From 611fb829a108174fe80f57a367acceed33894168 Mon Sep 17 00:00:00 2001 From: Maho Nakata Date: Fri, 22 Aug 2008 22:23:17 +0000 Subject: [PATCH] Update to 2.98. --- science/libghemical/Makefile | 24 ++-------- science/libghemical/distinfo | 6 +-- science/libghemical/files/patch-configure.ac | 47 +++----------------- science/libghemical/files/patch-f2c | 23 ---------- science/libghemical/pkg-plist | 15 ++++--- 5 files changed, 21 insertions(+), 94 deletions(-) delete mode 100644 science/libghemical/files/patch-f2c diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile index d4f5e9713f0c..b2cc267df2f3 100644 --- a/science/libghemical/Makefile +++ b/science/libghemical/Makefile @@ -5,10 +5,9 @@ # $FreeBSD$ PORTNAME= libghemical -PORTVERSION= 2.10 -PORTREVISION= 4 +PORTVERSION= 2.98 CATEGORIES= science -MASTER_SITES= http://www.uku.fi/~thassine/projects/download/ \ +MASTER_SITES= http://www.uku.fi/~thassine/projects/download/release20080731/ \ http://bioinformatics.org/ghemical/download/ DISTNAME= ${PORTNAME}-${PORTVERSION} @@ -28,25 +27,10 @@ USE_LDCONFIG= yes .include USE_FORTRAN= yes +USE_AUTOTOOLS= autoconf:262 +CONFIGURE_ARGS+= --enable-mpqc --enable-openbabel --enable-mopac7 CONFIGURE_ENV+= FC="${FC}" F77="${F77}" FFLAGS="${FFLAGS}" -.if exists(${LOCALBASE}/lib/libatlas_r.so) && !defined(WITH_BLAS) -WITH_ATLAS= yes -.endif -.if defined(WITH_ATLAS) -LIB_DEPENDS+= atlas.2:${PORTSDIR}/math/atlas -BLAS= -lf77blas -latlas -LAPACK= -lalapack -.else -LIB_DEPENDS+= blas.2:${PORTSDIR}/math/blas -LIB_DEPENDS+= lapack.4:${PORTSDIR}/math/lapack -BLAS= -lblas -LAPACK= -llapack -.endif - -CONFIGURE_ARGS+= --enable-mopac7 --enable-mpqc --enable-openbabel --with-blas="-L${LOCALBASE}/lib ${BLAS}" -with-lapack="-L${LOCALBASE}/lib ${LAPACK}" - -USE_AUTOTOOLS= autoconf:262 PLIST_SUB= LIBGHEMICAL_VERSION="${PORTVERSION}" .include diff --git a/science/libghemical/distinfo b/science/libghemical/distinfo index c23da640d46f..c55a9920b849 100644 --- a/science/libghemical/distinfo +++ b/science/libghemical/distinfo @@ -1,3 +1,3 @@ -MD5 (libghemical-2.10.tar.gz) = a248fc3aebf26582367326716f208594 -SHA256 (libghemical-2.10.tar.gz) = b0d6639d3b79f865cffb8cf4c2721f6bc7e81c562240a10441766358f4576a7e -SIZE (libghemical-2.10.tar.gz) = 690680 +MD5 (libghemical-2.98.tar.gz) = 9ca4a60ba9b98f3c5003ee2e1a0ffeb0 +SHA256 (libghemical-2.98.tar.gz) = b4b0f037ed6632c84c6074badeb65cf52d04cbc5580e258275295b7520bd8bf6 +SIZE (libghemical-2.98.tar.gz) = 716300 diff --git a/science/libghemical/files/patch-configure.ac b/science/libghemical/files/patch-configure.ac index 9487ccf730d7..be873d184dd0 100644 --- a/science/libghemical/files/patch-configure.ac +++ b/science/libghemical/files/patch-configure.ac @@ -1,48 +1,13 @@ ---- configure.ac.orig Mon Apr 24 19:58:14 2006 -+++ configure.ac Mon Jul 3 10:54:47 2006 -@@ -46,6 +46,16 @@ - ;; - esac - -+AC_ARG_WITH(blas, -+[ --with-blas Gives BLAS name you use(e.g., -lblas).], -+BLAS=$withval -+) -+ -+AC_ARG_WITH(lapack, -+[ --with-lapack Gives LAPACK name you use(e.g., -llapack).], -+LAPACK=$withval -+) -+ - AC_ARG_ENABLE(mpqc,[ --enable-mpqc compile with MPQC support],WITH_MPQC="$enableval",WITH_MPQC="no") - AC_ARG_ENABLE(mopac7,[ --enable-mopac7 compile with MOPAC7 support],WITH_MOPAC7="$enableval",WITH_MOPAC7="no") - ##removed20060208##AC_ARG_ENABLE(openbabel,[ --enable-openbabel compile with OpenBabel support],WITH_OPENBABEL="$enableval",WITH_OPENBABEL="no") -@@ -69,8 +79,26 @@ - AC_CHECK_LIB([m], [acos]) +--- configure.ac~ 2008-07-31 19:22:53.000000000 +0900 ++++ configure.ac 2008-08-23 06:17:58.000000000 +0900 +@@ -89,8 +89,8 @@ + AC_CHECK_LIB(m,acos,,[AC_MSG_ERROR([math library missing])]) if test $WITH_MPQC = yes; then - AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support])) - AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])) -+ -+#Blas and lapack ...actually not checked... -+BLAS="" -+ if test "$BLASNAME" = NONE; then -+ AC_MSG_ERROR([BLAS is required to complete the build]) -+ else -+ HAVE_BLAS="yes" -+ BLAS="$BLASNAME" -+ fi -+ -+ AC_SUBST(HAVE_BLAS) -+ -+LAPACK="" -+if test "$LAPACKNAME" = NONE; then -+ AC_MSG_ERROR([LAPACK is required to complete the build]) -+else -+ HAVE_LAPACK="yes" -+ LAPACK="$LAPACKNAME" -+fi -+ ++# AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support])) ++# AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])) AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no") if test "${HAVE_MPQC}" = "yes"; then AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC]) diff --git a/science/libghemical/files/patch-f2c b/science/libghemical/files/patch-f2c deleted file mode 100644 index be95ed1790cd..000000000000 --- a/science/libghemical/files/patch-f2c +++ /dev/null @@ -1,23 +0,0 @@ -We need -lf2c here... we will never depend on g2c. ---- Makefile.in~ Wed Jan 17 12:08:54 2007 -+++ Makefile.in Wed Jan 17 12:39:20 2007 -@@ -128,7 +128,7 @@ - LTLIBOBJS = @LTLIBOBJS@ - MAKEINFO = @MAKEINFO@ - MOPAC7_CFLAGS = @MOPAC7_CFLAGS@ --MOPAC7_LIBS = @MOPAC7_LIBS@ -+MOPAC7_LIBS = @MOPAC7_LIBS@ -lf2c - OBJEXT = @OBJEXT@ - PACKAGE = @PACKAGE@ - PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ - -why we need it here again? ---- libghemical.pc.in~ Tue Aug 1 19:46:49 2006 -+++ libghemical.pc.in Wed Jan 17 13:15:00 2007 -@@ -6,5 +6,5 @@ - Name: libghemical - Description: A library that contains molecular modelling functionality. - Version: @LIBVERSION@ --Libs: -L${libdir} -lghemical @SC_LIBS@ @MOPAC7_LIBS@ -+Libs: -L${libdir} -lghemical @SC_LIBS@ @MOPAC7_LIBS@ -lf2c - Cflags: -I${includedir}/ghemical @SC_CPPFLAGS@ @MOPAC7_CFLAGS@ diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist index eff439800d91..b0d626939960 100644 --- a/science/libghemical/pkg-plist +++ b/science/libghemical/pkg-plist @@ -17,14 +17,15 @@ include/ghemical/eng2_qm_mm.h include/ghemical/engine.h include/ghemical/geomopt.h include/ghemical/intcrd.h -include/ghemical/libghemicalconfig2.h include/ghemical/libghemicaldefine.h +include/ghemical/libghemical-features.h include/ghemical/mfinder.h include/ghemical/model.h include/ghemical/moldyn.h include/ghemical/notice.h include/ghemical/pop_ana.h include/ghemical/resonance.h +include/ghemical/sasaeval.h include/ghemical/search.h include/ghemical/seqbuild.h include/ghemical/tab_mm_default.h @@ -35,17 +36,17 @@ include/ghemical/typerule.h include/ghemical/utility.h include/ghemical/v3d.h @dirrm include/ghemical -lib/libghemical.so.0 +lib/libghemical.so.4 lib/libghemical.so lib/libghemical.la lib/libghemical.a lib/pkgconfig/libghemical.pc @dirrm lib/pkgconfig -share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino02.in -share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct02.in -share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont02.in -share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc02.in -share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99.dat +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino94_MOD.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct94.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont94.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc94_MOD.in +share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99_frcmod_ff99SB.dat share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/amino.txt share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/nucleic.txt share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/atomtypes.txt