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@gentoo.org>

6 files changed, 0 insertions, 277 deletions

diff --git a/profiles/package.mask b/profiles/package.mask
index 79e3e14868e0..0401b0d0b292 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -298,12 +298,6 @@ sci-electronics/vbs
 sci-chemistry/xyza2pipe
 
 # Arthur Zamarin <arthurzam@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 <arthurzam@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
 # doesn't match size and manifests. aqua depends on procheck.
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>nicolasbock@gentoo.org</email>
-		<name>Nicolas Bock</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@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
-}