commit: 2176533fcbc07aabe6a5c9a45e6bb1e499773592 Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> AuthorDate: Thu Sep 24 14:46:15 2020 +0000 Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> CommitDate: Thu Sep 24 14:46:25 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2176533f
sci-chemistry/vmd: Apply fixes to plugins Adapt patch to 1.9.4 Closes: https://bugs.gentoo.org/741978 Thanks-to: Hypoon Package-Manager: Portage-3.0.7, Repoman-3.0.1 Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> .../vmd/files/vmd-1.9.4-gentoo-plugins.patch | 604 +++++++++++++++++++++ sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 6 + 2 files changed, 610 insertions(+) diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch new file mode 100644 index 00000000000..c6ea769932f --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-plugins.patch @@ -0,0 +1,604 @@ +From c33a68684cd06424ec78c6983f93336109d91cb5 Mon Sep 17 00:00:00 2001 +From: Stefan Kuczera <[email protected]> +Date: Sat, 21 Jan 2017 13:20:45 +0100 +Subject: [PATCH] Squashed patches + +--- + plugins/Make-arch | 3 +- + plugins/Makefile | 20 +++--- + plugins/autopsf/Makefile | 4 +- + plugins/catdcd/Makefile | 4 +- + plugins/cionize/Makefile | 6 +- + plugins/clustalw/Makefile | 2 +- + plugins/cluster/Makefile | 2 +- + plugins/hesstrans/Makefile | 2 +- + plugins/libbiokit/Makefile | 14 ++-- + plugins/molfile_plugin/Makefile | 144 ++++++++++++++++++++-------------------- + plugins/phylotree/Makefile | 2 +- + plugins/rnaview/Makefile | 2 +- + plugins/stamp/Makefile | 2 +- + 13 files changed, 105 insertions(+), 102 deletions(-) + +diff --git a/plugins/Make-arch b/plugins/Make-arch +index 19d2b6c..937ad9e 100755 +--- a/plugins/Make-arch ++++ b/plugins/Make-arch +@@ -313,7 +313,8 @@ LINUX: + "AR = ar" \ + "NM = nm -p" \ + "RANLIB = touch" \ +- "SHLD = gcc -shared" ++ "SHLD = gcc -shared" \ ++ "SHXXLD = g++ -shared" + + LINUXALPHA: + $(MAKE) dynlibs staticlibs bins \ +diff --git a/plugins/Makefile b/plugins/Makefile +index 0fee349..6b07606 100755 +--- a/plugins/Makefile ++++ b/plugins/Makefile +@@ -150,25 +150,27 @@ distrib: + + include Make-arch + +-molfilelibs: +- cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1 +- cd molfile_plugin; $(MAKE) staticlibs && cd .. || exit 1 ++molfilelibs_static: ++ $(MAKE) -C molfile_plugin staticlibs ++ ++molfilelibs_dyn: ++ $(MAKE) -C molfile_plugin dynlibs + + win32molfilelibs: + cd molfile_plugin; $(MAKE) dynlibs && cd .. || exit 1 + cd molfile_plugin; $(MAKE) win32staticlibs && cd .. || exit 1 + +-dynlibs: molfilelibs +- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) dynlibs && cd .. || exit 1 ; done ++dynlibs: molfilelibs_dyn ++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir dynlibs; done + +-staticlibs: molfilelibs +- for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) staticlibs && cd .. || exit 1 ; done ++staticlibs: molfilelibs_static ++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir staticlibs; done + + win32staticlibs: win32molfilelibs + for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs && cd .. || exit 1 ; done + +-bins: +- for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) bins && cd .. || exit 1 ; done ++bins: molfilelibs_dyn ++ for dir in $(BUILDDIRS); do $(MAKE) -C $$dir bins; done + + win32bins: + for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE) win32bins && cd .. || exit 1 ; done +diff --git a/plugins/autopsf/Makefile b/plugins/autopsf/Makefile +index 3b35d10..8e1527e 100644 +--- a/plugins/autopsf/Makefile ++++ b/plugins/autopsf/Makefile +@@ -49,8 +49,8 @@ AUTOPSFOBJS=${ARCHDIR}/psfatom.o \ + + ${ARCHDIR}/psfcheck.so : ${AUTOPSFOBJS} + if [ -n "${TCLSHLD}" ]; \ +- then ${TCLSHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ +- else ${SHLD} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ ++ then ${TCLSHLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \ ++ else ${SHXXLD} ${LDFLAGS} $(LOPTO)$@ ${AUTOPSFOBJS} ${TCLLIB} ${TCLLDFLAGS}; \ + fi + + ${ARCHDIR}/psfatom.o : psfatom.h psfatom.C +diff --git a/plugins/catdcd/Makefile b/plugins/catdcd/Makefile +index d6c58c5..1637a3c 100644 +--- a/plugins/catdcd/Makefile ++++ b/plugins/catdcd/Makefile +@@ -45,8 +45,8 @@ ${ARCHDIR}/catdcd.exe : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfi + LINK ${CATDCDOBJS} /OUT:${ARCHDIR}/catdcd.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} + + # all other platforms +-${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a +- ${CXX} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm ++${ARCHDIR}/catdcd : ${CATDCDOBJS} ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${CATDCDOBJS} -o ${ARCHDIR}/catdcd -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm + + ${ARCHDIR}/hash.o: hash.h hash.c + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o +diff --git a/plugins/cionize/Makefile b/plugins/cionize/Makefile +index bcb2510..e02241b 100644 +--- a/plugins/cionize/Makefile ++++ b/plugins/cionize/Makefile +@@ -52,8 +52,8 @@ ${ARCHDIR}/cionize.exe : ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPI + LINK ${IONIZEOBJS} ${MGPOTOBJS} /OUT:${ARCHDIR}/cionize.exe /LIBPATH:${COMPILEDIR}/lib_${ARCH}/molfile libmolfile_plugin.lib ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} + + # all other platforms +-${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm ++${ARCHDIR}/cionize: ${IONIZEOBJS} ${MGPOTOBJS} ${ARCHDIR}/cionize.o ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.a ${COMPILEDIR}/lib_${ARCH}/molfile/libmolfile_plugin.h ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/cionize.o ${IONIZEOBJS} ${MGPOTOBJS} -o ${ARCHDIR}/cionize -L${COMPILEDIR}/lib_${ARCH}/molfile -lmolfile_plugin ${TCLLIB} ${TCLLDFLAGS} ${NETCDFLIB} ${NETCDFLDFLAGS} ${EXPATLIB} ${EXPATLDFLAGS} ${SQLITELIB} ${SQLITELDFLAGS} -lm + + ${ARCHDIR}/hash.o: hash.h hash.c + ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/hash.c $(COPTO)${ARCHDIR}/hash.o +@@ -66,7 +66,7 @@ ${ARCHDIR}/util.o: util.h util.c + + ${ARCHDIR}/getplugins.o: getplugins.h getplugins.c + ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/getplugins.c $(COPTO)${ARCHDIR}/getplugins.o +- ++ + ${ARCHDIR}/energythr.o: energythr.h energythr.c ${ARCHDIR}/util.o ${ARCHDIR}/threads.o + ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/energythr.c $(COPTO)${ARCHDIR}/energythr.o + +diff --git a/plugins/clustalw/Makefile b/plugins/clustalw/Makefile +index 6329f64..3443720 100644 +--- a/plugins/clustalw/Makefile ++++ b/plugins/clustalw/Makefile +@@ -66,7 +66,7 @@ OBJS = ${ARCHDIR}/alnscore.o \ + ${ARCHDIR}/clustalw.exe: ${OBJS} + LINK ${OBJS} /OUT:${ARCHDIR}/clustalw.exe + ${ARCHDIR}/clustalw: ${OBJS} +- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm ++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/clustalw -lm + + + # Objects. +diff --git a/plugins/cluster/Makefile b/plugins/cluster/Makefile +index 99d347e..c2d30ae 100644 +--- a/plugins/cluster/Makefile ++++ b/plugins/cluster/Makefile +@@ -48,7 +48,7 @@ ${ARCHDIR}/cluster.exe : ${OBJS} + + # all other platforms + ${ARCHDIR}/cluster : ${OBJS} +- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/cluster -lm + + ${ARCHDIR}/cluster.o: ${SRCDIR}/cluster.c + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/cluster.c $(COPTO)${ARCHDIR}/cluster.o +diff --git a/plugins/hesstrans/Makefile b/plugins/hesstrans/Makefile +index 76ee306..db46b82 100644 +--- a/plugins/hesstrans/Makefile ++++ b/plugins/hesstrans/Makefile +@@ -85,7 +85,7 @@ HESSTRANSOBJS=${ARCHDIR}/newmat1.o \ + ${ARCHDIR}/hesstrans.so : ${HESSTRANSOBJS} + if [ -n "${TCLSHLD}" ]; \ + then ${TCLSHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ +- else ${SHLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ ++ else ${SHXXLD} $(LOPTO)$@ ${HESSTRANSOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ + fi + + +diff --git a/plugins/libbiokit/Makefile b/plugins/libbiokit/Makefile +index 7a66d08..da764dd 100644 +--- a/plugins/libbiokit/Makefile ++++ b/plugins/libbiokit/Makefile +@@ -98,7 +98,7 @@ OBJS = ${DYNLIBOBJS} \ + ${ARCHDIR}/tcl_libbiokit.so : ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} + if [ -n "${TCLSHLD}" ]; \ + then ${TCLSHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ +- else ${SHLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ ++ else ${SHXXLD} $(LOPTO)$@ ${ARCHDIR}/tcl_libbiokit_wrap.o ${ARCHDIR}/tcl_libbiokit.o ${DYNLIBOBJS} ${TCLLIB} ${TCLLDFLAGS} ${LDFLAGS}; \ + fi + ${ARCHDIR}/tcl_libbiokit_wrap.o : ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp + ${CXX} ${CXXFLAGS} ${TCLINC} ${INCDIR} -c ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp $(COPTO)${ARCHDIR}/tcl_libbiokit_wrap.o +@@ -111,7 +111,7 @@ ${INTERFACESRCDIR}/tcl_libbiokit_wrap.cpp : ${INTERFACESRCDIR}/tcl_libbiokit.i + ${ARCHDIR}/percid.exe: ${ARCHDIR}/percid.o ${OBJS} + LINK ${ARCHDIR}/percid.o ${OBJS} /OUT:${ARCHDIR}/percid.exe + ${ARCHDIR}/percid: ${ARCHDIR}/percid.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/percid.o ${OBJS} -o ${ARCHDIR}/percid -lm + ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/percid.cpp $(COPTO)${ARCHDIR}/percid.o + +@@ -119,7 +119,7 @@ ${ARCHDIR}/percid.o: ${UTILSRCDIR}/percid.cpp + ${ARCHDIR}/qpair.exe: ${ARCHDIR}/qPair.o ${OBJS} + LINK ${ARCHDIR}/qPair.o ${OBJS} /OUT:${ARCHDIR}/qpair.exe + ${ARCHDIR}/qpair: ${ARCHDIR}/qPair.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/qPair.o ${OBJS} -o ${ARCHDIR}/qpair -lm + ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/qPair.cpp $(COPTO)${ARCHDIR}/qPair.o + +@@ -127,7 +127,7 @@ ${ARCHDIR}/qPair.o: ${UTILSRCDIR}/qPair.cpp + ${ARCHDIR}/rmsd.exe: ${ARCHDIR}/rmsd.o ${OBJS} + LINK ${ARCHDIR}/rmsd.o ${OBJS} /OUT:${ARCHDIR}/rmsd.exe + ${ARCHDIR}/rmsd: ${ARCHDIR}/rmsd.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/rmsd.o ${OBJS} -o ${ARCHDIR}/rmsd -lm + ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/rmsd.cpp $(COPTO)${ARCHDIR}/rmsd.o + +@@ -135,7 +135,7 @@ ${ARCHDIR}/rmsd.o: ${UTILSRCDIR}/rmsd.cpp + ${ARCHDIR}/q.exe: ${ARCHDIR}/Q.o ${OBJS} + LINK ${ARCHDIR}/Q.o ${OBJS} /OUT:${ARCHDIR}/q.exe + ${ARCHDIR}/q: ${ARCHDIR}/Q.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/Q.o ${OBJS} -o ${ARCHDIR}/q -lm + ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/Q.cpp $(COPTO)${ARCHDIR}/Q.o + +@@ -143,7 +143,7 @@ ${ARCHDIR}/Q.o: ${UTILSRCDIR}/Q.cpp + ${ARCHDIR}/seqqr.exe: ${ARCHDIR}/seqqr.o ${OBJS} + LINK ${ARCHDIR}/seqqr.o ${OBJS} /OUT:${ARCHDIR}/seqqr.exe + ${ARCHDIR}/seqqr: ${ARCHDIR}/seqqr.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/seqqr.o ${OBJS} -o ${ARCHDIR}/seqqr -lm + ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/seqqr.cpp $(COPTO)${ARCHDIR}/seqqr.o + +@@ -151,7 +151,7 @@ ${ARCHDIR}/seqqr.o: ${UTILSRCDIR}/seqqr.cpp + ${ARCHDIR}/structqr.exe : ${ARCHDIR}/structqr.o ${OBJS} + LINK ${ARCHDIR}/structqr.o ${OBJS} /OUT:${ARCHDIR}/structqr.exe + ${ARCHDIR}/structqr: ${ARCHDIR}/structqr.o ${OBJS} +- ${CXX} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${ARCHDIR}/structqr.o ${OBJS} -o ${ARCHDIR}/structqr -lm + ${ARCHDIR}/structqr.o: ${UTILSRCDIR}/structqr.cpp + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${UTILSRCDIR}/structqr.cpp $(COPTO)${ARCHDIR}/structqr.o + +diff --git a/plugins/molfile_plugin/Makefile b/plugins/molfile_plugin/Makefile +index 4c47615..1c77ddf 100644 +--- a/plugins/molfile_plugin/Makefile ++++ b/plugins/molfile_plugin/Makefile +@@ -15,7 +15,7 @@ + VPATH = src ../include ${ARCHDIR} + + SCCFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" +-SCXXFLAGS = $(CCFLAGS) $(DEF)"STATIC_PLUGIN" ++SCXXFLAGS = $(CXXFLAGS) $(DEF)"STATIC_PLUGIN" + + # + # Rules +@@ -206,209 +206,209 @@ + # + + abinitplugin.so: ${ARCHDIR}/abinitplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + amiraplugin.so: ${ARCHDIR}/amiraplugin.o + $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + avsplugin.so: ${ARCHDIR}/avsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + babelplugin.so: ${ARCHDIR}/babelplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + basissetplugin.so: ${ARCHDIR}/basissetplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + bgfplugin.so: ${ARCHDIR}/bgfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + binposplugin.so: ${ARCHDIR}/binposplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + biomoccaplugin.so: ${ARCHDIR}/biomoccaplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + brixplugin.so: ${ARCHDIR}/brixplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + carplugin.so: ${ARCHDIR}/carplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + ccp4plugin.so: ${ARCHDIR}/ccp4plugin.o + $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + corplugin.so: ${ARCHDIR}/corplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + cpmdplugin.so: ${ARCHDIR}/cpmdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + crdplugin.so: ${ARCHDIR}/crdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + cubeplugin.so: ${ARCHDIR}/cubeplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + dcdplugin.so: ${ARCHDIR}/dcdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + dlpolyplugin.so: ${ARCHDIR}/dlpolyplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + dsn6plugin.so: ${ARCHDIR}/dsn6plugin.o + $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + dxplugin.so: ${ARCHDIR}/dxplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + edmplugin.so: ${ARCHDIR}/edmplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + fs4plugin.so: ${ARCHDIR}/fs4plugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + gamessplugin.so: ${ARCHDIR}/gamessplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + graspplugin.so: ${ARCHDIR}/graspplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + grdplugin.so: ${ARCHDIR}/grdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + gridplugin.so: ${ARCHDIR}/gridplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + gromacsplugin.so: ${ARCHDIR}/gromacsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + jsplugin.so: ${ARCHDIR}/jsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + lammpsplugin.so: ${ARCHDIR}/lammpsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + mapplugin.so: ${ARCHDIR}/mapplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + mdfplugin.so: ${ARCHDIR}/mdfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + mol2plugin.so: ${ARCHDIR}/mol2plugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + moldenplugin.so: ${ARCHDIR}/moldenplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + molemeshplugin.so: ${ARCHDIR}/molemeshplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + msmsplugin.so: ${ARCHDIR}/msmsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + namdbinplugin.so: ${ARCHDIR}/namdbinplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + offplugin.so: ${ARCHDIR}/offplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + orcaplugin.so: ${ARCHDIR}/orcaplugin.o + $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + parm7plugin.so: ${ARCHDIR}/parm7plugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + parmplugin.so: ${ARCHDIR}/parmplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + pbeqplugin.so: ${ARCHDIR}/pbeqplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + pdbplugin.so: ${ARCHDIR}/pdbplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + pdbxplugin.so: ${ARCHDIR}/pdbxplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + phiplugin.so: ${ARCHDIR}/phiplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + pltplugin.so: ${ARCHDIR}/pltplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + plyplugin.so: ${ARCHDIR}/plyplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + pqrplugin.so: ${ARCHDIR}/pqrplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + psfplugin.so: ${ARCHDIR}/psfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + raster3dplugin.so: ${ARCHDIR}/raster3dplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + rst7plugin.so: ${ARCHDIR}/rst7plugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + situsplugin.so: ${ARCHDIR}/situsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + spiderplugin.so: ${ARCHDIR}/spiderplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + stlplugin.so: ${ARCHDIR}/stlplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + tinkerplugin.so: ${ARCHDIR}/tinkerplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + uhbdplugin.so: ${ARCHDIR}/uhbdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspchgcarplugin.so: ${ARCHDIR}/vaspchgcarplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspoutcarplugin.so: ${ARCHDIR}/vaspoutcarplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspparchgplugin.so: ${ARCHDIR}/vaspparchgplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspposcarplugin.so: ${ARCHDIR}/vaspposcarplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vasp5xdatcarplugin.so: ${ARCHDIR}/vasp5xdatcarplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspxdatcarplugin.so: ${ARCHDIR}/vaspxdatcarplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vaspxmlplugin.so: ${ARCHDIR}/vaspxmlplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + vtkplugin.so: ${ARCHDIR}/vtkplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + xbgfplugin.so: ${ARCHDIR}/xbgfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + xsfplugin.so: ${ARCHDIR}/xsfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + xyzplugin.so: ${ARCHDIR}/xyzplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + + ## + ## In-development plugins that aren't part of the build quite yet... + ## + cpmdlogplugin.so: ${ARCHDIR}/cpmdlogplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + gaussianplugin.so: ${ARCHDIR}/gaussianplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + + ## +@@ -416,31 +416,31 @@ + ## dependencies of some kind + ## + dmsplugin.so: ${ARCHDIR}/dmsplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(SQLITELIB) $(SQLITELDFLAGS) $(LDFLAGS) + + dtrplugin.so: ${ARCHDIR}/dtrplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + hoomdplugin.so: ${ARCHDIR}/hoomdplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(EXPATLIB) $(EXPATLDFLAGS) $(LDFLAGS) + + lmplugin.so: ${ARCHDIR}/lmplugin.o + $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(HDFLIB) $(HDFLDFLAGS) $(LDFLAGS) + + maeffplugin.so: ${ARCHDIR}/maeffplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(LDFLAGS) + + netcdfplugin.so: ${ARCHDIR}/netcdfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(NETCDFLIB) $(NETCDFLDFLAGS) $(LDFLAGS) + + tngplugin.so: ${ARCHDIR}/tngplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TNGLIB) $(TNGLDFLAGS) $(LDFLAGS) + + vtfplugin.so: ${ARCHDIR}/vtfplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) + + webpdbplugin.so: ${ARCHDIR}/webpdbplugin.o +- $(SHLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) ++ $(SHXXLD) $(LOPTO)${ARCHDIR}/$@ $? $(TCLLIB) $(TCLLDFLAGS) $(LDFLAGS) + + + # +diff --git a/plugins/phylotree/Makefile b/plugins/phylotree/Makefile +index 6442747..0aceb4d 100644 +--- a/plugins/phylotree/Makefile ++++ b/plugins/phylotree/Makefile +@@ -54,7 +54,7 @@ ${ARCHDIR}/upgmaclu.exe : ${OBJS} + + # all other platforms + ${ARCHDIR}/upgmaclu : ${OBJS} +- ${CXX} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm ++ ${CXX} ${LDFLAGS} ${CXXFLAGS} ${OBJS} -o ${ARCHDIR}/upgmaclu -lm + + ${ARCHDIR}/upgmaclu.o: ${SRCDIR}/upgmaclu.c + ${CXX} ${CXXFLAGS} ${INCDIR} -c ${SRCDIR}/upgmaclu.c $(COPTO)${ARCHDIR}/upgmaclu.o +diff --git a/plugins/rnaview/Makefile b/plugins/rnaview/Makefile +index 16f070a..da71248 100644 +--- a/plugins/rnaview/Makefile ++++ b/plugins/rnaview/Makefile +@@ -67,7 +67,7 @@ OBJS = ${ARCHDIR}/analyze.o \ + ${ARCHDIR}/rnaview.exe: ${OBJS} + LINK ${OBJS} /OUT:${ARCHDIR}/rnaview.exe + ${ARCHDIR}/rnaview: ${OBJS} +- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm ++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/rnaview -lm + + ${ARCHDIR}/analyze.o: ${SRCDIR}/analyze.c + ${CC} ${CCFLAGS} ${INCDIR} -c ${SRCDIR}/analyze.c $(COPTO)${ARCHDIR}/analyze.o +diff --git a/plugins/stamp/Makefile b/plugins/stamp/Makefile +index f0fb515..aa8f6b6 100644 +--- a/plugins/stamp/Makefile ++++ b/plugins/stamp/Makefile +@@ -101,7 +101,7 @@ OBJS = ${ARCHDIR}/a3to1.o \ + ${ARCHDIR}/stamp.exe: ${OBJS} + LINK ${OBJS} /OUT:${ARCHDIR}/stamp.exe + ${ARCHDIR}/stamp: ${OBJS} +- ${CC} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm ++ ${CC} ${LDFLAGS} ${CCFLAGS} ${OBJS} -o ${ARCHDIR}/stamp -lm + + + # Objects. +-- +2.5.5 + diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild index 8ffb5a09007..db9e4f49e52 100644 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild +++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild @@ -83,6 +83,10 @@ src_prepare() { cd "${WORKDIR}" xdg_src_prepare + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html + eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-plugins.patch + use cuda && cuda_sanitize # Prepare plugins @@ -117,6 +121,8 @@ src_prepare() { cd "${S}" || die eapply "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch + + # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.patch # PREFIX
