gentoo auto-resync : 13:06:2024 - 00:08:29

10 files changed, 0 insertions, 271 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 34d6d0622e3a..6508ad88c14e 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest
deleted file mode 100644
index a2f370898cec..000000000000
--- a/sci-libs/cifparse-obj/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX cifparse-obj-7.025-gcc5_6.patch 524 BLAKE2B 5cf4ce9f5c0615636b5701cd64613e01f0ac130ba4166fd12a8b92d7ffffc368fd5666ebdd8ac9cd983359a97ed4294e6f66e0984b3c826c56ecfa8b130cadef SHA512 f2469b15eb74192b61b78c165249e8b953c58d0f7478d38f1bebf8c2c884e95ad42ba18af23b1ea7e4915979b5d4f70c2637e083a14a2c40e20f83a09acf616e
-AUX cifparse-obj-7.105-makefile.patch 3790 BLAKE2B 11372dceab4e570e420bf639020769a1b1fb6f956a4ff75befcbb0016053d616cf271946ae0e6bb5667dffef863baa246f75fc34d36e80ddeb7e7c17a5befae7 SHA512 310f13e88f7dfb19ac2bdc003a2ab2f095583a90694d27232c1ab15a298bc88313e89590e062274da10d5eaba53f6bfcb3341d1d4f7d1c388520c75643364d61
-DIST cifparse-obj-v7.105-prod-src.tar.gz 931151 BLAKE2B c362fc528e0c88b41ef8433c6d0235ae0bd4055c8c1704d2f1be8ba8aa27a7526b3d19172f2a4ffda79c323140a54dcb2b0a2eb78f30780473c9bcfb2ab6c6f9 SHA512 d626aa055bdd6762eda4b5b04121f37fff3bc09460b12cd6cb80566545d23e5c08a8ad54fa184076932d2cff38aa9d91fa659fbe9a70d4a07b8b1677c28549f4
-EBUILD cifparse-obj-7.105.ebuild 1130 BLAKE2B ede8f1375068721147fd6628b4c3b7e16ed41a97df1d4a5403563e392499fa04a0a18b54371072beabb9a5df62632c8972fa053b801726874ec776007c58ffd5 SHA512 4e5529e47d5d40f0faa9f43341c234f6d228be6eeaeafba78da75b4ecb0c21e7ad602921cd5ebb0513e1c2a6c48ae205ee100944256474f8f90797b437ec8b24
-MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild
deleted file mode 100644
index 84c808a677e9..000000000000
--- a/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit 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/source/${MY_P}.tar.gz"
-
-LICENSE="PDB"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE=""
-
-RDEPEND=""
-DEPEND="
-	app-alternatives/yacc
-	app-alternatives/lex"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${PN}-7.025-gcc5_6.patch
-)
-
-src_prepare() {
-	default
-
-	sed \
-		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
-		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
-		-e "s:^\(F77=\).*:\1${FORTRANC}:g" \
-		-e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \
-		-e "s:-static::g" \
-		-i "${S}"/etc/make.* || die "Failed to fix makefile"
-}
-
-src_compile() {
-	# parallel make fails
-	emake -j1 \
-		C_OPT="${CFLAGS}" \
-		CXX_OPT="${CXXFLAGS}"
-}
-
-src_install() {
-	dolib.a lib/*
-	insinto /usr/include/${PN}
-	doins include/*
-}
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch
deleted file mode 100644
index 2ac0ec220d9e..000000000000
--- a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- etc/platform.sh | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/etc/platform.sh b/etc/platform.sh
-index ff0ab51..1b56ab1 100755
---- a/etc/platform.sh
-+++ b/etc/platform.sh
-@@ -60,7 +60,7 @@ case `uname -s` in
- #   Check if it is a Linux platform
-     Linux)
- #     Check if it is GCC version 4.x
--      gcc_ver=`gcc --version | grep -e " 4\."`
-+      gcc_ver=`gcc --version | grep -e " [456]\."`
-       if [[ -z $gcc_ver ]]
-       then
- #       It is not GCC version 4.x. Check if it is GCC version 3.x
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch
deleted file mode 100644
index 1716cd6390a4..000000000000
--- a/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch
+++ /dev/null
@@ -1,110 +0,0 @@
- etc/make.platform.gnu3 | 14 +++++++-------
- etc/make.platform.gnu4 | 16 ++++++++--------
- 2 files changed, 15 insertions(+), 15 deletions(-)
-
-diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
-index 54b0297..138fa47 100644
---- a/etc/make.platform.gnu3
-+++ b/etc/make.platform.gnu3
-@@ -107,8 +107,8 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \
-+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \
-   $(DEFINES) $(INCLUDES) 
- 
- ## C++ compiler
-@@ -128,14 +128,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-   $(DEFINES) $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
-+C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(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) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
-+C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
-    $(DEFINES) $(INCLUDES)
- 
- ## Fortran compiler
-@@ -145,7 +145,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -158,7 +158,7 @@ F77LIBS=
- STATIC_LINKING=-static
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
- LDFLAGS_NO_STATIC=$(ABI) -w
- 
- # Fortran linker
-diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
-index 6676f35..51681fa 100644
---- a/etc/make.platform.gnu4
-+++ b/etc/make.platform.gnu4
-@@ -107,11 +107,11 @@ NON_ANSI_C_FLAG=
- C_WARNINGS=$(WARNINGS)
- 
- # C compiler flags
--CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
--CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
-+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
-+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
- 
- ## C++ compiler
--## This part defines C++ compiler information
-+
- 
- # C++ compiler executable
- CCC=g++
-@@ -127,14 +127,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
- EXT=C
- 
- # C++ compiler flags
--C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-+C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
-   $(DEFINES) $(INCLUDES)
--C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
-+C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(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) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
-+C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
-   $(DEFINES) $(INCLUDES)
- 
- ## Fortran compiler
-@@ -144,7 +144,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
- F77=f77
- 
- # Fortran compiler flags
--FFLAGS=-O -u
-+FFLAGS=$(F_OPT)
- 
- # Additional Fortran libraries
- F77LIBS=
-@@ -157,7 +157,7 @@ F77LIBS=
- STATIC_LINKING=-static
- 
- # Linker flags
--LDFLAGS=$(ABI) -w $(STATIC_LINKING)
-+LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
- LDFLAGS_NO_STATIC=$(ABI) -w
- 
- # Fortran linker
diff --git a/sci-libs/cifparse-obj/metadata.xml b/sci-libs/cifparse-obj/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-libs/cifparse-obj/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/libghemical/Manifest b/sci-libs/libghemical/Manifest
deleted file mode 100644
index 12a3d071edfc..000000000000
--- a/sci-libs/libghemical/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX libghemical-2.98-gl.patch 402 BLAKE2B 6b2bf88b489bb99d2c851025c57941788eaecef9abcb623c4ac66c1090d862ad4623223e0ea99706d4079c1caf6591092e16b3d244275e2cb57f8c8f5731feec SHA512 bf0fee685f2f10f467d92f86db3dea47879651335c6966757e69bf7bac1f9a6ee18bd22c9a61f01ca1babc5c7e14cfc3caba382af764fd1a418ee70e32e2b1a6
-DIST libghemical-3.0.0.tar.gz 787947 BLAKE2B ea0bf4c8f257df3d22d5efdede83cea1ad2239692e98c87cdb44c7da3352956d5bc21c2c92f6ab8759cf6b8cad2d6041cb49d4532234ba8ff2d323db583c7d48 SHA512 71531e7bd72a7fa063dd35536a346f15e3c0fd0284112fa2f304580204b93552bd0c9a426cee22044b5dd1662e34e5d191d20af938e474561fe55f2394e7519e
-EBUILD libghemical-3.0.0.ebuild 802 BLAKE2B 45cd825b442247105150a05a85a523372e0ed6d3525251d01115bc6c95b45282592939d06bcb57da7ef044f8d766dcc6ddf3990dcba3413d83381228b05a55d9 SHA512 c5e55d1ea0ddcbc7a896191850835e42c763f6dfc671d806fb80b80449f2d8900a5822e933a54e0e4099d46bf91bc4628db7dbefe51cd04a46ddc5bd29689420
-MISC metadata.xml 892 BLAKE2B f130fdb96717717021a6a5b9d4313e06c96dfeff1a488abeaac379913e4de831ff9c652fc9fdf912c049a4bf211184e120811010570f2328d8a241209a1dfd94 SHA512 6ab95718eec65e26ee2c6c5b7e97cbd93ae3415796f9230c17b07b87572066021fae60182d1bf62ceb6a9bbb8d5f2f6cc06cff292bd80735c2c0f524f4100835
diff --git a/sci-libs/libghemical/files/libghemical-2.98-gl.patch b/sci-libs/libghemical/files/libghemical-2.98-gl.patch
deleted file mode 100644
index 8cea8aab636e..000000000000
--- a/sci-libs/libghemical/files/libghemical-2.98-gl.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-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/libghemical-3.0.0.ebuild b/sci-libs/libghemical/libghemical-3.0.0.ebuild
deleted file mode 100644
index de7e0299a0dc..000000000000
--- a/sci-libs/libghemical/libghemical-3.0.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-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"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.98-gl.patch )
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--enable-shared \
-		$(use_enable mopac7) \
-		$(use_enable mpqc) \
-		$(use_enable static-libs static)
-}
diff --git a/sci-libs/libghemical/metadata.xml b/sci-libs/libghemical/metadata.xml
deleted file mode 100644
index d7bc678f012b..000000000000
--- a/sci-libs/libghemical/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  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.
-  </longdescription>
-  <use>
-    <flag name="mopac7">Use <pkg>sci-chemistry/mopac7</pkg> for semi-empirical
-    calculations</flag>
-    <flag name="mpqc">Use <pkg>sci-chemistry/mpqc</pkg> for quantum-mechanical
-    calculations</flag>
-  </use>
-</pkgmetadata>