gentoo auto-resync : 07:12:2024 - 02:07:26

7 files changed, 0 insertions, 192 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index dfb62c2bb500..7c72c445ba81 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/molden/Manifest b/sci-chemistry/molden/Manifest
deleted file mode 100644
index 3a4aa389e311..000000000000
--- a/sci-chemistry/molden/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX molden-6.9-ldflags.patch 3244 BLAKE2B d5ddd71bade94310d9aaebb71c49dd138af46abbf65069920cfdc3b204cdb7fe21ce049bed90faeaf23da3ec5b9a1121bcab97d012e9ff8af9abdf5619953299 SHA512 2a8235c1bd07aff5ce9fb79d5a6b09353c63bb9fc157d7fe1ada397e567018f3052286a93a04df13573f2e561a6c1e302ee91822338c024e70654ce7dec488bd
-DIST molden6.9.tar.gz 8536291 BLAKE2B f50fd9c6303d215f3b1ea73136a8ecada07102a33cfc5831c412341731d00bd166f59bc260615d4a96c59d50a6a308087f02b637f8a8d36bf19f256ac407ba72 SHA512 dbb4a602f2957d0b1d5afb8748fb8ad012a41fb0dfa816b78e4d2748ea78ee39251846a549fce4b276641d4838a336ecd9cf02b92fcf9739adeb25bb550656ec
-EBUILD molden-6.9-r1.ebuild 1491 BLAKE2B b01b98c504dd7de6ae74864f6ad62b67fc36a0c802295db9e125626c3abb88c028451750bc175de6a9a4b999c91ad87e4c4a157ce446eb8fc95def9154b9e719 SHA512 7d1b31962697cefebb8b43e50bf0bbf59cbd775e19e2563205c7f8f74f06e2a8f92c7e144350a84339d2c5a666c13f6aab6ba7748b4309162b1685649b6a3a20
-MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/molden/files/molden-6.9-ldflags.patch b/sci-chemistry/molden/files/molden-6.9-ldflags.patch
deleted file mode 100644
index 9e8258aeacd7..000000000000
--- a/sci-chemistry/molden/files/molden-6.9-ldflags.patch
+++ /dev/null
@@ -1,87 +0,0 @@
-diff --git a/makefile b/makefile
-index f71a20df..564f9f4e 100644
---- a/makefile
-+++ b/makefile
-@@ -299,11 +299,11 @@ src/xwin.o:	src/xwin.c src/rots.h
- src/xwingl.o:	src/xwin.c src/rots.h
- 
- molden:	$(OBJS) src/mpdum.o src/xwin.o 
--	$(LDR) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS)
-+	$(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpdum.o src/xwin.o $(LIBS)
- 	mv molden bin/molden
- 
- gmolden:	$(OBJS) src/mpdum.o src/xwingl.o 
--	$(LDR) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG)
-+	$(LDR) $(LDFLAGS) -fno-builtin -o gmolden $(OBJS) src/mpdum.o src/xwingl.o $(LIBSG)
- 	mv gmolden bin/gmolden
- 
- ambfor/ambfor:	src/ambfor/*.f src/ambfor/*.c
-@@ -322,14 +322,14 @@ surf/surf:	src/surf/*.h src/surf/*.c
- # noxwin will not work as long as the old ocglbck calls arent in dummys
- 
- noxwin:	$(OBJS) $(DOBJ) src/mpdum.o
--	$(LDR) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm
-+	$(LDR) $(LDFLAGS) -o molden $(OBJS) $(DOBJ) src/mpdum.o -lm
- 	mv molden bin/molden.noxwin
- 
- # This version allows the fitting of multipole moments to the electrostatic
- # pontential
- 
- molden.mpfit:	$(OBJS) src/mpolefit.o src/xwinmp.o
--	$(LDR) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS)
-+	$(LDR) $(LDFLAGS) -o molden $(OBJS) src/mpolefit.o src/xwinmp.o $(LIBS)
- 	mv molden bin/molden.mpfit
- 
- src/xwinmp.o:	src/xwin.c
-@@ -340,18 +340,18 @@ src/xwingl.o:	src/xwin.c
- 	$(CC) $(CFLAGS) -DDOGL -c src/xwin.c -o src/xwingl.o
- 
- unmullik:	src/unmullik.o
--	$(LDR) -o bin/unmullik src/unmullik.o
-+	$(LDR) $(LDFLAGS) -o bin/unmullik src/unmullik.o
- 
- # short_wrl removes redundant vertices from molden's VRML2 files
- # with the courtesy of Andreas Klamt of COSMOSlogic
- #
- short_wrl:	src/short_wrl.o
--	$(LDR) -o bin/short_wrl src/short_wrl.o
-+	$(LDR) $(LDFLAGS) -o bin/short_wrl src/short_wrl.o
- 
- # conversion of CADPAC output to molden format
- 
- cad2mol:	src/cad2mol.o
--	$(LDR) -o bin/cad2mol src/cad2mol.o
-+	$(LDR) $(LDFLAGS) -o bin/cad2mol src/cad2mol.o
- 
- clean:
- 	rm -f src/$(OBJS) src/mpdum.o src/xwin.o src/xwingl.o bin/molden bin/gmolden bin/ambfor bin/ambmd bin/surf src/ambfor/*.o src/surf/*.o
-diff --git a/src/ambfor/makefile b/src/ambfor/makefile
-index 9938527e..5de7c65e 100644
---- a/src/ambfor/makefile
-+++ b/src/ambfor/makefile
-@@ -50,10 +50,10 @@ mpi:	FFLAGS = -c -g -ffast-math -funroll-loops -O3
- mpi:	ambfor.mpi ambmd.mpi
- 
- ambfor:	ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS)
--	$(LDR) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS)
-+	$(LDR) $(LDFLAGS) -o ambfor ambfor.o qvdw.o alloc.o optimise.o lbfgs.o $(OBJS) $(LIBS)
- 
- ambmd:	md.o verlet.o qvdw.o allocmd.o $(OBJS)
--	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
-+	$(LDR) $(LDFLAGS) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
- 
- ambfor.o:	ambfor.f
- 	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
-diff --git a/src/surf/Makefile b/src/surf/Makefile
-index 54b7af8e..f216c9eb 100644
---- a/src/surf/Makefile
-+++ b/src/surf/Makefile
-@@ -25,7 +25,7 @@ OBJS        = surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \
- 
- # make objects
- surf: $(OBJS) Makefile 
--	$(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE)
-+	$(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) $(LDFLAGS)
- 
- lint:
- 	lint $(INCLUDE) $(SRCS)
diff --git a/sci-chemistry/molden/metadata.xml b/sci-chemistry/molden/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/molden/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/molden/molden-6.9-r1.ebuild b/sci-chemistry/molden/molden-6.9-r1.ebuild
deleted file mode 100644
index 39ad93accf73..000000000000
--- a/sci-chemistry/molden/molden-6.9-r1.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit desktop fortran-2 flag-o-matic toolchain-funcs
-
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac"
-HOMEPAGE="https://www.theochem.ru.nl/molden/"
-SRC_URI="ftp://ftp.science.ru.nl/pub/Molden/${MY_P}.tar.gz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="MOLDEN"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="opengl"
-
-DEPEND="
-	x11-libs/libXmu
-	opengl? (
-		media-libs/freeglut
-		virtual/opengl
-		virtual/glu
-	)
-"
-RDEPEND="${DEPEND}
-	sci-chemistry/surf
-"
-
-PATCHES=(
-	"${FILESDIR}/${P}-ldflags.patch"
-)
-
-src_prepare() {
-	default
-	sed 's:shell g77:shell $(FC):g' -i makefile || die
-}
-
-src_compile() {
-	local args=()
-
-	# Use -mieee on alpha, according to the Makefile
-	use alpha && append-flags -mieee
-
-	# GCC 10 workaround
-	# bug #724556
-	append-fflags $(test-flags-FC -fallow-argument-mismatch)
-
-	args=(
-		CC="$(tc-getCC) ${CFLAGS}"
-		FC="$(tc-getFC)"
-		LDR="$(tc-getFC)"
-		FFLAGS="${FFLAGS}"
-	)
-
-	einfo "Building Molden..."
-	emake -j1 molden ambfor/ambfor ambfor/ambmd "${args[@]}"
-	if use opengl ; then
-		einfo "Building Molden OpenGL helper..."
-		emake -j1 "${args[@]}" gmolden
-	fi
-}
-
-src_install() {
-	dobin bin/molden bin/ambfor bin/ambmd
-	if use opengl; then
-		dobin bin/gmolden
-		doicon -s 64 haux/gmolden.png
-		make_desktop_entry gmolden MOLDEN gmolden
-	fi
-
-	dodoc HISTORY README REGISTER
-	cd doc || die
-	uncompress * && dodoc *
-}
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 14721b14d7ae..483bb56c226e 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,3 @@
-AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f
 AUX pymol-3.0.0-SceneGetDrawFlag-indexing.patch 821 BLAKE2B c854aa49441b308ab7f12265442961ddeb3633b71234bd554d45c3950c3ddcf457ac98e0aa1d226ec7ee3abbd2d0207cce97e40144cb81992f241c3a964b1bcc SHA512 326e04f988ff585a062a342b9553ab6b074102c0599b210a5dfa769cb8841e1619e74b670a2d673a80b81c5a9218e052829e0cc574049a1363741e762cac59e7
 AUX pymol-3.0.0-distutils-py3.12.patch 2620 BLAKE2B 802ef75cf22b408ff8e280c561f4954f7f4d816887107f8db36b85988c345948e7d2cfe97b099cb79794d61d3594666e12f90a64c1f0af2206458ade776a1a2b SHA512 3911207f1a03b19675105cd707d644e76258aa9ab58be3891833873d41b460f6161ac83d495a6bc58bf281831376d17186083d447269d755d2e69ee78e6fc5c2
 AUX pymol-3.0.0-eof-maeffplugin.patch 1071 BLAKE2B b28941bd3fddb534fe150b3d98ef6a17058b25b59717a15ca9a807812f05d98f3f7b2cedee9230eab0465c493bbf375325259260bb1cd0d03beafbb4a8f306d0 SHA512 b39846fa9b3b90d5952f22fdde323039bd09a5c43abdd7975bc72880854f22ae39a0d3d30a6640e98c6d7e8734306e00af3fdae555a4292e48ad7b46a83753f8
diff --git a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch b/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
deleted file mode 100644
index 080e5e8960e4..000000000000
--- a/sci-chemistry/pymol/files/pymol-2.5.0-format-security.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Michael Banck <mbanck@debian.org>
-Description: Fix "error: format not a string literal and no format arguments [-Werror=format-security]" (#759860)
-Forwarded: yes
-
---- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
-+++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
-@@ -2004,7 +2004,7 @@ namespace {
-       }
-     }
-     catch (std::exception &e) {
--      fprintf(stderr, "%s", e.what());
-+      fprintf(stderr, "Cannot write timestamp to mae file: %s\n", e.what());
-       return MOLFILE_ERROR;
-     }
-     return MOLFILE_SUCCESS;