Libraries needed to build the other RCSB Protein Data Bank tools.

(Portage version: 2.1_pre1)

6 files changed, 365 insertions, 0 deletions

diff --git a/sci-libs/cifparse-obj/ChangeLog b/sci-libs/cifparse-obj/ChangeLog
new file mode 100644
index 000000000000..651245fd60e8
--- /dev/null
+++ b/sci-libs/cifparse-obj/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-libs/cifparse-obj
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cifparse-obj/ChangeLog,v 1.1 2005/12/20 04:10:15 spyderous Exp $
+
+*cifparse-obj-6.302 (20 Dec 2005)
+
+  20 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/respect-flags-and-add-gcc4.patch, +metadata.xml,
+  +cifparse-obj-6.302.ebuild:
+  Libraries needed to build the other RCSB Protein Data Bank tools.
+
diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest
new file mode 100644
index 000000000000..ba1d508e262b
--- /dev/null
+++ b/sci-libs/cifparse-obj/Manifest
@@ -0,0 +1,5 @@
+MD5 ef4365b0a58450b9233b5c099f384a15 cifparse-obj-6.302.ebuild 796
+MD5 8ac8ad29e7eeb2dc15b2352cec3c1a55 files/digest-cifobj-loader-6.102 81
+MD5 88ff9a7be10296fc91b2f04eec9eaab3 files/digest-cifparse-obj-6.302 80
+MD5 2945df7eb475ba3da5fba282404ba5ec files/digest-validation-8.061 79
+MD5 445290482fdc500ef2e98a2035590a13 files/respect-flags-and-add-gcc4.patch 10289
diff --git a/sci-libs/cifparse-obj/cifparse-obj-6.302.ebuild b/sci-libs/cifparse-obj/cifparse-obj-6.302.ebuild
new file mode 100644
index 000000000000..939443998241
--- /dev/null
+++ b/sci-libs/cifparse-obj/cifparse-obj-6.302.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cifparse-obj/cifparse-obj-6.302.ebuild,v 1.1 2005/12/20 04:10:15 spyderous Exp $
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}-v${PV}-prod-src"
+DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format"
+HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	epatch ${FILESDIR}/respect-flags-and-add-gcc4.patch
+	cd ${S}
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		${S}/etc/make.*
+}
+
+src_compile() {
+	emake || die "make failed"
+}
+
+src_install() {
+	dolib.a lib/*
+	insinto /usr/include/rcsb
+	doins include/*
+}
diff --git a/sci-libs/cifparse-obj/files/digest-cifparse-obj-6.302 b/sci-libs/cifparse-obj/files/digest-cifparse-obj-6.302
new file mode 100644
index 000000000000..8ce357369a68
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/digest-cifparse-obj-6.302
@@ -0,0 +1 @@
+MD5 027e5501b68816fbc846ea31c4ee06aa cifparse-obj-v6.302-prod-src.tar.gz 782727
diff --git a/sci-libs/cifparse-obj/files/respect-flags-and-add-gcc4.patch b/sci-libs/cifparse-obj/files/respect-flags-and-add-gcc4.patch
new file mode 100644
index 000000000000..79d4914edf58
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/respect-flags-and-add-gcc4.patch
@@ -0,0 +1,302 @@
+diff -urN -x make.log -x Makefile.platform cifparse-obj-v6.302-prod-src.orig/etc/make.platform.gnu3 cifparse-obj-v6.302-prod-src/etc/make.platform.gnu3
+--- cifparse-obj-v6.302-prod-src.orig/etc/make.platform.gnu3	2005-04-26 06:12:57.000000000 -0700
++++ cifparse-obj-v6.302-prod-src/etc/make.platform.gnu3	2005-12-18 22:50:21.000000000 -0800
+@@ -107,8 +107,8 @@
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -125,12 +125,12 @@
+ # This variable specifies how to compile the C code. If it is set to C,
+ # that indicates that C code will be compiled with the C++ compiler.
+ # Otherwise it will be compiled with C compiler.
+-EXT=C
++EXT=c
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -144,7 +144,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+diff -urN -x make.log -x Makefile.platform cifparse-obj-v6.302-prod-src.orig/etc/make.platform.gnu4 cifparse-obj-v6.302-prod-src/etc/make.platform.gnu4
+--- cifparse-obj-v6.302-prod-src.orig/etc/make.platform.gnu4	1969-12-31 16:00:00.000000000 -0800
++++ cifparse-obj-v6.302-prod-src/etc/make.platform.gnu4	2005-12-18 22:55:17.000000000 -0800
+@@ -0,0 +1,202 @@
++##########################################################################
++##
++##  File:    make.plaform.gnu4
++##  Purpose: This file is a Linux platform makefile that supports GNU 4.x
++##           compiler suite.
++##
++##########################################################################
++
++#-----Lexer and Parser section-------------------------------------------#
++
++# Lexer executable
++LEX=flex
++
++# Lexer flags
++LEXFLAGS=-Cfr -L
++
++# Parser executable
++YACC=bison
++
++# Parser flags
++YACCFLAGS=-d -v -l
++
++#------------------------------------------------------------------------#
++
++#-----Compilers section--------------------------------------------------#
++
++## ABI
++## This part defines an application binary interface to be used with the
++## compiler suite.
++ABI= 
++
++## Warnings flags
++## This part defines warnings related flags
++
++# WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
++# warnings as errors.
++
++# ALL_WARNINGS defines flags to instruct all compilers to report all
++# warnings.
++ALL_WARNINGS=-Wall
++
++# NO_DEPRECATED defines flags to instruct C++ compiler not to report
++# warnings about deprecated constructs still used in C++ code.
++NO_DEPRECATED=-Wno-deprecated
++
++# Collect all general warnings related flags
++WARNINGS=$(WARNINGS_AS_ERRORS) $(ALL_WARNINGS)
++
++## Platform specifics
++## This part defines platform specific information
++
++# Endianess.
++# Should be defined only for big endian platforms. Otherwise
++# it must be left undefined, which indicates little endian platform.
++#ENDIANESS=-DBIG_ENDIAN_PLATFORM
++ 
++# OS indicator. Should be defined only if SunOS is the platform
++#PLATFORM_OS=-DSUN_OS
++ 
++# Collect all platform related flags
++PLATFORM=$(ENDIANESS) $(PLATFORM_OS)
++
++## Compiler capabilities/restrictions related defines
++## This part defines variables based on the capabilities or restrictions
++## of the compiler suite used on the platform.
++
++# If STRCASECMP_OPTION is defined, that indicates that the compiler
++# suite/supporting libraries support strcasecmp() function.
++STRCASECMP_OPTION=-DHAVE_STRCASECMP
++
++# If INCL_TEMPLATE_SRC_OPTION is defined, that indicates that
++# compiler must include template method definition in template
++# header files in order to properly compile templates.
++INCL_TEMPLATE_SRC_OPTION=-DINCL_TEMPLATE_SRC
++
++# If PLACEMENT_NEW_OPTION is defined, that indicates that the compiler
++# suite/supporting libraries support placement new/delete operators.
++PLACEMENT_NEW_OPTION=-DHAVE_PLACEMENT_NEW
++
++# Collect all compiler capabilities/restrictions
++COMPILER=$(STRCASECMP_OPTION) $(INCL_TEMPLATE_SRC_OPTION) \
++  $(PLACEMENT_NEW_OPTION)
++
++# Collect all global defines
++GDEFINES=$(PLATFORM) $(COMPILER)
++
++# Collect all defines from global defines and defines specified in
++# module makefile
++DEFINES=$(GDEFINES) $(LDEFINES)
++
++## Global include directories
++GINCLUDES= 
++
++# Collect all include directories from global include directories and
++# include directories specified in module makefile
++INCLUDES=$(LINCLUDES) $(GINCLUDES) 
++
++## C compiler
++## This part defines C compiler information
++
++# C compiler executable
++CC=gcc
++
++# C compiler ANSI/NON-ANSI flags
++ANSI_C_FLAG=-ansi
++NON_ANSI_C_FLAG=
++C_WARNINGS=$(WARNINGS)
++
++# C compiler flags
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++               $(INCLUDES) 
++
++## C++ compiler
++## This part defines C++ compiler information
++
++# C++ compiler executable
++CCC=g++
++
++# C++ compiler ANSI/NON-ANSI flags
++ANSI_C_PLUS_FLAG=-ansi
++NON_ANSI_C_PLUS_FLAG=-traditional-cpp
++C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
++
++# This variable specifies how to compile the C code. If it is set to C,
++# that indicates that C code will be compiled with the C++ compiler.
++# Otherwise it will be compiled with C compiler.
++EXT=c
++
++# C++ compiler flags
++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++        $(INCLUDES)
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++                 $(DEFINES) $(INCLUDES)
++# C++FLAGS_RELAXED should be set to avoid warnings reported by third party
++# source code that is not maintained by PDB
++C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
++        $(INCLUDES)
++
++## Fortran compiler
++## This part defines Fortran compiler information
++
++# Fortran compiler executable
++F77=gfortran
++
++# Fortran compiler flags
++FFLAGS=$(F_OPT)
++
++# Additional Fortran libraries
++F77LIBS=
++
++#------------------------------------------------------------------------#
++
++#-----Linkers section----------------------------------------------------#
++
++# Static linking option. If not defined, dynamic linking is used.
++STATIC_LINKING=-static
++
++# Linker flags
++LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC=$(ABI) -w
++
++# Fortran linker
++F77_LINKER=gfortran
++
++#------------------------------------------------------------------------#
++
++#-----Archiver section---------------------------------------------------#
++
++# Archiver executable
++AR=ar
++
++# Archiver flags
++AR_GETFLAGS=xv
++AR_PUTFLAGS=rcvs
++
++#------------------------------------------------------------------------#
++
++#-----Ranlib-------------------------------------------------------------#
++
++RANLIB=true
++
++#------------------------------------------------------------------------#
++
++#-----Installer----------------------------------------------------------#
++
++INSTALL=../etc/cifinstall
++INSTALLOPTS=-m 0444 
++
++#------------------------------------------------------------------------#
++
++#-----Stripper-----------------------------------------------------------#
++
++STRIP=strip
++
++#------------------------------------------------------------------------#
++
++#-----Shell--------------------------------------------------------------#
++
++SHELL=/bin/sh
++
++#------------------------------------------------------------------------#
+diff -urN -x make.log -x Makefile.platform cifparse-obj-v6.302-prod-src.orig/etc/platform.sh cifparse-obj-v6.302-prod-src/etc/platform.sh
+--- cifparse-obj-v6.302-prod-src.orig/etc/platform.sh	2005-04-26 06:12:57.000000000 -0700
++++ cifparse-obj-v6.302-prod-src/etc/platform.sh	2005-12-18 22:50:21.000000000 -0800
+@@ -47,23 +47,31 @@
+     ;;
+ 
+     Linux)
+-#     Check if it is GCC version 3.x
+-      gcc_ver=`gcc --version | grep -e " 3\."`
++#     Check if it is GCC version 4.x
++      gcc_ver=`gcc --version | grep -e " 4\."`
+       if [[ -z $gcc_ver ]]
+       then
+-#     It is not GCC version 3.x. Check if it is GCC version 2.x
+-        gcc_ver=`gcc --version | grep -e "2\."`
++#       It is not GCC version 4.x. Check if it is GCC version 3.x
++        gcc_ver=`gcc --version | grep -e " 3\."`
+         if [[ -z $gcc_ver ]]
+         then
+-#         It is not GCC version 2.x either. Production can not be compiled.
+-          sysid="unknown"
++#         It is not GCC version 3.x. Check if it is GCC version 2.x
++          gcc_ver=`gcc --version | grep -e "2\."`
++          if [[ -z $gcc_ver ]]
++          then
++#           It is not GCC version 2.x either. Production can not be compiled.
++            sysid="unknown"
++          else
++#           It is GCC version 2.x
++            sysid="gnu2"
++          fi
+         else
+-#         It is GCC version 2.x
+-          sysid="gnu2"
++#         It is GCC version 3.x
++          sysid="gnu3"
+         fi
+       else
+-#       It is GCC version 3.x
+-        sysid="gnu3"
++#       It is GCC version 4.x
++        sysid="gnu4"
+       fi
+     ;;
+ 
+diff -urN -x make.log -x Makefile.platform cifparse-obj-v6.302-prod-src.orig/Makefile cifparse-obj-v6.302-prod-src/Makefile
+--- cifparse-obj-v6.302-prod-src.orig/Makefile	2005-04-26 06:12:57.000000000 -0700
++++ cifparse-obj-v6.302-prod-src/Makefile	2005-12-18 22:50:21.000000000 -0800
+@@ -54,7 +54,7 @@
+ 		echo "------------------------------------------------------------"; \
+ 		echo "**** Making $$libdir ****"; \
+ 		echo "------------------------------------------------------------"; \
+-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
++		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" install) || exit 1; \
+ 	done
+ 
+ debug:
diff --git a/sci-libs/cifparse-obj/metadata.xml b/sci-libs/cifparse-obj/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-libs/cifparse-obj/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>