HISTORY README REGISTER || die "failed to install docs."
+	cd doc
+	uncompress * && dodoc * || die "failed to install docs."
+}
diff --git a/sci-chemistry/molden/molden-4.8-r1.ebuild b/sci-chemistry/molden/molden-4.8-r1.ebuild
new file mode 100644
index 000000000000..52bbc291e319
--- /dev/null
+++ b/sci-chemistry/molden/molden-4.8-r1.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molden/molden-4.8-r1.ebuild,v 1.1 2010/06/24 16:03:06 jlec Exp $
+
+EAPI="3"
+
+inherit eutils flag-o-matic fortran toolchain-funcs
+
+FORTRAN="g77 gfortran"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac."
+HOMEPAGE="http://www.cmbi.kun.nl/~schaft/molden/molden.html"
+SRC_URI="ftp://ftp.cmbi.kun.nl/pub/molgraph/${PN}/${MY_P}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ia64 ~x86"
+IUSE="opengl"
+
+RDEPEND="
+	x11-libs/libXmu
+	opengl? (
+		virtual/glut
+		virtual/opengl )"
+DEPEND="${RDEPEND}
+	app-editors/vim"
+	# vim provides ex, which the build system uses (surf/Makefile, at least)
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-ambfor.patch
+	epatch "${FILESDIR}"/${P}-overflow.patch
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+	epatch "${FILESDIR}"/${PN}-4.7-implicit-dec.patch
+	sed 's:makedepend:gccmakedep:g' -i surf/Makefile
+}
+
+src_compile() {
+	# Use -mieee on alpha, according to the Makefile
+	use alpha && append-flags -mieee
+
+	# Honor CC, CFLAGS, FC, and FFLAGS from environment;
+	# unfortunately a bash bug prevents us from doing typeset and
+	# assignment on the same line.
+	typeset -a args
+	args=( CC="$(tc-getCC) ${CFLAGS}" \
+		FC="${FORTRANC}" LDR="${FORTRANC}" FFLAGS="${FFLAGS}" )
+
+	einfo "Building Molden..."
+	emake -j1 "${args[@]}" || die "molden emake failed"
+	if use opengl ; then
+		einfo "Building Molden OpenGL helper..."
+		emake -j1 "${args[@]}" moldenogl || die "moldenogl emake failed"
+	fi
+}
+
+src_install() {
+	dobin ${PN} g${PN} || die "failed to install molden executable."
+	if use opengl ; then
+		dobin ${PN}ogl || die "failed to install moldenogl."
+	fi
+
+	dodoc HISTORY README REGISTER || die "failed to install docs."
+	cd doc
+	uncompress * && dodoc * || die "failed to install docs."
+}