Date: Thu, 25 Sep 2014 11:04:03 +0000 (UTC) From: John Marino <marino@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r369236 - in head/science: ghemical libghemical libint mpqc Message-ID: <201409251104.s8PB43lY004283@svn.freebsd.org>
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Author: marino Date: Thu Sep 25 11:04:02 2014 New Revision: 369236 URL: http://svnweb.freebsd.org/changeset/ports/369236 QAT: https://qat.redports.org/buildarchive/r369236/ Log: science: Fix mpqc, libint and unbreak ghemical, and libghemical atomically science/ghemical would not link because libghemical.so (from science/ libghemical port) had never been properly linked. Links to all mpqc "SC" libraries were added to LDFLAGS to rectify this. The configure breakage and solution is described below. After the version of lang/gcc was bumped from 4.7 to 4.8, science/libghemical ceased to configure and it was marked broken. After recreating the conftest, it was discovered that two versions incompatible versions of libgcc_s.so were getting pulled in by the realtime linker: the base version and the gcc48 ports version. The base version was getting pulled in by science/libint. To unbreak libghemical, libint is now built with lang/gcc. It was necessary to force libtool to link with LDFLAGS that Mk/bsd.gcc.mk sets so that the runpaths match across libraries used by libghemical. When science/mpqc was staged, it utilized libtool which renumbered all the library versions from 8.0.1 to 7.1.0. This was caused by the age component being greater than 0. By patching configure.in with a new version, we can generate major SHLIB of 8 again. While here, fix the bin/sc-config tool to remove a bad include cflag. With this fixes, science/ghemical builds successfully. Bump all 4 of these ports, remove any BROKEN designation and remove redundant @dirrm in pkg-plist Modified: head/science/ghemical/Makefile head/science/ghemical/pkg-plist head/science/libghemical/Makefile head/science/libghemical/pkg-plist head/science/libint/Makefile head/science/libint/pkg-plist head/science/mpqc/Makefile head/science/mpqc/pkg-plist Modified: head/science/ghemical/Makefile ============================================================================== --- head/science/ghemical/Makefile Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/ghemical/Makefile Thu Sep 25 11:04:02 2014 (r369236) @@ -3,7 +3,7 @@ PORTNAME= ghemical PORTVERSION= 3.0.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/release20111012/ \ http://bioinformatics.org/ghemical/download/current @@ -25,7 +25,8 @@ USES= fortran gettext gmake pkgconfig USE_GNOME= glib20 gtk20 libglade2 USE_GL= glut GNU_CONFIGURE= yes -CONFIGURE_ARGS= --enable-gamess --enable-mpqc --enable-openbabel --enable-gtk --enable-threads --enable-mopac7 +CONFIGURE_ARGS= --enable-gamess --enable-mpqc --enable-openbabel --enable-gtk \ + --enable-threads --enable-mopac7 PLIST_SUB= GHEMICAL_VERSION="${PORTVERSION}" CPPFLAGS= -I${LOCALBASE}/include Modified: head/science/ghemical/pkg-plist ============================================================================== --- head/science/ghemical/pkg-plist Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/ghemical/pkg-plist Thu Sep 25 11:04:02 2014 (r369236) @@ -151,18 +151,3 @@ share/ghemical/%%GHEMICAL_VERSION%%/pixm %%NLS%%share/locale/pt_BR/LC_MESSAGES/ghemical.mo %%NLS%%share/locale/ru/LC_MESSAGES/ghemical.mo %%NLS%%share/locale/sq/LC_MESSAGES/ghemical.mo -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/pixmaps -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs/images -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/user-docs -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/glade -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/tautomeric_shift_keto_enol -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/sigmatropic_rearrangement_Cope -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/cycloaddition_Diels-Alder -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_methide_shift -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/carbocation_rearrangement_hydride_shift -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/SN2-reaction -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search/E2-reaction -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples/transition_state_search -@dirrm share/ghemical/%%GHEMICAL_VERSION%%/examples -@dirrm share/ghemical/%%GHEMICAL_VERSION%% -@dirrm share/ghemical Modified: head/science/libghemical/Makefile ============================================================================== --- head/science/libghemical/Makefile Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/libghemical/Makefile Thu Sep 25 11:04:02 2014 (r369236) @@ -3,7 +3,7 @@ PORTNAME= libghemical PORTVERSION= 3.0.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/release20111012/ \ http://bioinformatics.org/ghemical/download/current @@ -11,8 +11,6 @@ MASTER_SITES= http://bioinformatics.org/ MAINTAINER= ports@FreeBSD.org COMMENT= Support libraries of science/ghemical port -BROKEN= Fails to configure - BUILD_DEPENDS= obabel:${PORTSDIR}/science/openbabel \ intltool-update:${PORTSDIR}/textproc/intltool \ ld:${PORTSDIR}/devel/binutils @@ -26,7 +24,13 @@ USE_LDCONFIG= yes CONFIGURE_ARGS+= --enable-mpqc CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib +LDFLAGS= -L${LOCALBASE}/lib -lSCbasis -lSCcints -lSCclass \ + -lSCcontainer -lSCdft -lSCgroup -lSCintv3 -lSCisosurf \ + -lSCkeyval -lSCmbpt -lSCmbptr12 -lSCmisc -lSCmolecule \ + -lSCoint3 -lSCoptimize -lSCoptions -lSCpsi -lSCref \ + -lSCrender -lSCscf -lSCscmat -lSCsolvent -lSCstate \ + -lSCsymmetry -lSCwfn \ + -lgfortran -lpthread -lblas -llapack PLIST_SUB= LIBGHEMICAL_VERSION="${PORTVERSION}" INSTALL_TARGET= install-strip Modified: head/science/libghemical/pkg-plist ============================================================================== --- head/science/libghemical/pkg-plist Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/libghemical/pkg-plist Thu Sep 25 11:04:02 2014 (r369236) @@ -36,7 +36,6 @@ include/ghemical/typedef.h include/ghemical/typerule.h include/ghemical/utility.h include/ghemical/v3d.h -@dirrm include/ghemical lib/libghemical.so.5.0.1 lib/libghemical.so.5 lib/libghemical.so @@ -74,13 +73,3 @@ share/locale/mk/LC_MESSAGES/libghemical. share/locale/pt_BR/LC_MESSAGES/libghemical.mo share/locale/ru/LC_MESSAGES/libghemical.mo share/locale/sq/LC_MESSAGES/libghemical.mo -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52 -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/amber -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/builder -@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%% -@dirrm share/libghemical Modified: head/science/libint/Makefile ============================================================================== --- head/science/libint/Makefile Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/libint/Makefile Thu Sep 25 11:04:02 2014 (r369236) @@ -3,14 +3,21 @@ PORTNAME= libint PORTVERSION= 1.1.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= http://www.files.chem.vt.edu/chem-dept/valeev/software/libint/src/ MAINTAINER= ports@FreeBSD.org COMMENT= Evaluate the integrals in modern atomic and molecular theory +# USE_GCC=yes is required because libint is used with mpqc which is built +# by gfortran48 (from lang/gcc) and these two libraries each try to pull in +# a different version of libgcc_s.so which fails. Forcing this port to +# build with lang/gcc as well resolves the conflict that manifests in +# science/libghemical + USES= perl5 gmake libtool +USE_GCC= yes USE_LDCONFIG= yes ALL_TARGET= # empty @@ -18,7 +25,8 @@ GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared post-patch: - @${REINPLACE_CMD} -e 's|echo aout|echo elf|' ${WRKSRC}/configure + @${REINPLACE_CMD} -e 's| -rpath|${LDFLAGS} -rpath|g' \ + ${WRKSRC}/src/lib/MakeVars.in post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so Modified: head/science/libint/pkg-plist ============================================================================== --- head/science/libint/pkg-plist Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/libint/pkg-plist Thu Sep 25 11:04:02 2014 (r369236) @@ -15,6 +15,3 @@ lib/libr12-stable.so.1 lib/libr12-stable.so.1.0.0 lib/libr12.a lib/libr12.so -@dirrm include/libderiv -@dirrm include/libint -@dirrm include/libr12 Modified: head/science/mpqc/Makefile ============================================================================== --- head/science/mpqc/Makefile Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/mpqc/Makefile Thu Sep 25 11:04:02 2014 (r369236) @@ -3,7 +3,7 @@ PORTNAME= mpqc PORTVERSION= 2.3.1 -PORTREVISION= 23 +PORTREVISION= 24 CATEGORIES= science parallel MASTER_SITES= SF @@ -16,12 +16,11 @@ GNU_CONFIGURE= yes USES= fortran gmake libtool perl5 tar:bzip2 USE_AUTOTOOLS= autoconf USE_LDCONFIG= yes -MPQC_COMMAND= ${PREFIX}/bin/mpqc CONFIGURE_ARGS+=--with-cc=${CC} \ --with-cxx=${CXX} \ --with-f77=${FC} \ - --with-include="-I${WRKDIR} -I${LOCALBASE}/include" \ + --with-include="-I${LOCALBASE}/include" \ --with-libdirs="-L${LOCALBASE}/lib ${LDFLAGS}" \ --with-blas="${BLAS}" \ --with-lapack="${LAPACK}" \ @@ -84,6 +83,11 @@ CFLAGS+= -O2 -ffast-math CXXFLAGS+= -O2 -ffast-math .endif +post-patch: + # To get so.8.0.1, we need to -version-info to show 8.1.0 + # <current>:<rev>:<age> => so.(current-age).(age).(rev) + ${REINPLACE_CMD} -e 's|\[8:0:1\]|\[8:1:0\]|' ${WRKSRC}/configure.in + do-build: (cd ${WRKSRC} && ${MAKE_CMD}) .if ${PORT_OPTIONS:MDOCS} Modified: head/science/mpqc/pkg-plist ============================================================================== --- head/science/mpqc/pkg-plist Thu Sep 25 11:03:20 2014 (r369235) +++ head/science/mpqc/pkg-plist Thu Sep 25 11:04:02 2014 (r369236) @@ -353,108 +353,108 @@ include/scdirlist.h @dirrm include/chemistry lib/libSCbasis.a lib/libSCbasis.so -lib/libSCbasis.so.7 -lib/libSCbasis.so.7.1.0 +lib/libSCbasis.so.8 +lib/libSCbasis.so.8.0.1 lib/libSCcints.so -lib/libSCcints.so.7 -lib/libSCcints.so.7.1.0 +lib/libSCcints.so.8 +lib/libSCcints.so.8.0.1 lib/libSCcints.a lib/libSCclass.a lib/libSCclass.so -lib/libSCclass.so.7 -lib/libSCclass.so.7.1.0 +lib/libSCclass.so.8 +lib/libSCclass.so.8.0.1 lib/libSCcontainer.a lib/libSCcontainer.so -lib/libSCcontainer.so.7 -lib/libSCcontainer.so.7.1.0 +lib/libSCcontainer.so.8 +lib/libSCcontainer.so.8.0.1 lib/libSCdft.a lib/libSCdft.so -lib/libSCdft.so.7 -lib/libSCdft.so.7.1.0 +lib/libSCdft.so.8 +lib/libSCdft.so.8.0.1 lib/libSCgroup.a lib/libSCgroup.so -lib/libSCgroup.so.7 -lib/libSCgroup.so.7.1.0 +lib/libSCgroup.so.8 +lib/libSCgroup.so.8.0.1 lib/libSCintv3.a lib/libSCintv3.so -lib/libSCintv3.so.7 -lib/libSCintv3.so.7.1.0 +lib/libSCintv3.so.8 +lib/libSCintv3.so.8.0.1 lib/libSCisosurf.a lib/libSCisosurf.so -lib/libSCisosurf.so.7 -lib/libSCisosurf.so.7.1.0 +lib/libSCisosurf.so.8 +lib/libSCisosurf.so.8.0.1 lib/libSCkeyval.a lib/libSCkeyval.so -lib/libSCkeyval.so.7 -lib/libSCkeyval.so.7.1.0 +lib/libSCkeyval.so.8 +lib/libSCkeyval.so.8.0.1 lib/libSCmbpt.a lib/libSCmbpt.so -lib/libSCmbpt.so.7 -lib/libSCmbpt.so.7.1.0 +lib/libSCmbpt.so.8 +lib/libSCmbpt.so.8.0.1 lib/libSCmbptr12.so -lib/libSCmbptr12.so.7 -lib/libSCmbptr12.so.7.1.0 +lib/libSCmbptr12.so.8 +lib/libSCmbptr12.so.8.0.1 lib/libSCmbptr12.a lib/libSCmisc.a lib/libSCmisc.so -lib/libSCmisc.so.7 -lib/libSCmisc.so.7.1.0 +lib/libSCmisc.so.8 +lib/libSCmisc.so.8.0.1 lib/libSCmolecule.a lib/libSCmolecule.so -lib/libSCmolecule.so.7 -lib/libSCmolecule.so.7.1.0 +lib/libSCmolecule.so.8 +lib/libSCmolecule.so.8.0.1 lib/libSCoint3.a lib/libSCoint3.so -lib/libSCoint3.so.7 -lib/libSCoint3.so.7.1.0 +lib/libSCoint3.so.8 +lib/libSCoint3.so.8.0.1 lib/libSCoptimize.a lib/libSCoptimize.so -lib/libSCoptimize.so.7 -lib/libSCoptimize.so.7.1.0 +lib/libSCoptimize.so.8 +lib/libSCoptimize.so.8.0.1 lib/libSCoptions.a lib/libSCoptions.so -lib/libSCoptions.so.7 -lib/libSCoptions.so.7.1.0 +lib/libSCoptions.so.8 +lib/libSCoptions.so.8.0.1 lib/libSCpsi.a lib/libSCpsi.so -lib/libSCpsi.so.7 -lib/libSCpsi.so.7.1.0 +lib/libSCpsi.so.8 +lib/libSCpsi.so.8.0.1 lib/libSCref.a lib/libSCref.so -lib/libSCref.so.7 -lib/libSCref.so.7.1.0 +lib/libSCref.so.8 +lib/libSCref.so.8.0.1 lib/libSCrender.a lib/libSCrender.so -lib/libSCrender.so.7 -lib/libSCrender.so.7.1.0 +lib/libSCrender.so.8 +lib/libSCrender.so.8.0.1 lib/libSCscf.a lib/libSCscf.so -lib/libSCscf.so.7 -lib/libSCscf.so.7.1.0 +lib/libSCscf.so.8 +lib/libSCscf.so.8.0.1 lib/libSCscmat.a lib/libSCscmat.so -lib/libSCscmat.so.7 -lib/libSCscmat.so.7.1.0 +lib/libSCscmat.so.8 +lib/libSCscmat.so.8.0.1 lib/libSCsolvent.a lib/libSCsolvent.so -lib/libSCsolvent.so.7 -lib/libSCsolvent.so.7.1.0 +lib/libSCsolvent.so.8 +lib/libSCsolvent.so.8.0.1 lib/libSCstate.a lib/libSCstate.so -lib/libSCstate.so.7 -lib/libSCstate.so.7.1.0 +lib/libSCstate.so.8 +lib/libSCstate.so.8.0.1 lib/libSCsymmetry.a lib/libSCsymmetry.so -lib/libSCsymmetry.so.7 -lib/libSCsymmetry.so.7.1.0 +lib/libSCsymmetry.so.8 +lib/libSCsymmetry.so.8.0.1 lib/libSCwfn.a lib/libSCwfn.so -lib/libSCwfn.so.7 -lib/libSCwfn.so.7.1.0 +lib/libSCwfn.so.8 +lib/libSCwfn.so.8.0.1 lib/libmpqc.a lib/libmpqc.so -lib/libmpqc.so.7 -lib/libmpqc.so.7.1.0 +lib/libmpqc.so.8 +lib/libmpqc.so.8.0.1 %%DOCS%%man/man1/mpqc.1.gz %%DOCS%%man/man1/mpqcrun.1.gz %%DOCS%%man/man1/scls.1.gz
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