diff options
Diffstat (limited to 'sci-chemistry/molden')
| -rw-r--r-- | sci-chemistry/molden/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-chemistry/molden/files/molden-4.7-glibc-2.11.patch | 116 | ||||
| -rw-r--r-- | sci-chemistry/molden/files/molden-4.7-implicit-dec.patch | 12 | ||||
| -rw-r--r-- | sci-chemistry/molden/files/molden-4.7-ldflags.patch | 13 | ||||
| -rw-r--r-- | sci-chemistry/molden/files/molden-4.8-ldflags.patch | 17 | ||||
| -rw-r--r-- | sci-chemistry/molden/molden-4.7-r1.ebuild | 67 | ||||
| -rw-r--r-- | sci-chemistry/molden/molden-4.8-r1.ebuild | 68 |
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." +} |