From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Aug 22 2012 - 04:41:21 CDT

Thanks John,

I updated the CVS but now I get other missing directory error (see below):

Best,
Vlad

Copying volutil 1.3 files to
Copying vmddebug 1.0 files to
/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/vmddebug1.0
Copying vmdmovie 1.9 files to
/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/vmdmovie1.9
/bin/sh: line 0: cd: vmdprefs: No such file or directory
make: *** [distrib] Error 1

On 08/21/2012 06:06 PM, Vlad Cojocaru wrote:
> Dear all,
>
> I am trying to compile the vmd cvs code downloaded today and while
> building the plugins, I get the error below (build script also
> provided below).
> It looks as if some gif files are missing .... Does anybody know how
> to fix this ?
>
> Thanks
> Vlad
>
> ----------------script used to build plugins ----------------
> #!/bin/bash
>
> export TCLINC="-I/usr/include"
> export TCLLIB="-L/usr/lib64"
>
> export NETCDFINC="-I/usr/include"
> export NETCDFLIB="-I/usr/lib64"
>
> make clean
> make LINUXAMD64 TCLINC=$TCLINC TCLLIB=$TCLLIB NETCDFINC=$NETCDFINC
> NETCDFLIB=$NETCDFLIB 2>&1 | tee make.log
> export PLUGINDIR="/usr/local/apps/vmd/2012-08-21-SRC/lib/plugins"
> make distrib 2>&1 | tee make_distrib.log
>
> exit
>
> -----------------error--------------------
> Copying molfile plugins to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins destination area
> abinitplugin.so ...
> biomoccaplugin.so ...
> cpmdplugin.so ...
> psfplugin.so ...
> pdbplugin.so ...
> dcdplugin.so ...
> babelplugin.so ...
> gromacsplugin.so ...
> parmplugin.so ...
> crdplugin.so ...
> namdbinplugin.so ...
> binposplugin.so ...
> graspplugin.so ...
> msmsplugin.so ...
> stlplugin.so ...
> offplugin.so ...
> cubeplugin.so ...
> edmplugin.so ...
> ccp4plugin.so ...
> dsn6plugin.so ...
> brixplugin.so ...
> pltplugin.so ...
> raster3dplugin.so ...
> parm7plugin.so ...
> rst7plugin.so ...
> tinkerplugin.so ...
> uhbdplugin.so ...
> vaspchgcarplugin.so ...
> vaspparchgplugin.so ...
> vaspposcarplugin.so ...
> vaspoutcarplugin.so ...
> vaspxdatcarplugin.so ...
> vaspxmlplugin.so ...
> dlpolyplugin.so ...
> lammpsplugin.so ...
> vtfplugin.so ...
> xyzplugin.so ...
> corplugin.so ...
> moldenplugin.so ...
> phiplugin.so ...
> pbeqplugin.so ...
> grdplugin.so ...
> situsplugin.so ...
> dxplugin.so ...
> spiderplugin.so ...
> mapplugin.so ...
> avsplugin.so ...
> fs4plugin.so ...
> pqrplugin.so ...
> mol2plugin.so ...
> gridplugin.so ...
> carplugin.so ...
> mdfplugin.so ...
> gamessplugin.so ...
> xsfplugin.so ...
> bgfplugin.so ...
> xbgfplugin.so ...
> jsplugin.so ...
> dtrplugin.so ...
> maeffplugin.so ...
> basissetplugin.so ...
> webpdbplugin.so ...
> netcdfplugin.so ...
> hoomdplugin.so ...
> dmsplugin.so ...
> libmolfile_plugin.a ...
> libmolfile_plugin.h ...
> libmolfile_plugin.lib ...
> libmolfile_plugin.h ...
> Copying apbsrun 1.3 files to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/apbsrun1.3
> Copying atomedit 1.0 files to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/atomedit1.0
> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
> restricted \write18 enabled.
> entering extended mode
> (./ug.tex
> LaTeX2e <2009/09/24>
> Babel <v3.8l> and hyphenation patterns for english, dumylang,
> nohyphenation, ge
> rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek,
> ibycus, arabi
> c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian,
> czech, danis
> h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic,
> farsi, finnis
> h, french, galician, german, ngerman, swissgerman, monogreek, greek,
> hungarian,
> icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
> marathi, or
> iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
> kurmanji,
> lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
> nynorsk, pol
> ish, portuguese, romanian, russian, sanskrit, serbian, serbianc,
> slovak, sloven
> ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
> welsh, loaded
> .
> (/usr/share/texmf/tex/latex/base/article.cls
> Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
> (/usr/share/texmf/tex/latex/base/size10.clo))
> (/usr/share/texmf/tex/latex/graphics/graphicx.sty
> (/usr/share/texmf/tex/latex/graphics/keyval.sty)
> (/usr/share/texmf/tex/latex/graphics/graphics.sty
> (/usr/share/texmf/tex/latex/graphics/trig.sty)
> (/usr/share/texmf/tex/latex/latexconfig/graphics.cfg)
> (/usr/share/texmf/tex/latex/pdftex-def/pdftex.def
> (/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
> (/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty))))
> (/usr/lib/texmf/tex/latex/html/html.sty
> (/usr/share/texmf/tex/latex/hyperref/hyperref.sty
> (/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
> (/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
> (/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
> (/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
> (/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
> (/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
> (/usr/share/texmf/tex/latex/url/url.sty))
>
> Package hyperref Message: Driver (autodetected): hpdftex.
>
> (/usr/share/texmf/tex/latex/hyperref/hpdftex.def
> (/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty)))
> (./ug_macros.tex)
> No file ug.aux.
> (/usr/share/texmf/tex/context/base/supp-pdf.mkii
> [Loading MPS to PDF converter (version 2006.09.02).]
> ) (/usr/share/texmf/tex/latex/oberdiek/epstopdf-base.sty
> (/usr/share/texmf/tex/latex/oberdiek/grfext.sty)
> (/usr/share/texmf/tex/latex/latexconfig/epstopdf-sys.cfg))
> (/usr/share/texmf/tex/latex/hyperref/nameref.sty
> (/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty))
> (./ug_title.tex)
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] (./ug_text.tex
> Underfull \hbox (badness 10000) in paragraph at lines 10--11
>
> (/usr/share/texmf/tex/latex/base/omscmr.fd)
> <autoimd-diagram.pdf, id=19, 301.125pt x 288.07625pt>
> <use autoimd-diagram.pdf>
>
> LaTeX Warning: Reference `fig:autoimd-diagram' on page 3 undefined on
> input lin
> e 31.
>
> [3 <./autoimd-diagram.pdf>]
>
> LaTeX Warning: Reference `par:customize' on page 4 undefined on input
> line 58.
>
>
> LaTeX Warning: Reference `fig:autoimd-GUI' on page 4 undefined on
> input line 78
> .
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 78--79
>
> <autoimd-GUI.pdf, id=45, 431.6125pt x 298.11375pt> <use autoimd-GUI.pdf>
>
> LaTeX Warning: Reference `fig:simsettings-GUI' on page 4 undefined on
> input lin
> e 85.
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 85--86
>
> <simsettings-GUI.pdf, id=46, 543.02875pt x 443.6575pt>
> <use simsettings-GUI.pdf>
> Underfull \hbox (badness 10000) in paragraph at lines 91--92
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 96--97
>
> [4 <./autoimd-GUI.pdf>]
> Underfull \hbox (badness 10000) in paragraph at lines 100--101
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 104--105
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 106--107
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 111--112
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 115--116
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 118--119
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 125--126
>
> [5 <./simsettings-GUI.pdf>]
> Underfull \hbox (badness 10000) in paragraph at lines 130--131
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 134--135
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 140--141
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 170--171
>
> [6]
> Underfull \hbox (badness 10000) in paragraph at lines 194--195
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 207--208
>
> [7]
> Underfull \hbox (badness 10000) in paragraph at lines 254--255
>
> ) [8] (./ug.aux)
>
> Package rerunfilecheck Warning: File `ug.out' has changed.
> (rerunfilecheck) Rerun to get outlines right
> (rerunfilecheck) or use package `bookmark'.
>
>
> LaTeX Warning: There were undefined references.
>
>
> LaTeX Warning: Label(s) may have changed. Rerun to get
> cross-references right.
>
> )
> (see the transcript file for additional
> information)</usr/share/texmf/fonts/typ
> e1/public/amsfonts/cm/cmbx10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
>
> cm/cmbx12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/
>
> share/texmf/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf/fonts/ty
>
> pe1/public/amsfonts/cm/cmr12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
>
> cm/cmr17.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmr6.pfb></usr/sh
>
> are/texmf/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texmf/fonts/type1
>
> /public/amsfonts/cm/cmr8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/c
>
> msl8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar
>
> e/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf/fonts/type1
>
> /public/amsfonts/cm/cmtt10.pfb>
> Output written on ug.pdf (8 pages, 319257 bytes).
> Transcript written on ug.log.
> This is pdfTeX, Version 3.1415926-2.3-1.40.12 (TeX Live 2011)
> restricted \write18 enabled.
> entering extended mode
> (./ug.tex
> LaTeX2e <2009/09/24>
> Babel <v3.8l> and hyphenation patterns for english, dumylang,
> nohyphenation, ge
> rman-x-2009-06-19, ngerman-x-2009-06-19, afrikaans, ancientgreek,
> ibycus, arabi
> c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian,
> czech, danis
> h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic,
> farsi, finnis
> h, french, galician, german, ngerman, swissgerman, monogreek, greek,
> hungarian,
> icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam,
> marathi, or
> iya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian,
> kurmanji,
> lao, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal,
> nynorsk, pol
> ish, portuguese, romanian, russian, sanskrit, serbian, serbianc,
> slovak, sloven
> ian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian,
> welsh, loaded
> .
> (/usr/share/texmf/tex/latex/base/article.cls
> Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
> (/usr/share/texmf/tex/latex/base/size10.clo))
> (/usr/share/texmf/tex/latex/graphics/graphicx.sty
> (/usr/share/texmf/tex/latex/graphics/keyval.sty)
> (/usr/share/texmf/tex/latex/graphics/graphics.sty
> (/usr/share/texmf/tex/latex/graphics/trig.sty)
> (/usr/share/texmf/tex/latex/latexconfig/graphics.cfg)
> (/usr/share/texmf/tex/latex/pdftex-def/pdftex.def
> (/usr/share/texmf/tex/generic/oberdiek/infwarerr.sty)
> (/usr/share/texmf/tex/generic/oberdiek/ltxcmds.sty))))
> (/usr/lib/texmf/tex/latex/html/html.sty
> (/usr/share/texmf/tex/latex/hyperref/hyperref.sty
> (/usr/share/texmf/tex/generic/oberdiek/hobsub-hyperref.sty
> (/usr/share/texmf/tex/generic/oberdiek/hobsub-generic.sty))
> (/usr/share/texmf/tex/generic/ifxetex/ifxetex.sty)
> (/usr/share/texmf/tex/latex/oberdiek/kvoptions.sty)
> (/usr/share/texmf/tex/latex/hyperref/pd1enc.def)
> (/usr/share/texmf/tex/latex/latexconfig/hyperref.cfg)
> (/usr/share/texmf/tex/latex/url/url.sty))
>
> Package hyperref Message: Driver (autodetected): hpdftex.
>
> (/usr/share/texmf/tex/latex/hyperref/hpdftex.def
> (/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty)))
> (./ug_macros.tex)
> (./ug.aux) (/usr/share/texmf/tex/context/base/supp-pdf.mkii
> [Loading MPS to PDF converter (version 2006.09.02).]
> ) (/usr/share/texmf/tex/latex/oberdiek/epstopdf-base.sty
> (/usr/share/texmf/tex/latex/oberdiek/grfext.sty)
> (/usr/share/texmf/tex/latex/latexconfig/epstopdf-sys.cfg))
> (/usr/share/texmf/tex/latex/hyperref/nameref.sty
> (/usr/share/texmf/tex/generic/oberdiek/gettitlestring.sty)) (./ug.out)
> (./ug.out) (./ug_title.tex)
> [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.ma
> p}] (./ug.toc) [2] (./ug_text.tex
> Underfull \hbox (badness 10000) in paragraph at lines 10--11
>
> (/usr/share/texmf/tex/latex/base/omscmr.fd)
> <autoimd-diagram.pdf, id=55, 301.125pt x 288.07625pt>
> <use autoimd-diagram.pdf> [3 <./autoimd-diagram.pdf>]
> Underfull \hbox (badness 10000) in paragraph at lines 78--79
>
> <autoimd-GUI.pdf, id=82, 431.6125pt x 298.11375pt> <use autoimd-GUI.pdf>
> Underfull \hbox (badness 10000) in paragraph at lines 85--86
>
> <simsettings-GUI.pdf, id=84, 543.02875pt x 443.6575pt>
> <use simsettings-GUI.pdf>
> Underfull \hbox (badness 10000) in paragraph at lines 91--92
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 96--97
>
> [4 <./autoimd-GUI.pdf>]
> Underfull \hbox (badness 10000) in paragraph at lines 100--101
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 104--105
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 106--107
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 111--112
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 115--116
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 118--119
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 125--126
>
> [5 <./simsettings-GUI.pdf>]
> Underfull \hbox (badness 10000) in paragraph at lines 130--131
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 134--135
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 140--141
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 170--171
>
> [6]
> Underfull \hbox (badness 10000) in paragraph at lines 194--195
>
>
> Underfull \hbox (badness 10000) in paragraph at lines 207--208
>
> [7]
> Underfull \hbox (badness 10000) in paragraph at lines 254--255
>
> ) [8] (./ug.aux) )
> (see the transcript file for additional
> information)</usr/share/texmf/fonts/typ
> e1/public/amsfonts/cm/cmbx10.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
>
> cm/cmbx12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmbx8.pfb></usr/
>
> share/texmf/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/share/texmf/fonts/ty
>
> pe1/public/amsfonts/cm/cmr12.pfb></usr/share/texmf/fonts/type1/public/amsfonts/
>
> cm/cmr17.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmr6.pfb></usr/sh
>
> are/texmf/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texmf/fonts/type1
>
> /public/amsfonts/cm/cmr8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/c
>
> msl8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar
>
> e/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf/fonts/type1
>
> /public/amsfonts/cm/cmtt10.pfb>
> Output written on ug.pdf (8 pages, 322174 bytes).
> Transcript written on ug.log.
> Copying autoimd 1.7 files to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/autoimd1.7
> Copying autoionize 1.3 files to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/autoionize1.3
> Copying bendix 1.0 files to
> /usr/local/apps/vmd/2012-08-21-SRC/lib/plugins/noarch/tcl/bendix1.0
> cp: cannot stat `doc/GUI-tips.gif': No such file or directory
> cp: cannot stat `doc/Monsieur_Bendix_smaller_still.gif': No such file
> or directory
> make[1]: *** [distrib] Error 1
> make: *** [distrib] Error 1
>

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru