gentoo resync : 25.08.2020

8 files changed, 0 insertions, 297 deletions

diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest
deleted file mode 100644
index 483d19fd9cfe..000000000000
--- a/sci-chemistry/sparky/Manifest
+++ /dev/null
@@ -1,8 +0,0 @@
-AUX 3.115-fix-c++14.patch 849 BLAKE2B fde4158bf18e4cba23e0bb93972b10236e88e8cd3db055b81e328ff2fbddd38c8f6a051525e949b237adebd7a534aaa7639863aa17c3536fe35387e930ca5806 SHA512 80bbfe8a2e853f8be84ed48da99605805a42bb05b091c851ddbefb5513745cdf51c5396e97ad4e3be7dd199270fb069e239e0c24f6642d956fd6571d8b14a7e1
-AUX 3.115-ldflags.patch 2713 BLAKE2B 26873b508c9b0ecd5122712b8e599393bdf1787e9608b4e7e451d1db95ba2831af42e8f9d2637181f21e3206689bd115601fdcb7b48c0011cc30a83037bec087 SHA512 1c439cc04af3e8e403257ccd45eecb16f0e36d4b51a28ab5ddda269bde271d23a20bb453cda48e03f58c31a9a614d4b19ca2b6aa7f75bdfec1f79b70e8c361de
-AUX 3.115-makefile.patch 580 BLAKE2B 4beeca38c910e583235d2aef66137165fe4ae58f48591e4567f50a1d702ea0391e467dd6f4baab4019a05a8b5051329b0485fc1cc56a38c6bfcbd53a06034a09 SHA512 9ddd99de93656301f307aabb3284e86fe68f4c7957f0b5ff81da4615f850fc36b686908de84816f0ff8a3d75169ccd0d4d7cb5bb8afd88d96c913f766e7ee19a
-AUX 3.115-paths.patch 415 BLAKE2B 9e959f54626f3eb34e963a571cb9a92e92f87af4fd593972490dc3bf299ba8b9e42a47768f78ea8463f0fb1c76274ec334be8f4d5b1e52d339aa90eec7b7dd19 SHA512 44c44c99cf2c5c51c8e506267efc4efc50eb2277ccdab362943da0c45c63f9e797ae699e99eda3ce6ca0b4e0a886393d1917ce8614eea3086e97446fc3c0c674
-AUX 3.115-wrapper-r1.patch 1518 BLAKE2B a5dd56c76a36f1a1e67599b1dcb25ba9f8edd639220d9f3c248d64b7bee88a108482137ec70acb5ee466048abf5939122842ae827ffba23dcef7c895dbf20f56 SHA512 be2c18a40ceabdb1c25a7849e1ee00438092f264c486e93b3bfb412fc417902a3b22b672d28a6cc104fedc5477ea2c0de66bc40dd5d4d607ed0201eee4d368a7
-DIST sparky-source-3.115.tar.gz 4103686 BLAKE2B c7811aa135b10f21b8807447e2ab173f407ccc1446ff1307006f7f885e6e69983647991600720e02e4e738bb68338de01bc5d57577eacf20298db6d53a54b183 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89
-EBUILD sparky-3.115-r2.ebuild 3192 BLAKE2B 172ded57706c8aac3a4f9d268fd75f410d35dffc9c26352695c3961c2508dc08773e3a9c857d530ab47341ac3977daac78939661d14c8334da4eadba7852e610 SHA512 f2f5fe11666e85feca9d90c5fb6c9d93f42b9bde269f311a943c37b334d617d7dcdbc5ee45cb555fb6af278a648c0c0ab4ec28027143675ee0cc2c77dc41c10a
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/sparky/files/3.115-fix-c++14.patch b/sci-chemistry/sparky/files/3.115-fix-c++14.patch
deleted file mode 100644
index 3a05ea7d85ce..000000000000
--- a/sci-chemistry/sparky/files/3.115-fix-c++14.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Fix the custom new/new[] operators in order to account for changed
-noexcept semantics in C++11.
-See also: https://bugs.gentoo.org/show_bug.cgi?id=596012
-
-Patch by Peter Levine
-
---- a/c++/memalloc.cc
-+++ b/c++/memalloc.cc
-@@ -39,7 +39,10 @@
- 
- // ----------------------------------------------------------------------------
- //
--void *operator new(size_t size) throw(std::bad_alloc)
-+void *operator new(size_t size)
-+#if __cplusplus < 201103L
-+throw(std::bad_alloc)
-+#endif
- {
-   void *value = allocate(size);
-   if (tracking_memory)
-@@ -72,7 +75,10 @@
- 
- // ----------------------------------------------------------------------------
- //
--void *operator new[](size_t size) throw(std::bad_alloc)
-+void *operator new[](size_t size)
-+#if __cplusplus < 201103L
-+throw(std::bad_alloc)
-+#endif
- {
-   void *value = allocate(size);
-   if (tracking_memory)
diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch
deleted file mode 100644
index bd4020387682..000000000000
--- a/sci-chemistry/sparky/files/3.115-ldflags.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/c++/Makefile b/c++/Makefile
-index aeb4daa..5cab356 100644
---- a/c++/Makefile
-+++ b/c++/Makefile
-@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
- 	chmod 755 $@
- 
- sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
--	$(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS)
- 
- ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS)
--	$(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS)
--	$(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
-+	$(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
- 
- spy.so: python.o $(SPARKY_OBJS)
--	$(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS)
- 
- winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc
- 	$(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc
-@@ -161,7 +161,7 @@ python.o: python.cc
- 	$(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
- 
- _tkinter.so: _tkinter.o
--	$(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS)
-+	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS)
- 
- _tkinter.o: _tkinter.c
- 	$(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c
-@@ -188,8 +188,8 @@ PYLDFLAGS	= -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION)
- PYIFLAGS	= -I$(PYTHON_INC)
- 
- debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS)
--	$(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
--		$(LDFLAGS) $(PYLDFLAGS) $(LDLIBS)
-+	$(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
-+		$(PYLDFLAGS) $(LDLIBS)
- 
- main-debug.o: main-debug.cc
- 	$(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc
diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch
deleted file mode 100644
index 7c810dcbd8ae..000000000000
--- a/sci-chemistry/sparky/files/3.115-makefile.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/Makefile b/Makefile
-index bb27034..30979bd 100644
---- a/Makefile
-+++ b/Makefile
-@@ -48,6 +48,12 @@ TKINTER_PYMOD	= _tkinter$(PYMOD_SUFFIX)
- all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
- 	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
- 
-+libraries:
-+	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD)
-+
-+binaries:
-+	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky
-+
- Makefile.dep TAGS: force
- 	cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
- 
diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch
deleted file mode 100644
index 20d9a801ecd6..000000000000
--- a/sci-chemistry/sparky/files/3.115-paths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/c++/paths.h b/c++/paths.h
-index 2a21366..38aff52 100644
---- a/c++/paths.h
-+++ b/c++/paths.h
-@@ -19,7 +19,7 @@
- // Installation subdirectories and files
- //
- #define SPARKY_MANUAL		"manual"
--#define SPARKY_LIB		"lib"
-+#define SPARKY_LIB		"."
- #define SPARKY_PRINT		"print-prolog.ps"	// under lib directory
- #define SPARKY_RESOURCE		"Sparky"		// under lib directory
- #define SPARKY_SAMPLE_DATA	"example"
diff --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
deleted file mode 100644
index d83b5b8510cc..000000000000
--- a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/bin/sparky b/bin/sparky
-index 8b51212..270723a 100644
---- a/bin/sparky
-+++ b/bin/sparky
-@@ -4,18 +4,6 @@
- #
- 
- # -----------------------------------------------------------------------------
--# Figure out Sparky installation directory from $0.
--#
--set sparky_exe = "$0"
--while (-l "$sparky_exe")
--  set ls_sparky_exe = `ls -l "$sparky_exe"`
--  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
--end
--set sparky_bin = `dirname "$sparky_exe"`
--set sparky_bin = `cd "$sparky_bin"; pwd`
--set sparky_inst = `dirname "$sparky_bin"`
--
--# -----------------------------------------------------------------------------
- # Sparky uses the SPARKY_INSTALL environment variable to find its
- # application resource file and print prolog file.
- #
-@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL		"$sparky_inst"
- # If Python is available start Sparky as a Python extension.
- # Otherwise the standalone version of Sparky is started.
- #
--set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5"
-+set PYTHON = GENTOO_PYTHON
- if (! -e "$PYTHON") then
-   set PYTHON = python2.5
- endif
-@@ -79,7 +67,7 @@ if ($status == 0) then
-   # ---------------------------------------------------------------------------
-   # Add the Sparky package and Tkinter to the Python path
-   #
--  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk"
-+  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky"
-   if ($?PYTHONPATH) then
-     setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH"
-   else
diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/sparky/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://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/sparky/sparky-3.115-r2.ebuild b/sci-chemistry/sparky/sparky-3.115-r2.ebuild
deleted file mode 100644
index e664747fea13..000000000000
--- a/sci-chemistry/sparky/sparky-3.115-r2.ebuild
+++ /dev/null
@@ -1,117 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit flag-o-matic prefix python-single-r1 toolchain-funcs
-
-DESCRIPTION="Graphical NMR assignment and integration program for large polymers"
-HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/"
-SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz"
-
-LICENSE="sparky"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
-	app-shells/tcsh
-	dev-lang/tcl:0=
-	dev-lang/tk:0="
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${PN}"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-wrapper-r1.patch
-	"${FILESDIR}"/${PV}-paths.patch
-	"${FILESDIR}"/${PV}-makefile.patch
-	"${FILESDIR}"/${PV}-fix-c++14.patch
-)
-
-pkg_setup() {
-	python-single-r1_pkg_setup
-	TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-	PYVER=${EPYTHON#python}
-}
-
-src_prepare() {
-	default
-
-	sed -i \
-		-e "s:^\(set PYTHON =\).*:\1 ${PYTHON}:g" \
-		-e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \
-		-e "s:tcl8.4:tcl${TKVER}:g" \
-		-e "s:tk8.4:tk${TKVER}:g" \
-		-e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \
-		"${S}"/bin/sparky || die
-	eprefixify "${S}"/bin/sparky
-}
-
-src_compile() {
-	emake \
-		SPARKY="${S}" \
-		PYTHON_VERSION="${PYVER}" \
-		PYTHON_PREFIX="${EPREFIX}/usr" \
-		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
-		PYTHON_INC="$(python_get_includedir)" \
-		TK_PREFIX="${EPREFIX}/usr" \
-		TCLTK_VERSION="${TKVER}" \
-		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
-		CXX="$(tc-getCXX)" \
-		CC="$(tc-getCC)" \
-		LDSHARED="-shared" \
-		binaries
-
-	rm c++/*.o || die
-
-	emake \
-		SPARKY="${S}" \
-		PYTHON_VERSION="${PYVER}" \
-		PYTHON_PREFIX="${EPREFIX}/usr" \
-		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
-		PYTHON_INC="$(python_get_includedir)" \
-		TK_PREFIX="${EPREFIX}/usr" \
-		TCLTK_VERSION="${TKVER}" \
-		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
-		CXX="$(tc-getCXX)" \
-		CC="$(tc-getCC)" \
-		CXXFLAGS="${CXXFLAGS} -fPIC" \
-		CFLAGS="${CFLAGS} -fPIC" \
-		LDSHARED="-shared -fPIC" \
-		libraries
-}
-
-src_install() {
-	# The symlinks are needed to avoid hacking the complete code to fix the locations
-	dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN}
-
-	insinto /usr/share/${PN}/
-	doins lib/{print-prolog.ps,Sparky}
-	dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps
-	dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky
-
-	python_moduleinto ${PN}
-	python_domodule python/*.py c++/{spy.so,_tkinter.so}
-	dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python
-
-	rm manual/{pkzip.cfg,Makefile} || die
-	mv {manual/,}manual.ps || die
-	local DOCS=( README manual.ps )
-	local HTML_DOCS=( manual/. )
-	einstalldocs
-	newdoc python/README README.python
-	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual
-
-	if use examples; then
-		dodoc -r example
-		dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example
-	fi
-}