gentoo resync : 25.08.2020

7 files changed, 0 insertions, 316 deletions

diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest
deleted file mode 100644
index 18b6162cbafa..000000000000
--- a/sci-chemistry/eden/Manifest
+++ /dev/null
@@ -1,7 +0,0 @@
-AUX 5.3-makefile-fixes.patch 1647 BLAKE2B ead9023a9ae4c2a94a22de4ff5ef97f89b7602e914ebcc0a3295eb53a3cdf25639d9c8d74b14b9f75f2c5009812b8a23afd51432accfa2daec80484e4b5c4a49 SHA512 3ec4f8ba8d3b600b729bfb32cef3fb1f82a1f51a485ebab143e01052ea1487a78c3395c902079fe0e5d5c3df8a2a83b2ce4d37d823e1d89426087874ec47391d
-AUX eden-5.3-format-security.patch 3202 BLAKE2B a548dbb384d497a07806bcf9e25141d07a75a0381802b080eec02f14b6018e66c7d5b2a4c0caefc679d43736e15c4b00e460a82e3d40e65188a364d28469bde3 SHA512 01e100fe5481a73de2efa6652fe38c19337eae0dc13557ef0ad3e3a4f186becbfb8831aece0a619c08541e1a667e999c47b28438ec431f056c44f12849662c12
-AUX eden-5.3-impl-dec.patch 899 BLAKE2B 667a43677ff28192277ad3e259aa093ca03a05aa55bde0a175885823d2e48ddc64989c72e2c47884ff22c840addd87df9ea5925eeb6f20397be403f0e92cf44e SHA512 e89f1e0c028099e305a79befa558a86bc47d050c1e30394178999c7a1568bae9c3e525953bf152888690e0e1607dd72c522d2995f45b1eccfb9f7bf75e7866c2
-AUX makefile-fixes.patch 837 BLAKE2B fc20ba8c98e333b90bc3e028d572810fabe6305ec929a52aab5c4491b80fd370a604729ae29b22d078e872693fcab3e7d84f82524f29c09be74c8b41c128ec2f SHA512 818fe1d23fa940cb533afcb9e84bdc5c719651005136304ca66d368fc21cf4d7a1facb0a383c9689ab1658632cec30969322fdffccadae941a754900542237e7
-DIST eden_V5.3.tar.gz 1139981 BLAKE2B 237f054accbba72fcde3a43716915a8037412a26aee861839c4a6e404276126a3955e6e0a3c76078b2253658f3ab9bcf8ad628bba059421c5171d0394c41052b SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5
-EBUILD eden-5.3-r2.ebuild 1845 BLAKE2B c6b996398a511372ca4f8cec15d923056997747fc8c0bb37c1b88c57dc794d4aa304eca0bbfafc1d3d740d9f7534202da9113871c32f8d9a2adfe1f444971819 SHA512 5de7c7da62d7819ee74c8983ba5f222853995d9fae865a7a0802c7ee583f3406d6dbbdc335b3ad60c138d5642d6eb3df683c7a6f26ab91afd39707b63b1579a0
-MISC metadata.xml 383 BLAKE2B daa13ce13128bd1cd96fd95b063788d796bab9a455b7e552abfb76f2ce62369a3eaced99a7b53f248d99289774cfb8ff45b0848e759f3a2e6f89122f1e214141 SHA512 e23cc36f53622230ac9c70cb886cd9812e4bfefba8c0912059b3f072e063c235ba52cce893ea3b49ba05dda047097ba505c4ce5c53248d5acf720f16e123be84
diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild
deleted file mode 100644
index 8bf667224ba8..000000000000
--- a/sci-chemistry/eden/eden-5.3-r2.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils multilib python-r1 toolchain-funcs
-
-MY_P="${PN}_V${PV}"
-
-DESCRIPTION="A crystallographic real-space electron-density refinement & optimization program"
-HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/"
-SRC_URI="mirror://gentoo/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="double-precision"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	sci-libs/fftw:2.1
-	sci-libs/gsl
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-SRC="${S}/source"
-
-pkg_setup() {
-	export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}"
-}
-
-src_prepare() {
-	epatch \
-		"${FILESDIR}"/${PV}-makefile-fixes.patch \
-		"${FILESDIR}"/${P}-impl-dec.patch \
-		"${FILESDIR}"/${P}-format-security.patch
-
-	sed -i \
-		-e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \
-		-e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \
-		-e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \
-		-e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \
-		-e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \
-		${SRC}/Makefile || die
-
-	if ! use double-precision; then
-		sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die
-		EDEN_EXE="s${PN}"
-	else
-		EDEN_EXE="d${PN}"
-	fi
-}
-
-src_compile() {
-	emake CC=$(tc-getCC) -C ${SRC}
-}
-
-src_install() {
-	emake -C ${SRC} install
-
-	python_foreach_impl python_newscript python/${PN}.py i${PN}
-	python_foreach_impl python_domodule python/FileListDialog.py
-
-	rm python/*py || die
-	insinto ${EDENHOME}/python
-	doins python/*
-
-	insinto ${EDENHOME}/help
-	doins help/*
-
-	insinto ${EDENHOME}/tools
-	doins tools/*
-
-	dodoc manual/UserManual.pdf
-
-	cat >> "${T}"/60${PN} <<- EOF
-	EDENHOME="${EDENHOME}"
-	EOF
-
-	doenvd "${T}"/60${PN}
-
-	dosym ${EDEN_EXE} /usr/bin/${PN}
-}
diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch
deleted file mode 100644
index 632358341784..000000000000
--- a/sci-chemistry/eden/files/5.3-makefile-fixes.patch
+++ /dev/null
@@ -1,60 +0,0 @@
- source/Makefile |   17 ++++++++++-------
- 1 files changed, 10 insertions(+), 7 deletions(-)
-
-diff --git a/source/Makefile b/source/Makefile
-index 46d89cc..aa751c7 100644
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -78,8 +78,10 @@ CFLAGS		=   -Wall -pipe -g3
- #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
- #CFLAGS		=   -Wall -O3 -march=i686 
- ifneq ($(FFTW),/usr/local)
-+ifneq ($(FFTW),/usr)
- CFLAGS		+= -I$(INC)
- endif
-+endif
- 
- #			NOTE:
- # DOUBLESWITCH = ON	for double precision;
-@@ -91,15 +93,15 @@ endif
- DOUBLESWITCH 	= ON
- 
- ifeq ($(DOUBLESWITCH),ON)
--LDFLAGS	 = -L$(LIB) -ldfftw -lm  
-+LIBS	 = -L$(LIB) -ldfftw -lm  
- CFLAGS	+= -DDOUBLE 
- TARGET	 = deden
- else
--LDFLAGS	 = -L$(LIB) -lsfftw -lm  
-+LIBS	 = -L$(LIB) -lsfftw -lm  
- TARGET	 = seden
- endif
- 
--LDFLAGS += -g -lgsl -lgslcblas 
-+LIBS += -lgsl -lgslcblas 
- 
- # GSL_PREFIX:= /sw/lib
- # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a 
-@@ -120,17 +122,18 @@ OBJ	= 	addmaps.o   apodfc.o   apodfo.o     back.o     cadhkl.o  \
- all:		eden	fbyteswap 
- 
- eden:  		eden.o   $(OBJ)
--		$(CC)  $^ $(LDFLAGS) -o $@
-+		$(CC)  $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- fbyteswap:	fbyteswap.c		
--		$(CC) -o $@ $^
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- install:	all
-+		mkdir -p $(BIN)
- 		mv fbyteswap $(BIN)
- 		mv eden $(BIN)/$(TARGET)
- 		chmod 751 $(BIN)/$(TARGET)
--		chmod +x mkeden.csh
--		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
-+#		chmod +x mkeden.csh
-+#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
- 
- dist:		clean
- 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch
deleted file mode 100644
index 04b5ecfddebb..000000000000
--- a/sci-chemistry/eden/files/eden-5.3-format-security.patch
+++ /dev/null
@@ -1,96 +0,0 @@
- source/back.c     | 2 +-
- source/concosts.c | 4 ++--
- source/count.c    | 4 ++--
- source/eden.c     | 2 +-
- source/util.c     | 4 ++--
- 5 files changed, 8 insertions(+), 8 deletions(-)
-
-diff --git a/source/back.c b/source/back.c
-index fd517b9..185a02b 100644
---- a/source/back.c
-+++ b/source/back.c
-@@ -112,7 +112,7 @@ void	back_main(int argc, char *argv[])
-           ballpark(caller) ;
- 
-      if (argc > optind+2)
--	  sprintf(sf_filename, argv[optind+2]) ;
-+	  sprintf(sf_filename, "%s", argv[optind+2]) ;
- 
-   /*********************************************
-   Pull off prefix defining whereabouts of input 
-diff --git a/source/concosts.c b/source/concosts.c
-index d62d2e3..590f073 100644
---- a/source/concosts.c
-+++ b/source/concosts.c
-@@ -452,7 +452,7 @@ void	prepare_singlets(char *filename)
-                       sprintf(message, 
- 		      "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", 
-                       s, p, n, phase, *(checks+n), phase-*(checks+n)) ;
--                      fprintf(fp_log, message) ;
-+                      fprintf(fp_log, "%s", message) ;
-                  }
-               } 
- 		/***********************************************
-@@ -556,7 +556,7 @@ void	prepare_triplets(char *filename)
- 		 sprintf(message, 
- "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n",
- 		   newh, newk, newl, t_h[q], t_k[q], t_l[q]) ;
--		 fprintf(fp_log, message) ;
-+		 fprintf(fp_log, "%s", message) ;
- 		 legal_triplet = FALSE ;
-               }
-            }
-diff --git a/source/count.c b/source/count.c
-index c3bc390..ca13008 100644
---- a/source/count.c
-+++ b/source/count.c
-@@ -460,12 +460,12 @@ void	print_el_count(char *filename,
-      }
- 
-      sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ;
--     fprintf(fp, message) ;
-+     fprintf(fp, "%s", message) ;
-      printTwice(message) ;
- 
-      sprintf(message, "Count of all remaining electrons: %g %g %g\n", 
-      remainder0*volvox, remainder1*volvox, remainder2*volvox) ;
--     fprintf(fp, message) ;
-+     fprintf(fp, "%s", message) ;
-      printTwice(message) ;
- 
-      fclose(fp) ;
-diff --git a/source/eden.c b/source/eden.c
-index dea3246..5a9b389 100644
---- a/source/eden.c
-+++ b/source/eden.c
-@@ -319,7 +319,7 @@ int	main(int argc, char *argv[])
- 
-      get_unique_logname() ;
- 
--     sprintf(command_line, argv[0]) ;
-+     sprintf(command_line, "%s", argv[0]) ;
- 
-      for (k = 1; k < argc; k++) { 
-          strcat(command_line, " ") ;
-diff --git a/source/util.c b/source/util.c
-index 6fff179..41c624c 100644
---- a/source/util.c
-+++ b/source/util.c
-@@ -266,7 +266,7 @@ void	printTwice(char *mess)	/* send info to terminal (stdout) and to log */
-  
- void	prompt(char *mess)	/* Send message to user, await reply */
- {
--    fprintf(stdout, mess) ;
-+    fprintf(stdout, "%s", mess) ;
- 
-     while (fgets(terminp, MAXSTRING, stdin) != NULL)  {
- 	if ((int)strlen(terminp) > 0) 
-@@ -722,7 +722,7 @@ void	start_record()
-      int	k ;
- 
-      rec_length = k = sprintf(record, "\n") ;
--     rec_length += sprintf(record+k, timestamp()) ;
-+     rec_length += sprintf(record+k, "%s", timestamp()) ;
-      k = rec_length ;
- 
-      if ((cwd = getcwd(NULL, 120)) == NULL) 
diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
deleted file mode 100644
index af67508d090e..000000000000
--- a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
+++ /dev/null
@@ -1,28 +0,0 @@
- source/fbyteswap.c |    1 +
- source/util.c      |    1 +
- 2 files changed, 2 insertions(+), 0 deletions(-)
-
-diff --git a/source/fbyteswap.c b/source/fbyteswap.c
-index 83015b9..c9033c3 100644
---- a/source/fbyteswap.c
-+++ b/source/fbyteswap.c
-@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes.
- 
- #include <stdio.h>
- #include <fcntl.h>
-+#include <unistd.h>
- #include <sys/stat.h>
- #include <sys/types.h>
- void byteswap();
-diff --git a/source/util.c b/source/util.c
-index 6fff179..ca7a957 100644
---- a/source/util.c
-+++ b/source/util.c
-@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes.
- 
- *******************************************************************************/
- #include  <sys/time.h>	/* ... for picking up date & time	*/
-+#include <time.h>
- #include  <signal.h>	/* ... for capturing kill		*/
- #include  "util.h"
- 
diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch
deleted file mode 100644
index 4cfff3f515df..000000000000
--- a/sci-chemistry/eden/files/makefile-fixes.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -ur eden.orig/source/Makefile eden/source/Makefile
---- eden.orig/source/Makefile	2004-10-18 10:40:03.000000000 -0700
-+++ eden/source/Makefile	2005-12-15 22:32:45.000000000 -0800
-@@ -78,8 +78,10 @@
- #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
- #CFLAGS		=   -Wall -O3 -march=i686 
- ifneq ($(FFTW),/usr/local)
-+ifneq ($(FFTW),/usr)
- CFLAGS		+= -I$(INC)
- endif
-+endif
- 
- #			NOTE:
- # DOUBLESWITCH = ON	for double precision;
-@@ -129,8 +131,8 @@
- 		mv fbyteswap $(BIN)
- 		mv eden $(BIN)/$(TARGET)
- 		chmod 751 $(BIN)/$(TARGET)
--		chmod +x mkeden.csh
--		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
-+#		chmod +x mkeden.csh
-+#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
- 
- dist:		clean
- 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml
deleted file mode 100644
index 6113635247f3..000000000000
--- a/sci-chemistry/eden/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-  <use>
-    <flag name="double-precision">More precise calculations at the expense of
-    speed</flag>
-  </use>
-</pkgmetadata>