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sci-chemistry/ambertools: Remove last-rited pkg, #612740

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This commit is contained in:
Michał Górny
2017-06-15 09:56:52 +02:00
parent 160ccd2925
commit 4eaa6cd670
5 changed files with 0 additions and 547 deletions
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4
profiles/package.mask
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@@ -511,11 +511,7 @@ x11-terms/rxvt
# #
# sci-biology/mammoth - #612738, not touched since 2015, added in 2007, # sci-biology/mammoth - #612738, not touched since 2015, added in 2007,
# not bumped since; homepage gone # not bumped since; homepage gone
#
# sci-chemistry/ambertools - #612740, not touched since 2013, added
# in 2011, not bumped since; includes sci-chemistry/acpype as a revdep
sci-biology/mammoth sci-biology/mammoth
sci-chemistry/ambertools
# Bernard Cafarelli <voyageur@gentoo.org> (8 May 2017) # Bernard Cafarelli <voyageur@gentoo.org> (8 May 2017)
# Coordinated conversion to wxGTK:3.0-gtk3 # Coordinated conversion to wxGTK:3.0-gtk3

2
sci-chemistry/ambertools/Manifest
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@@ -1,2 +0,0 @@
DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c
DIST ambertools-1.5-bugfix_1-10.patch.xz 31708 SHA256 5773aaa8a2478ad478f0f3afafaa39669002c31ebe755c0d12ff277ce9ab8352

143
sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
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@@ -1,143 +0,0 @@
# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=4
inherit eutils fortran-2 multilib toolchain-funcs
DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
HOMEPAGE="http://ambermd.org/#AmberTools"
SRC_URI="
AmberTools-${PV}.tar.bz2
mirror://gentoo/${P}-bugfix_1-10.patch.xz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux"
IUSE="mpi openmp static-libs X"
RESTRICT="fetch"
RDEPEND="
virtual/cblas
virtual/lapack
sci-libs/clapack
sci-libs/arpack
sci-libs/cifparse-obj
sci-chemistry/mopac7
sci-libs/netcdf
sci-libs/fftw:2.1
sci-chemistry/reduce"
DEPEND="${RDEPEND}
dev-util/byacc
dev-libs/libf2c
sys-devel/ucpp
virtual/pkgconfig"
S="${WORKDIR}/amber11"
pkg_nofetch() {
einfo "Go to ${HOMEPAGE} and get ${A}"
einfo "Place it in ${DISTDIR}"
}
pkg_setup() {
fortran-2_pkg_setup
if use openmp; then
tc-has-openmp || \
die "Please select an openmp capable compiler like gcc[openmp]"
fi
AMBERHOME="${S}"
}
src_prepare() {
epatch \
"${WORKDIR}/${P}-bugfix_1-10.patch" \
"${FILESDIR}/${P}-gentoo.patch"
cd AmberTools/src
rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
}
src_configure() {
cd AmberTools/src
sed \
-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) --libs lapack) -lclapack:g" \
-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) --libs blas cblas):g" \
-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
-e "s:fc=g77:fc=$(tc-getFC):g" \
-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) --libs netcdf):g" \
-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
-e "s:-O3::g" \
-i configure || die
sed -e "s:arsecond_:arscnd_:g" \
-i sff/time.c \
-i sff/sff.h \
-i sff/sff.c || die
sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
-i nss/Makefile || die
local myconf
use X || myconf="${myconf} -noX11"
for x in mpi openmp; do
use ${x} && myconf="${myconf} -${x}"
done
./configure \
${myconf} \
-nobintraj \
-nomdgx \
-nopython \
-nomtkpp \
gnu
# $(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
}
src_compile() {
cd AmberTools/src
emake
}
src_install() {
rm -r bin/chemistry bin/MMPBSA_mods
rm bin/ante-MMPBSA.py bin/extractFrcmod.py
for x in bin/*
do dobin ${x} || die
done
rm "${ED}/usr/bin/yacc"
dobin AmberTools/src/antechamber/mopac.sh
sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
-i "${ED}/usr/bin/mopac.sh" || die
# Make symlinks untill binpath for amber will be fixed
dodir /usr/share/${PN}/bin
cd "${ED}/usr/bin"
for x in *; do
dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
done
cd "${S}"
# sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
# -i "${ED}/usr/bin/xleap" \
# -i "${ED}/usr/bin/tleap" || die
dodoc doc/AmberTools.pdf doc/leap_pg.pdf
use static-libs && dolib.a lib/*
insinto /usr/include/${PN}
doins include/*
insinto /usr/share/${PN}
doins -r dat
cd AmberTools
doins -r benchmarks examples test
cat >> "${T}"/99ambertools <<- EOF
AMBERHOME="${EPREFIX}/usr/share/ambertools"
EOF
doenvd "${T}"/99ambertools
}

386
sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch
View File

@@ -1,386 +0,0 @@
diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
--- amber11.orig/AmberTools/src/configure 2011-04-14 15:30:55.000000000 +0300
+++ amber11/AmberTools/src/configure 2011-06-04 12:26:45.000000000 +0300
@@ -293,7 +293,8 @@
echo "Your AMBERHOME environment variable is not set! It should be set to"
echo "$ambhome NOT doing so may cause errors when you compile. Continue"
echo "anyway? (yes or no)"
- read answer
+ #read answer
+ answer='yes'
if [ "$answer" = 'yes' -o "$answer" = 'Yes' -o "$answer" = 'YES' -o "$answer" = 'y' -o "$answer" = 'Y' ]; then
echo ""
echo "Continuing anyway... Setting AMBERHOME to $ambhome temporarily"
@@ -356,11 +357,11 @@
mpi_flag=
lex=flex
flibs_mkl=
-lapack=install
-blas=install
+lapack=skip
+blas=skip
f2c=skip
-ucpp=install
-cpp="\$(BINDIR)/ucpp -l"
+ucpp=skip
+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
#-----------------------------------
# skip building of sleap?
@@ -1655,24 +1656,24 @@
#--------------------------------------------------------------------------
# Configure fftw-3.2.2:
#--------------------------------------------------------------------------
- if [ "$mdgx" = 'yes' ]; then
- mdgxflag="--prefix=$AMBERHOME --disable-fortran"
- echo
- echo "Configuring fftw-3.2.2 (may be time-consuming)..."
- echo
- cd fftw-3.2.2 && \
- env CC="$cc" CFLAGS="$cflags $cnooptflags" \
- ./configure $mdgxflag > ../fftw3_config.log 2>&1
- ncerror=$?
- if [ $ncerror -gt 0 ]; then
- echo " Error: FFTW configure returned $ncerror"
- echo " FFTW configure failed! Check the fftw3_config.log file."
- exit 1
- else
- echo " fftw-3.2.2 configure succeeded."
- fi
- cd ..
- fi
+ #if [ "$mdgx" = 'yes' ]; then
+ # mdgxflag="--prefix=$AMBERHOME --disable-fortran"
+ # echo
+ # echo "Configuring fftw-3.2.2 (may be time-consuming)..."
+ # echo
+ # cd fftw-3.2.2 && \
+ # env CC="$cc" CFLAGS="$cflags $cnooptflags" \
+ # ./configure $mdgxflag > ../fftw3_config.log 2>&1
+ # ncerror=$?
+ # if [ $ncerror -gt 0 ]; then
+ # echo " Error: FFTW configure returned $ncerror"
+ # echo " FFTW configure failed! Check the fftw3_config.log file."
+ # exit 1
+ # else
+ # echo " fftw-3.2.2 configure succeeded."
+ # fi
+ # cd ..
+ #fi
#--------------------------------------------------------------------------
# Configure python
@@ -1792,27 +1793,27 @@
echo
echo "Configuring fftw-2.1.5 (may be time-consuming)..."
echo
- cd fftw-2.1.5
- if [ "$mpi" = 'yes' ]; then
- ./configure $rismflag --enable-mpi \
- CC="$cc" CFLAGS="$cflags $coptflags" \
- F77="$fc" FFLAGS="$fflags $foptflags" \
- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
- else
- ./configure $rismflag \
- CC="$cc" CFLAGS="$cflags $coptflags" \
- F77="$fc" FFLAGS="$fflags $foptflags" \
- FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
- fi
- ncerror=$?
- if [ $ncerror -gt 0 ]; then
- echo " Error: fftw configure returned $ncerror"
- echo " fftw configure failed! Check the fftw2_config.log file."
- exit 1
- else
- echo " fftw-2.1.5 configure succeeded."
- fi
- cd ..
+ # cd fftw-2.1.5
+ # if [ "$mpi" = 'yes' ]; then
+ # ./configure $rismflag --enable-mpi \
+ # CC="$cc" CFLAGS="$cflags $coptflags" \
+ # F77="$fc" FFLAGS="$fflags $foptflags" \
+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+ # else
+ # ./configure $rismflag \
+ # CC="$cc" CFLAGS="$cflags $coptflags" \
+ # F77="$fc" FFLAGS="$fflags $foptflags" \
+ # FLIBS="$flibs_arch" > ../fftw2_config.log 2>&1
+ # fi
+ # ncerror=$?
+ # if [ $ncerror -gt 0 ]; then
+ # echo " Error: fftw configure returned $ncerror"
+ # echo " fftw configure failed! Check the fftw2_config.log file."
+ # exit 1
+ # else
+ # echo " fftw-2.1.5 configure succeeded."
+ # fi
+ # cd ..
flibs_fftw2="-ldrfftw -ldfftw"
if [ "$mpi" = 'yes' ]; then
flibs_fftw2="-ldrfftw_mpi -ldfftw_mpi $flibs_fftw2"
diff -urN amber11.orig/AmberTools/src/cpptraj/src/Makefile_at amber11/AmberTools/src/cpptraj/src/Makefile_at
--- amber11.orig/AmberTools/src/cpptraj/src/Makefile_at 2011-04-14 15:30:16.000000000 +0300
+++ amber11/AmberTools/src/cpptraj/src/Makefile_at 2011-05-20 00:45:48.000000000 +0300
@@ -65,8 +65,8 @@
-/bin/rm FindDepend.o
-/bin/rm findDepend
-cpptraj$(SFX): $(NETCDFLIB) $(OBJECTS)
- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB)
+cpptraj$(SFX): $(OBJECTS)
+ $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(NETCDFLIB) $(ZLIB) $(BZLIB) -lgomp
$(NETCDFLIB): ../../netcdf_config.log
cd ../../netcdf/src && $(MAKE) install
diff -urN amber11.orig/AmberTools/src/Makefile amber11/AmberTools/src/Makefile
--- amber11.orig/AmberTools/src/Makefile 2011-04-14 15:30:12.000000000 +0300
+++ amber11/AmberTools/src/Makefile 2011-05-19 23:36:36.000000000 +0300
@@ -8,15 +8,15 @@
install: $(INSTALLTYPE)
-serial: configured_serial $(NETCDFLIB) $(PYINSTALL) $(MTKPP)
+serial: configured_serial
@echo "Starting installation of ${AMBERTOOLS} serial at `date`".
# utility routines and libraries:
- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
(cd byacc && $(MAKE) install )
- (cd arpack && $(MAKE) install );
- (cd lapack && $(MAKE) $(LAPACK) )
- (cd blas && $(MAKE) $(BLAS) )
- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+# (cd arpack && $(MAKE) install );
+# (cd lapack && $(MAKE) $(LAPACK) )
+# (cd blas && $(MAKE) $(BLAS) )
+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
(cd etc && $(MAKE) install )
(cd chamber && $(MAKE) install )
(cd pbsa && $(MAKE) install )
@@ -32,7 +32,7 @@
(cd cpptraj && $(MAKE) $(CPPTRAJ))
# miscellaneous:
- (cd reduce && $(MAKE) install )
+# (cd reduce && $(MAKE) install )
# leap and gleap:
(cd leap && $(MAKE) install )
@@ -42,7 +42,7 @@
(cd rism && $(MAKE) install )
# nab:
- (cd cifparse && $(MAKE) install )
+# (cd cifparse && $(MAKE) install )
(cd sff && $(MAKE) install )
(cd pbsa && $(MAKE) libinstall )
(cd nab && $(MAKE) install )
@@ -63,19 +63,19 @@
@echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
@echo ""
-nabonly: $(NETCDFLIB)
+nabonly:
# utility routines and libraries:
- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
+# (cd ucpp-1.3 && $(MAKE) $(UCPP) )
(cd byacc && $(MAKE) install )
- (cd arpack && $(MAKE) install );
- (cd lapack && $(MAKE) $(LAPACK) )
- (cd blas && $(MAKE) $(BLAS) )
- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
+# (cd arpack && $(MAKE) install );
+# (cd lapack && $(MAKE) $(LAPACK) )
+# (cd blas && $(MAKE) $(BLAS) )
+# (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
(cd pbsa && $(MAKE) libinstall )
(cd rism && $(MAKE) install )
# nab:
- (cd cifparse && $(MAKE) install )
+# (cd cifparse && $(MAKE) install )
(cd sff && $(MAKE) install )
(cd nab && $(MAKE) install )
(cd nss && $(MAKE) install )
diff -urN amber11.orig/AmberTools/src/mdgx/Makefile amber11/AmberTools/src/mdgx/Makefile
--- amber11.orig/AmberTools/src/mdgx/Makefile 2011-04-14 15:30:17.000000000 +0300
+++ amber11/AmberTools/src/mdgx/Makefile 2011-05-20 12:44:38.000000000 +0300
@@ -109,7 +109,7 @@
FFTW_LIBS = $(LIBDIR)/libfftw3.a
-mdgx$(SFX) : $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB)
+mdgx$(SFX) : $(MDGX_OBJS)
$(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \
-o $@ $(MDGX_OBJS) $(FFTW_LIBS) $(NETCDFLIB) $(LM)
diff -urN amber11.orig/AmberTools/src/pbsa/Makefile amber11/AmberTools/src/pbsa/Makefile
--- amber11.orig/AmberTools/src/pbsa/Makefile 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/pbsa/Makefile 2011-05-19 22:27:40.000000000 +0300
@@ -148,7 +148,7 @@
)
#---------------------------------------------------------------------------
-pbsa$(SFX): $(OBJ) syslib netlib c9x-complex configured_serial
+pbsa$(SFX): $(OBJ) syslib configured_serial
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
../lib/nxtsec.o ../lib/random.o \
$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
@@ -158,7 +158,7 @@
../lib/nxtsec.o ../lib/random.o \
$(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
-simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o $(FLIBSF) \
$(LDFLAGS) $(AMBERLDFLAGS)
@@ -194,15 +194,15 @@
sfflib:
cd ../sff && $(MAKE) install
-netlib:
- cd ../lapack && $(MAKE) $(LAPACK)
- cd ../blas && $(MAKE) $(BLAS)
- cd ../arpack && $(MAKE) install
-
-c9x-complex:
- @if test $(C9XCOMPLEX) != "skip"; then \
- cd ../c9x-complex && $(MAKE) libmc.a; \
- fi
+#netlib:
+# cd ../lapack && $(MAKE) $(LAPACK)
+# cd ../blas && $(MAKE) $(BLAS)
+# cd ../arpack && $(MAKE) install
+
+#c9x-complex:
+# @if test $(C9XCOMPLEX) != "skip"; then \
+# cd ../c9x-complex && $(MAKE) libmc.a; \
+# fi
%.LIBPBSA.o: %.f
$(FPP) $(FPPFLAGS) $(AMBERFPPFLAGS) -DLIBPBSA $< > _$<
diff -urN amber11.orig/AmberTools/src/ptraj/Makefile amber11/AmberTools/src/ptraj/Makefile
--- amber11.orig/AmberTools/src/ptraj/Makefile 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/Makefile 2011-05-19 23:38:36.000000000 +0300
@@ -57,25 +57,25 @@
pubfft.o: pubfft.f
$(FC) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
-rdparm$(SFX): libs $(NETCDFLIB) $(OBJECTS)
+rdparm$(SFX): libs $(OBJECTS)
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
-o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
-ptraj$(SFX): libs netlib $(NETCDFLIB) $(OBJECTS)
+ptraj$(SFX): libs $(OBJECTS)
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
-o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
-ptraj.MPI$(SFX): libs netlib $(PNETCDFLIB) $(OBJECTS)
+ptraj.MPI$(SFX): libs $(PNETCDFLIB) $(OBJECTS)
$(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
-o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
libs:
cd pdb && $(MAKE)
- cd ../arpack && $(MAKE)
+# cd ../arpack && $(MAKE)
-netlib:
- cd ../lapack && $(MAKE) $(LAPACK)
- cd ../blas && $(MAKE) $(BLAS)
+#netlib:
+# cd ../lapack && $(MAKE) $(LAPACK)
+# cd ../blas && $(MAKE) $(BLAS)
clean:
cd pdb && $(MAKE) clean
diff -urN amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h amber11/AmberTools/src/ptraj/netcdf_ptraj.h
--- amber11.orig/AmberTools/src/ptraj/netcdf_ptraj.h 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/netcdf_ptraj.h 2011-05-19 22:30:43.000000000 +0300
@@ -4,7 +4,7 @@
# include "../../include/pnetcdf.h"
# define nc_strerror ncmpi_strerror
# else
-# include "../../include/netcdf.h"
+# include <netcdf.h>
# endif
#endif
diff -urN amber11.orig/AmberTools/src/ptraj/ptraj.h amber11/AmberTools/src/ptraj/ptraj.h
--- amber11.orig/AmberTools/src/ptraj/ptraj.h 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/ptraj/ptraj.h 2011-06-04 13:25:01.000000000 +0300
@@ -94,7 +94,7 @@
#define nc_strerror ncmpi_strerror
#include "../../include/pnetcdf.h"
#else
-#include "../../include/netcdf.h"
+#include <netcdf.h>
#endif
#endif
diff -urN amber11.orig/AmberTools/src/rism/Makefile amber11/AmberTools/src/rism/Makefile
--- amber11.orig/AmberTools/src/rism/Makefile 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/rism/Makefile 2011-05-20 01:07:26.000000000 +0300
@@ -49,7 +49,7 @@
mdiis_orig_c.o mdiis_blas_c.o mdiis_blas2_c.o mdiis_c.o \
fce_c.o erfcfun.o safemem.o blend.o timer_c.o
-librism: $(LIBOBJ) $(FLIBS_FFTW2)
+librism: $(LIBOBJ)
$(AR) $(LIBDIR)/$@.a $(LIBOBJ)
$(RANLIB) $(LIBDIR)/$@.a
diff -urN amber11.orig/AmberTools/src/sff/AmberNetcdf.c amber11/AmberTools/src/sff/AmberNetcdf.c
--- amber11.orig/AmberTools/src/sff/AmberNetcdf.c 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/sff/AmberNetcdf.c 2011-05-20 10:49:06.000000000 +0300
@@ -27,7 +27,7 @@
#endif
#ifdef BINTRAJ
-#include "../../include/netcdf.h"
+#include <netcdf.h>
#define NCFRAME "frame"
#define NCSPATIAL "spatial"
diff -urN amber11.orig/AmberTools/src/sff/Makefile amber11/AmberTools/src/sff/Makefile
--- amber11.orig/AmberTools/src/sff/Makefile 2011-04-14 15:30:19.000000000 +0300
+++ amber11/AmberTools/src/sff/Makefile 2011-05-20 09:53:27.000000000 +0300
@@ -1,7 +1,7 @@
include ../config.h
.c.o:
- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) -o $@ $<
+ $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFLIB) -o $@ $<
OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o \
diff -urN amber11.orig/AmberTools/src/sqm/Makefile amber11/AmberTools/src/sqm/Makefile
--- amber11.orig/AmberTools/src/sqm/Makefile 2011-04-14 15:30:20.000000000 +0300
+++ amber11/AmberTools/src/sqm/Makefile 2011-05-19 22:31:49.000000000 +0300
@@ -77,7 +77,7 @@
install: sqm$(SFX)
mv sqm$(SFX) $(BINDIR)
-sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
$(FC) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
$(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
@@ -94,10 +94,10 @@
sys:
cd ../lib; $(MAKE) sys.a
-netlib:
- cd ../lapack; $(MAKE) $(LAPACK)
- cd ../blas; $(MAKE) $(BLAS)
- cd ../arpack && $(MAKE) install
+#netlib:
+# cd ../lapack; $(MAKE) $(LAPACK)
+# cd ../blas; $(MAKE) $(BLAS)
+# cd ../arpack && $(MAKE) install
clean:
/bin/rm -f *.o _*.f *.mod *.d sqm$(SFX)

12
sci-chemistry/ambertools/metadata.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
<email>alexxy@gentoo.org</email>
<name>Alexey Shvetsov</name>
</maintainer>
<maintainer type="project">
<email>sci-chemistry@gentoo.org</email>
<name>Gentoo Chemistry Project</name>
</maintainer>
</pkgmetadata>