VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 01 2004 - 09:37:17 CDT

Lubos,
  You need to specify the TCLINC and TCLLIB with valid compile
switches, like this:
  gmake NETBSD TCLINC="-I/usr/pkg/include" TCLLIB="-L/usr/pkg/lib"

Try that and let me know if you still have problems.

  John

On Wed, Sep 01, 2004 at 09:18:16AM +0200, Lubos Vrbka wrote:
> 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
> _@_" 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078