VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 22 2012 - 09:34:30 CDT

Vlad,
  Please try doing a "cvs update -PAd" in the top level plugins directory
to make sure you get the new vmdprefs plugin. That should solve the error
you got below.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2012 at 11:41:21AM +0200, Vlad Cojocaru wrote:
> 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))
> >
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> >
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> >(/usr/share/texmf/tex/latex/oberdiek/rerunfilecheck.sty)))
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> >(/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
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> >
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> >
> >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
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> >msl8.pfb></usr/share/texmf/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/shar
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> >e/texmf/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texmf/fonts/type1
> >
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> >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))
> >
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> >
> >(/usr/share/texmf/tex/latex/hyperref/hpdftex.def
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> >(./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)
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> >[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.ma
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> >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
>
> 

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