From c33a68684cd06424ec78c6983f93336109d91cb5 Mon Sep 17 00:00:00 2001 From: Stefan Kuczera 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