commit: 4eaa6cd670cab66f894fb4f3a2bbc537814ee78b Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Thu Jun 15 07:56:52 2017 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Thu Jun 15 08:01:02 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4eaa6cd6
sci-chemistry/ambertools: Remove last-rited pkg, #612740 profiles/package.mask | 4 - sci-chemistry/ambertools/Manifest | 2 - sci-chemistry/ambertools/ambertools-1.5-r1.ebuild | 143 -------- .../ambertools/files/ambertools-1.5-gentoo.patch | 386 --------------------- sci-chemistry/ambertools/metadata.xml | 12 - 5 files changed, 547 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 385ed17ae7f..ad287dfb688 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -511,11 +511,7 @@ x11-terms/rxvt # # sci-biology/mammoth - #612738, not touched since 2015, added in 2007, # 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-chemistry/ambertools # Bernard Cafarelli <[email protected]> (8 May 2017) # Coordinated conversion to wxGTK:3.0-gtk3 diff --git a/sci-chemistry/ambertools/Manifest b/sci-chemistry/ambertools/Manifest deleted file mode 100644 index 747dbffa95d..00000000000 --- a/sci-chemistry/ambertools/Manifest +++ /dev/null @@ -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 diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild deleted file mode 100644 index 35204fa921e..00000000000 --- a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild +++ /dev/null @@ -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 -} diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch deleted file mode 100644 index 0e41d26d6f9..00000000000 --- a/sci-chemistry/ambertools/files/ambertools-1.5-gentoo.patch +++ /dev/null @@ -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)/[email protected] $(LIBOBJ) - $(RANLIB) $(LIBDIR)/[email protected] - -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) diff --git a/sci-chemistry/ambertools/metadata.xml b/sci-chemistry/ambertools/metadata.xml deleted file mode 100644 index d10bde235ea..00000000000 --- a/sci-chemistry/ambertools/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="person"> - <email>[email protected]</email> - <name>Alexey Shvetsov</name> - </maintainer> -<maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata>
