From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-libs/libghemical/Manifest | 3 ++ .../files/2.00-really-find-blas-and-lapack.patch | 24 ++++++++++++ .../libghemical/files/libghemical-2.98-gcc43.patch | 43 ++++++++++++++++++++++ .../libghemical/files/libghemical-2.98-gl.patch | 13 +++++++ .../libghemical/files/libghemical-2.99.1-gl.patch | 26 +++++++++++++ sci-libs/libghemical/files/libghemical-gcc43.patch | 21 +++++++++++ sci-libs/libghemical/libghemical-2.00.ebuild | 38 +++++++++++++++++++ sci-libs/libghemical/libghemical-2.99.1.ebuild | 42 +++++++++++++++++++++ sci-libs/libghemical/libghemical-3.0.0.ebuild | 42 +++++++++++++++++++++ sci-libs/libghemical/metadata.xml | 18 +++++++++ 10 files changed, 270 insertions(+) create mode 100644 sci-libs/libghemical/Manifest create mode 100644 sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch create mode 100644 sci-libs/libghemical/files/libghemical-2.98-gcc43.patch create mode 100644 sci-libs/libghemical/files/libghemical-2.98-gl.patch create mode 100644 sci-libs/libghemical/files/libghemical-2.99.1-gl.patch create mode 100644 sci-libs/libghemical/files/libghemical-gcc43.patch create mode 100644 sci-libs/libghemical/libghemical-2.00.ebuild create mode 100644 sci-libs/libghemical/libghemical-2.99.1.ebuild create mode 100644 sci-libs/libghemical/libghemical-3.0.0.ebuild create mode 100644 sci-libs/libghemical/metadata.xml (limited to 'sci-libs/libghemical') diff --git a/sci-libs/libghemical/Manifest b/sci-libs/libghemical/Manifest new file mode 100644 index 00000000000..e95eb151f36 --- /dev/null +++ b/sci-libs/libghemical/Manifest @@ -0,0 +1,3 @@ +DIST libghemical-2.00.tar.gz 629479 SHA256 e873b3042df75fa1c9f37fc99f2ff14227965ed13c7680169f714ab6575d5f21 +DIST libghemical-2.99.1.tar.gz 778812 SHA256 f9b6df3c1e98a524f90644ebaaebb804792f391ca383c0f92b609060dc485d9f +DIST libghemical-3.0.0.tar.gz 787947 SHA256 db8c3add0aa1f94c21016d60fa3f66fb194e56b8e9fceaa3860c603700efc3ac SHA512 71531e7bd72a7fa063dd35536a346f15e3c0fd0284112fa2f304580204b93552bd0c9a426cee22044b5dd1662e34e5d191d20af938e474561fe55f2394e7519e WHIRLPOOL fae8e49a2136460013296e0a23a56513a36941ece73013a1a21b530abdfbabfba2b5098457b70a9cd1694759995ffeae01250d05034e0c1186fd2f47af52af08 diff --git a/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch new file mode 100644 index 00000000000..bef730abbe4 --- /dev/null +++ b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch @@ -0,0 +1,24 @@ +diff -urN libghemical-2.00.orig/configure.ac libghemical-2.00/configure.ac +--- libghemical-2.00.orig/configure.ac 2006-05-12 23:31:06.000000000 -0700 ++++ libghemical-2.00/configure.ac 2006-05-12 23:54:20.000000000 -0700 +@@ -69,8 +69,18 @@ + AC_CHECK_LIB([m], [acos]) + + if test $WITH_MPQC = yes; then +- AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support])) +- AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])) ++ AC_CHECK_LIB([blas], [dgemm_], HAVE_BLAS="yes", , -lpthread) ++ AC_CHECK_LIB([blas], [dgemm], HAVE_BLAS="yes", , -lpthread) ++ AC_CHECK_LIB([blas], [dgemm__], HAVE_BLAS="yes", , -lpthread) ++ if test "x${HAVE_BLAS}" = "x"; then ++ AC_MSG_ERROR([Cannot find blas library needed for MPQC support]) ++ fi ++ AC_CHECK_LIB([lapack], [cheev_], HAVE_LAPACK="yes", , -lpthread) ++ AC_CHECK_LIB([lapack], [cheev], HAVE_LAPACK="yes", , -lpthread) ++ AC_CHECK_LIB([lapack], [cheev__], HAVE_LAPACK="yes", , -lpthread) ++ if test "x${HAVE_LAPACK}" = "x"; then ++ AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]) ++ fi + AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no") + if test "${HAVE_MPQC}" = "yes"; then + AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC]) diff --git a/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch b/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch new file mode 100644 index 00000000000..d92d31d93b7 --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-2.98-gcc43.patch @@ -0,0 +1,43 @@ +--- src/atom.h.orig 2008-06-09 03:59:34.262567972 -0500 ++++ src/atom.h 2008-06-09 04:00:07.136698792 -0500 +@@ -10,6 +10,8 @@ + #ifndef ATOM_H + #define ATOM_H + ++#include ++#include + #include "libghemicaldefine.h" + #include "libghemicalconfig2.h" + +--- src/notice.h.orig 2008-06-09 04:00:24.472509840 -0500 ++++ src/notice.h 2008-06-09 04:00:44.608265748 -0500 +@@ -10,6 +10,7 @@ + #ifndef NOTICE_H + #define NOTICE_H + ++#include + #include "libghemicaldefine.h" + #include "libghemicalconfig2.h" + +--- src/sasaeval.cpp 2008-08-01 09:39:01.000000000 +0530 ++++ src/sasaeval.cpp 2008-08-01 09:40:33.000000000 +0530 +@@ -21,6 +21,9 @@ + #include "sasaeval.h" + + #include "engine.h" ++#include ++#include ++using namespace std; + + // the surface area code apparently contains some bugs, since it sometimes + // crashes. another possibility is that the surface area math contains some +--- src/sasaeval.h 2008-07-31 00:40:08.000000000 +0530 ++++ src/sasaeval.h 2008-08-01 09:40:04.000000000 +0530 +@@ -24,6 +24,7 @@ + #define SASAEVAL_H + + #include "typedef.h" ++#include + + struct cg_nbt3_nl; // SASA neighbor list. + diff --git a/sci-libs/libghemical/files/libghemical-2.98-gl.patch b/sci-libs/libghemical/files/libghemical-2.98-gl.patch new file mode 100644 index 00000000000..8cea8aab636 --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-2.98-gl.patch @@ -0,0 +1,13 @@ +diff --git a/src/typedef.h b/src/typedef.h +index 8d2efcc..1e304e8 100644 +--- a/src/typedef.h ++++ b/src/typedef.h +@@ -27,7 +27,7 @@ + + // comment this out if you have no GL/gl.h available... + +-#define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? ++// #define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? + + // added by Robert Williams for Compaq cxx, alpha 11/28/01 + diff --git a/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch new file mode 100644 index 00000000000..ad46079e945 --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch @@ -0,0 +1,26 @@ +diff --git a/configure.ac b/configure.ac +index b01e5fa..943890b 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -151,7 +151,7 @@ fi + # Checks for header files. + # ^^^^^^^^^^^^^^^^^^^^^^^^ + +-AC_CHECK_HEADERS([GL/gl.h]) ++# AC_CHECK_HEADERS([GL/gl.h]) + + # Checks for typedefs, structures, and compiler characteristics. + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diff --git a/src/typedef.h b/src/typedef.h +index 8d2efcc..0ba62fe 100644 +--- a/src/typedef.h ++++ b/src/typedef.h +@@ -27,7 +27,7 @@ + + // comment this out if you have no GL/gl.h available... + +-#define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? ++// #define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? + + // added by Robert Williams for Compaq cxx, alpha 11/28/01 + diff --git a/sci-libs/libghemical/files/libghemical-gcc43.patch b/sci-libs/libghemical/files/libghemical-gcc43.patch new file mode 100644 index 00000000000..53db5fba4d9 --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-gcc43.patch @@ -0,0 +1,21 @@ +--- src/atom.h.orig 2008-06-09 03:59:34.262567972 -0500 ++++ src/atom.h 2008-06-09 04:00:07.136698792 -0500 +@@ -10,6 +10,8 @@ + #ifndef ATOM_H + #define ATOM_H + ++#include ++#include + #include "libghemicaldefine.h" + #include "libghemicalconfig2.h" + +--- src/notice.h.orig 2008-06-09 04:00:24.472509840 -0500 ++++ src/notice.h 2008-06-09 04:00:44.608265748 -0500 +@@ -10,6 +10,7 @@ + #ifndef NOTICE_H + #define NOTICE_H + ++#include + #include "libghemicaldefine.h" + #include "libghemicalconfig2.h" + diff --git a/sci-libs/libghemical/libghemical-2.00.ebuild b/sci-libs/libghemical/libghemical-2.00.ebuild new file mode 100644 index 00000000000..7e7c489336e --- /dev/null +++ b/sci-libs/libghemical/libghemical-2.00.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://www.bioinformatics.org/ghemical/download/${P}.tar.gz" +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ppc x86" +IUSE="mopac7 mpqc" +RDEPEND="mopac7? ( sci-chemistry/mopac7 ) + mpqc? ( >=sci-chemistry/mpqc-2.3.1-r1 + virtual/blas + virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_unpack() { + unpack ${A} + epatch "${FILESDIR}"/${PV}-really-find-blas-and-lapack.patch + cd "${S}" + eautoreconf +} + +src_compile() { + econf \ + $(use_enable mopac7) \ + $(use_enable mpqc) \ + || die "configure failed" + emake || die "make failed" +} + +src_install() { + make DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-libs/libghemical/libghemical-2.99.1.ebuild b/sci-libs/libghemical/libghemical-2.99.1.ebuild new file mode 100644 index 00000000000..3c5ebbfe764 --- /dev/null +++ b/sci-libs/libghemical/libghemical-2.99.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="mopac7 mpqc static-libs" + +RDEPEND=" + mopac7? ( >=sci-chemistry/mopac7-1.13-r1 ) + mpqc? ( + >=sci-chemistry/mpqc-2.3.1-r1 + virtual/blas + virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gl.patch + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable mopac7) \ + $(use_enable mpqc) \ + $(use_enable static-libs static) +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-libs/libghemical/libghemical-3.0.0.ebuild b/sci-libs/libghemical/libghemical-3.0.0.ebuild new file mode 100644 index 00000000000..d1d3dbf4418 --- /dev/null +++ b/sci-libs/libghemical/libghemical-3.0.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="3" + +inherit autotools eutils + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="mopac7 mpqc static-libs" + +RDEPEND=" + mopac7? ( >=sci-chemistry/mopac7-1.13-r1 ) + mpqc? ( + >=sci-chemistry/mpqc-2.3.1-r1 + virtual/blas + virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.98-gl.patch + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable mopac7) \ + $(use_enable mpqc) \ + $(use_enable static-libs static) +} + +src_install() { + emake DESTDIR="${D}" install || die "install failed" +} diff --git a/sci-libs/libghemical/metadata.xml b/sci-libs/libghemical/metadata.xml new file mode 100644 index 00000000000..e94fba7a2bf --- /dev/null +++ b/sci-libs/libghemical/metadata.xml @@ -0,0 +1,18 @@ + + + +sci-chemistry + +Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models +and molecular mechanics models (there is an experimental Tripos 5.2-like force +field for organic molecules). Also a tool for reduced protein models is +included. Geometry optimization, molecular dynamics and a large set of +visualization tools are currently available. + + + Use sci-chemistry/mopac7 for semi-empirical + calculations + Use sci-chemistry/mpqc for quantum-mechanical + calculations + + -- cgit v1.2.1