commit: 140e19b020538b51f589747c5525883061c7f970 Author: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> AuthorDate: Fri Jul 19 11:29:05 2024 +0000 Commit: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> CommitDate: Fri Jul 19 11:34:41 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=140e19b0
sci-chemistry/namd: treeclean Bug: https://bugs.gentoo.org/686856 Bug: https://bugs.gentoo.org/686858 Bug: https://bugs.gentoo.org/686860 Bug: https://bugs.gentoo.org/934228 Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org> profiles/package.mask | 6 -- sci-chemistry/namd/Manifest | 1 - sci-chemistry/namd/files/namd-2.10-gentoo.patch | 124 ------------------------ sci-chemistry/namd/files/namd-2.7-iml-dec.patch | 24 ----- sci-chemistry/namd/metadata.xml | 12 --- sci-chemistry/namd/namd-2.10.ebuild | 110 --------------------- 6 files changed, 277 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 79e3e14868e0..0401b0d0b292 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -297,12 +297,6 @@ sci-electronics/vbs # Removal on 2024-07-14. Bug #934232. sci-chemistry/xyza2pipe -# Arthur Zamarin <arthur...@gentoo.org> (2024-06-14) -# EAPI=6, not maintained for ~7 years in gentoo, waiting for version -# bump. Fetch restricted, and fails to build after manual fetch. -# Removal on 2024-07-14. Bugs #934228, #686860, #686858, #686856. -sci-chemistry/namd - # Arthur Zamarin <arthur...@gentoo.org> (2024-06-14) # EAPI=6, not maintained in Gentoo for a long time. procheck is # fetch restricted, and the file you download from upstream diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest deleted file mode 100644 index ffe7e0c005e5..000000000000 --- a/sci-chemistry/namd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST NAMD_2.10_Source.tar.gz 9200234 BLAKE2B fe348a21309b279640da81ed4dd5447c1e6e467866270dc1730b26d02d5518b45bd662211c3cbe228bd8d9885edb062cf5d245d634bcd38773c36873febd2ee6 SHA512 3712a03841fad76c502ac4e41469162ff78e6152560d0f6855d61d2b5583241a661e2a3e7446029b56a6f6f1100f25cb51b2c3df6571542397961d3bb625bc92 diff --git a/sci-chemistry/namd/files/namd-2.10-gentoo.patch b/sci-chemistry/namd/files/namd-2.10-gentoo.patch deleted file mode 100644 index ffef6dc3ad68..000000000000 --- a/sci-chemistry/namd/files/namd-2.10-gentoo.patch +++ /dev/null @@ -1,124 +0,0 @@ -diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw NAMD_2.10_Source/arch/Linux-x86_64.fftw ---- NAMD_2.10_Source.orig/arch/Linux-x86_64.fftw 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/arch/Linux-x86_64.fftw 2015-03-06 17:54:46.641162629 -0700 -@@ -1,7 +1,7 @@ - --FFTDIR=/Projects/namd2/fftw/linux-x86_64 -+FFTDIR=/usr - FFTINCL=-I$(FFTDIR)/include --FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw -+FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw - FFTFLAGS=-DNAMD_FFTW - FFT=$(FFTINCL) $(FFTFLAGS) - -diff -Naur NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl NAMD_2.10_Source/arch/Linux-x86_64.tcl ---- NAMD_2.10_Source.orig/arch/Linux-x86_64.tcl 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/arch/Linux-x86_64.tcl 2015-03-06 17:54:46.641162629 -0700 -@@ -1,9 +1,9 @@ - - #TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64 --TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded -+TCLDIR=/usr - TCLINCL=-I$(TCLDIR)/include - #TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl --TCLLIB=-L$(TCLDIR)/lib -ltcl8.5 -ldl -lpthread -+#TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl -lpthread - TCLFLAGS=-DNAMD_TCL - TCL=$(TCLINCL) $(TCLFLAGS) - -diff -Naur NAMD_2.10_Source.orig/Makefile NAMD_2.10_Source/Makefile ---- NAMD_2.10_Source.orig/Makefile 2015-03-06 17:53:44.170416075 -0700 -+++ NAMD_2.10_Source/Makefile 2015-03-06 18:01:32.645966590 -0700 -@@ -389,10 +389,10 @@ - $(DSTDIR)/stringhash.o - - # definitions for Charm routines --CHARMC = $(CHARM)/bin/charmc --CHARMXI = $(CHARM)/bin/charmc --CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1 --CHARMLIB = $(CHARM)/lib -+CHARMC = /usr/bin/charmc -+CHARMXI = /usr/bin/charmc -+CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1 -+CHARMLIB = /usr/gentoo-libdir - CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -module CkMulticast - #CHARM_MODULES = -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB - #CHARM_MODULES = -module msa -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -@@ -418,7 +418,7 @@ - - # Add new executables here. - --BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb charmrun -+BINARIES = namd2 psfgen sortreplicas flipdcd flipbinpdb - - # This should be rebuilt at every compile, but not on Win32. - BUILDINFO = $(DSTDIR)/buildinfo -@@ -434,7 +434,7 @@ - - namd2: $(MKINCDIR) $(MKDSTDIR) $(OBJS) $(LIBS) - $(MAKEBUILDINFO) -- $(CHARMC) -verbose -ld++-option \ -+ $(CHARMC) $(LDFLAGS) -verbose -ld++-option \ - '$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS) $(CXXMICOPTS)' \ - "$(CHARM_MODULES)" -language charm++ \ - $(BUILDINFO).o \ -@@ -484,11 +484,8 @@ - charmd_faceless.exe: - $(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe - --charmrun.exe: -- $(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe -- - psfgen: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) -- $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm -+ $(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm - - psfgen.exe: $(MKDSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL) - $(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm -@@ -506,7 +503,7 @@ - $(CC) $(CFLAGS) -o diffbinpdb $(SRCDIR)/diffbinpdb.c -lm - - flipdcd: $(SRCDIR)/flipdcd.c -- $(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \ - echo "#!/bin/sh\necho unavailable on this platform" > $@; \ - chmod +x $@ - -@@ -516,7 +513,7 @@ - chmod +x $@ - - fixdcd: $(SRCDIR)/fixdcd.c -- $(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c - - dumpdcd: $(SRCDIR)/dumpdcd.c - $(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c -@@ -711,9 +708,7 @@ - - DOC_FILES = README.txt announce.txt license.txt notes.txt - --RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen charmrun namd2 -- --WINDOWS_RELEASE_FILES = $(LIBCUDARTSO) $(WINDOWSBINARIES) $(TCLDLL) -+RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb sortreplicas psfgen namd2 - - release: all - $(ECHO) Creating release $(RELEASE_DIR_NAME) -@@ -724,17 +719,9 @@ - for f in `find $(RELEASE_DIR_NAME)/lib -name CVS`; do \ - /bin/rm -rf $$f; \ - done -- if [ -r $(CHARM)/bin/charmd ]; then \ -- $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \ -- fi -- if [ -r $(CHARM)/bin/charmd_faceless ]; then \ -- $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \ -- fi - chmod -R a+rX $(RELEASE_DIR_NAME) - tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME) - gzip $(RELEASE_DIR_NAME).tar -- echo $(CHARM) -- ls -l $(CHARM)/lib - -for f in $(RELEASE_FILES); do echo $$f; $(LDD) $(RELEASE_DIR_NAME)/$$f; done - - winrelease: winall diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch deleted file mode 100644 index e5ee3bd6c818..000000000000 --- a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c -index 94b71ba..01a2529 100644 ---- a/src/flipbinpdb.c -+++ b/src/flipbinpdb.c -@@ -9,6 +9,7 @@ - #include <sys/mman.h> - #include <fcntl.h> - #include <stdio.h> -+#include <stdlib.h> - - #ifndef MAP_FILE - #define MAP_FILE 0 -diff --git a/src/flipdcd.c b/src/flipdcd.c -index 8ec85b7..1c23433 100644 ---- a/src/flipdcd.c -+++ b/src/flipdcd.c -@@ -13,6 +13,7 @@ - #include <sys/mman.h> - #include <fcntl.h> - #include <stdio.h> -+#include <stdlib.h> - - #ifndef MAP_FILE - #define MAP_FILE 0 diff --git a/sci-chemistry/namd/metadata.xml b/sci-chemistry/namd/metadata.xml deleted file mode 100644 index 11bbcb9bf2c8..000000000000 --- a/sci-chemistry/namd/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>nicolasb...@gentoo.org</email> - <name>Nicolas Bock</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/namd/namd-2.10.ebuild b/sci-chemistry/namd/namd-2.10.ebuild deleted file mode 100644 index 76a34c5a0a19..000000000000 --- a/sci-chemistry/namd/namd-2.10.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -MY_PN="NAMD" - -inherit multilib toolchain-funcs flag-o-matic - -DESCRIPTION="A powerful and highly parallelized molecular dynamics code" -HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"; -SRC_URI="${MY_PN}_${PV}_Source.tar.gz" - -LICENSE="namd" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -RESTRICT="fetch" - -RDEPEND=" - >=sys-cluster/charm-6.5.1-r2 - sci-libs/fftw:3.0 - dev-lang/tcl:0=" - -DEPEND="${RDEPEND} - virtual/pkgconfig - app-shells/tcsh" - -NAMD_ARCH="Linux-x86_64-g++" - -NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"; - -S="${WORKDIR}/${MY_PN}_${PV}_Source" - -PATCHES=( - # apply a few small fixes to make NAMD compile and - # link to the proper libraries - "${FILESDIR}"/namd-2.10-gentoo.patch - "${FILESDIR}"/namd-2.7-iml-dec.patch -) - -pkg_nofetch() { - echo - einfo "Please download ${MY_PN}_${PV}_Source.tar.gz from" - einfo "${NAMD_DOWNLOAD}" - einfo "after agreeing to the license and then move it to" - einfo "your DISTDIR directory." - einfo "Be sure to select the ${PV} version!" - echo -} - -src_prepare() { - CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3) - - default - - sed \ - -e "/CHARMBASE =/s:= .*:= /usr/bin/charm-${CHARM_VERSION}:" \ - -i Make.charm || die - - # Remove charm distribution. We don't need it. - rm -f charm-*.tar || die - - # proper compiler and cflags - sed \ - -e "s/g++.*/$(tc-getCXX)/" \ - -e "s/gcc.*/$(tc-getCC)/" \ - -e "s/CXXOPTS = .*/CXXOPTS = ${CXXFLAGS} ${LDFLAGS}/" \ - -e "s/COPTS = .*/COPTS = ${CFLAGS} ${LDFLAGS}/" \ - -i arch/${NAMD_ARCH}.arch || die - - sed \ - -e "s/gentoo-libdir/$(get_libdir)/g" \ - -e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \ - -i Makefile || die "Failed gentooizing Makefile." - sed -e "s@/lib@/$(get_libdir)@g" -e '/FFTDIR=/s@=.*@=/usr@' -i arch/Linux-x86_64.fftw3 || die - sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || die -} - -src_configure() { - # configure - ./config ${NAMD_ARCH} --with-fftw3 --charm-arch . || die -} - -src_compile() { - # build namd - cd "${S}/${NAMD_ARCH}" || die - TCLLIB="$($(tc-getPKG_CONFIG) --libs tcl) -ldl -pthread" \ - emake -} - -src_install() { - dodoc announce.txt license.txt notes.txt - cd "${S}/${NAMD_ARCH}" || die - - # the binaries - dobin ${PN}2 psfgen flipbinpdb flipdcd -} - -pkg_postinst() { - echo - einfo "For detailed instructions on how to run and configure" - einfo "NAMD please consults the extensive documentation at" - einfo "http://www.ks.uiuc.edu/Research/namd/"; - einfo "and the NAMD tutorials available at" - einfo "http://www.ks.uiuc.edu/Training/Tutorials/"; - einfo "Have fun :)" - echo -}
