VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Wed Sep 01 2004 - 02:18:16 CDT

hi John,

> Are you using GNU make or the BSD make utility? I suspect that
> the real problem here may be the make utility. If you're not using
> GNU make, go get a copy of it, compile it, install it as "gmake" or
> something that doesn't conflict with the BSD make utility, and then
> do the build using "gmake" instead of make. That will hopefully
> solve the problem.
i have both of them, my gmake is
        GNU Make 3.80
i am using it as
        gmake NETBSD TCLINC="/usr/pkg/include" TCLLIB="/usr/pkg/lib"
but i get
gmake dynlibs staticlibs \
"ARCH = NETBSD" \
"COPTO = -o " \
"LOPTO = -o " \
"CC = gcc" \
"CXX = g++" \
"CCFLAGS = -O2 -Wall -ansi" \
"CXXFLAGS = -O2 -Wall" \
"TCLLDFLAGS = -ltcl84" \
"NM = nm -p" \
"RANLIB = ranlib" \
gmake[1]: Entering directory `/scratch/vrbka/software/vmd/plugins'
for dir in apbsrun autoionize cliptool contactmap exectool imdmenu
membrane navigate pdbtool ramaplot rmsd solvate timeline vmdmovie
vmdtkcon zoomseq molfile_plugin psfgen autoimd ; do cd $dir && gmake
dynlibs && cd .. ; done
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/apbsrun'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/apbsrun'
gmake[2]: Entering directory
`/scratch/vrbka/software/vmd/plugins/autoionize'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/autoionize'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/cliptool'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/cliptool'
gmake[2]: Entering directory
`/scratch/vrbka/software/vmd/plugins/contactmap'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/contactmap'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/exectool'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/exectool'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/imdmenu'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/imdmenu'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/membrane'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/membrane'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/navigate'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/navigate'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/pdbtool'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/pdbtool'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/ramaplot'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/ramaplot'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/rmsd'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/rmsd'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/solvate'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/solvate'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/timeline'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/timeline'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/vmdmovie'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/vmdmovie'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/vmdtkcon'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/vmdtkcon'
gmake[2]: Entering directory `/scratch/vrbka/software/vmd/plugins/zoomseq'
gmake[2]: Nothing to be done for `dynlibs'.
gmake[2]: Leaving directory `/scratch/vrbka/software/vmd/plugins/zoomseq'
gmake[2]: Entering directory
`/scratch/vrbka/software/vmd/plugins/molfile_plugin'
Building Molecule File Reader plugins
gcc -O2 -Wall -ansi -I../include -Isrc -c src/cpmdplugin.c -o
../compile/lib_NETBSD/molfile/cpmdplugin.o
src/cpmdplugin.c: In function `vmdplugin_register':
src/cpmdplugin.c:202: warning: dereferencing type-punned pointer will
break strict-aliasing rules
src/cpmdplugin.c: At top level:
src/cpmdplugin.c:82: warning: `read_cpmd_structure' defined but not used
o ../compile/lib_NETBSD/molfile/cpmdplugin.so
../compile/lib_NETBSD/molfile/cpmdplugin.o
gmake[2]: o: Command not found
gmake[2]: [cpmdplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/psfplugin.c -o
../compile/lib_NETBSD/molfile/psfplugin.o
src/psfplugin.c: In function `vmdplugin_register':
src/psfplugin.c:423: warning: dereferencing type-punned pointer will
break strict-aliasing rules
o ../compile/lib_NETBSD/molfile/psfplugin.so
../compile/lib_NETBSD/molfile/psfplugin.o
gmake[2]: o: Command not found
gmake[2]: [psfplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/pdbplugin.c -o
../compile/lib_NETBSD/molfile/pdbplugin.o
src/pdbplugin.c: In function `vmdplugin_register':
src/pdbplugin.c:442: warning: dereferencing type-punned pointer will
break strict-aliasing rules
o ../compile/lib_NETBSD/molfile/pdbplugin.so
../compile/lib_NETBSD/molfile/pdbplugin.o
gmake[2]: o: Command not found
gmake[2]: [pdbplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/dcdplugin.c -o
../compile/lib_NETBSD/molfile/dcdplugin.o
src/dcdplugin.c: In function `vmdplugin_register':
src/dcdplugin.c:388: warning: dereferencing type-punned pointer will
break strict-aliasing rules
src/dcdplugin.c: At top level:
src/endianswap.h:32: warning: `swap2_unaligned' defined but not used
src/endianswap.h:96: warning: `swap2_aligned' defined but not used
src/fastio.h:231: warning: `fio_read_int32' defined but not used
src/fastio.h:235: warning: `fio_write_str' defined but not used
o ../compile/lib_NETBSD/molfile/dcdplugin.so
../compile/lib_NETBSD/molfile/dcdplugin.o
gmake[2]: o: Command not found
gmake[2]: [dcdplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/babelplugin.c -o
../compile/lib_NETBSD/molfile/babelplugin.o
src/readpdb.h:205: warning: `write_raw_pdb_record' defined but not used
src/vmddir.h:132: warning: `vmd_file_is_executable' defined but not used
o ../compile/lib_NETBSD/molfile/babelplugin.so
../compile/lib_NETBSD/molfile/babelplugin.o
gmake[2]: o: Command not found
gmake[2]: [babelplugin.so] Error 127 (ignored)
g++ -O2 -Wall -I../include -Isrc -c src/gromacsplugin.C -o
../compile/lib_NETBSD/molfile/gromacsplugin.o
src/endianswap.h:32: warning: `void swap2_unaligned(void*, long int)'
defined
    but not used
src/endianswap.h:46: warning: `void swap4_unaligned(void*, long int)'
defined
    but not used
src/endianswap.h:65: warning: `void swap8_unaligned(void*, long int)'
defined
    but not used
src/endianswap.h:96: warning: `void swap2_aligned(void*, long int)'
defined but
    not used
o ../compile/lib_NETBSD/molfile/gromacsplugin.so
../compile/lib_NETBSD/molfile/gromacsplugin.o
gmake[2]: o: Command not found
gmake[2]: [gromacsplugin.so] Error 127 (ignored)
g++ -O2 -Wall -I../include -Isrc -c src/parmplugin.C -o
../compile/lib_NETBSD/molfile/parmplugin.o
o ../compile/lib_NETBSD/molfile/parmplugin.so
../compile/lib_NETBSD/molfile/parmplugin.o
gmake[2]: o: Command not found
gmake[2]: [parmplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/crdplugin.c -o
../compile/lib_NETBSD/molfile/crdplugin.o
src/crdplugin.c: In function `vmdplugin_register':
src/crdplugin.c:214: warning: dereferencing type-punned pointer will
break strict-aliasing rules
src/crdplugin.c:215: warning: dereferencing type-punned pointer will
break strict-aliasing rules
o ../compile/lib_NETBSD/molfile/crdplugin.so
../compile/lib_NETBSD/molfile/crdplugin.o
gmake[2]: o: Command not found
gmake[2]: [crdplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/namdbinplugin.c -o
../compile/lib_NETBSD/molfile/namdbinplugin.o
src/namdbinplugin.c: In function `vmdplugin_register':
src/namdbinplugin.c:235: warning: dereferencing type-punned pointer will
break strict-aliasing rules
o ../compile/lib_NETBSD/molfile/namdbinplugin.so
../compile/lib_NETBSD/molfile/namdbinplugin.o
gmake[2]: o: Command not found
gmake[2]: [namdbinplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi -I../include -Isrc -c src/binposplugin.c -o
../compile/lib_NETBSD/molfile/binposplugin.o
src/binposplugin.c: In function `vmdplugin_register':
src/binposplugin.c:247: warning: dereferencing type-punned pointer will
break strict-aliasing rules
o ../compile/lib_NETBSD/molfile/binposplugin.so
../compile/lib_NETBSD/molfile/binposplugin.o
gmake[2]: o: Command not found
gmake[2]: [binposplugin.so] Error 127 (ignored)
gcc -O2 -Wall -ansi /usr/pkg/include -I../include -Isrc -c
src/webpdbplugin.c -o ../compile/lib_NETBSD/molfile/webpdbplugin.o
gcc: cannot specify -o with -c or -S and multiple compilations
gmake[2]: *** [../compile/lib_NETBSD/molfile/webpdbplugin.o] Error 1
gmake[2]: Leaving directory
`/scratch/vrbka/software/vmd/plugins/molfile_plugin'
cd: can't cd to psfgen
cd: can't cd to autoimd
gmake[1]: *** [dynlibs] Error 2
gmake[1]: Leaving directory `/scratch/vrbka/software/vmd/plugins'
gmake: *** [NETBSD] Error 2

problem lies in the "o" command - what is that?

regards,
lubos 

-- 
Lubos
_@_"