[BioC] makecdfenv

Jenny Drnevich drnevich at uiuc.edu
Tue Dec 12 20:09:05 CET 2006 

Hi Weijin,

We were having the same problem, and you may have already found the 
solution using Martin's suggestion. But if not, this is it: You can turn 
off making the documentation for cdf or probe packages (which really aren't 
needed...) using

R CMD INSTALL --docs=none ehtapops520389fcdf

or it might have been NONE or "none" - I forget which worked in the end.

Cheers,
Jenny

At 02:14 PM 12/11/2006, Martin Morgan wrote:
>Weijin
>
> >From the DOS command prompt you should be able to type
>
>c:\>hhc /?
>
>and get a message summarizing usage, along the lines of.
>
>Usage:   hhc <filename>
>     where <filename> = an HTML Help project file
>Example: hhc myfile.hhp
>
>If not, then your PATH variable is incorrect, e.g., wrong punctuation
>separating elements (should be a semi-coloon). Another possibility is
>that the Perl being used is not the one you expect (e.g., cygwin perl,
>rather than Windows. The command perl --version should help; I'm not
>sure if this is really likely to be a problem). Depending on the
>reasons for creating the package, You might also try
>
>R CMD INSTALL --help
>
>to learn how to avoid producing 'chm' files.
>
>This is definitely a Windows configuration issue, with the answer
>being meticulous (even paranoid) adherence to the official
>recommendations.
>
>Hope that helps; it's difficult to get right the first time but easier
>the second,
>
>Martin
>
>"Weiyin Zhou" <weiyin.zhou at exonhit-usa.com> writes:
>
> > Hi Martin,
> >
> > Many thanks for your help.  I solved that error message.
> >
> > Now, I got other error messages as fellow:
> >
> > C:\>R CMD INSTALL ehtapops520389fcdf
> >
> > latex: not found
> > latex: not found
> > latex: not found
> >
> > ---------- Making package ehtapops520389fcdf ------------
> > latex: not found
> >   adding build stamp to DESCRIPTION
> > latex: not found
> > latex: not found
> > latex: not found
> >   installing R files
> > latex: not found
> >   installing data files
> > latex: not found
> >   installing man source files
> >   installing indices
> > latex: not found
> >   not zipping data
> >   installing help
> >  >>> Building/Updating help pages for package 'ehtapops520389fcdf'
> >      Formats: text html latex example chm
> >   ehtapops520389fcdf                text    html    latex
> >   geometry                          text    html    latex   example
> > hhc: not found
> > cp: cannot stat `C://ehtapops520389fcdf/chm/ehtapops520389fcdf.chm': No
> > such file or directory
> > make[1]: *** [chm-ehtapops520389fcdf] Error 1
> > make: *** [pkg-ehtapops520389fcdf] Error 2
> > *** Installation of ehtapops520389fcdf failed ***
> >
> > Removing 'C:/R/R-2.4.0/library/ehtapops520389fcdf'
> >
> > I installed Microsoft HTML Help Workshop at my C drive
> > (C:\HTML_Help_Workshop).  I looked in this folder, there is hhc, which
> > is the HTML Help Compiler.  I set the Path for this folder after tools
> > and Perl from my computer environment variables.  Why it said "hhc: not
> > found"?
> >
> > Thanks in advance,
> >
> > Weiyin
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> > Sent: Saturday, December 09, 2006 9:08 AM
> > To: Wolfgang Huber
> > Cc: Weiyin Zhou; bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] makecdfenv
> >
> > Dr. Zhou
> >
> > Probably a more comprehensive set of instructions is in the 'R
> > Installation and Administration' manual, section 3. This is available
> > from
> >
> > http://cran.r-project.org
> >
> > and visiting the 'Manuals' link. There is also a less formal guide on
> > the Bioconductor developer wiki at
> >
> > http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows
> >
> > The error below is because your system is not locating the set of R
> > tools correctly; Rtools (see the pages referenced above) needs to be
> > in front of windows system entries in the 'PATH' environment
> > variable.
> >
> > Hope that helps
> >
> > Martin
> >
> > "Wolfgang Huber" <huber at ebi.ac.uk> writes:
> >
> >> Dear Dr. Zhou,
> >>
> >> this seems to be general problem with the computer system on which you
> > are
> >> trying to build the CDF package, rather than a specific makecdfenv
> >> problem. I am not an expert for Windows, but please consult
> >> http://www.murdoch-sutherland.com/Rtools/
> >> for information on how to install packages from source format (i.e.
> > what
> >> you get from make.cdf.package) on your Windows system.
> >>
> >>  Best wishes
> >>  Wolfgang Huber
> >>
> >> <quote who="Weiyin Zhou">
> >>> Hi Dr. Huber,
> >>>
> >>>
> >>>
> >>> I have sent below e-mail to bioconductor several days ago.  But no
> >>> response.  I really need your help.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> I was trying to create CDF package on window using following
> > commands:
> >>>
> >>>
> >>>
> >>>> make.cdf.package("APOP.cdf", species="Homo_sapiens")
> >>>
> >>>
> >>>
> >>> It created a subdirectory apopcdf in my working directory.  Then at
> >>> terminal, I typed:
> >>>
> >>>> R CMD INSTALL apopcdf
> >>>
> >>>
> >>>
> >>> Here is the error message I got:
> >>>
> >>>
> >>>
> >>> Microsoft (R) Program Maintenance Utility   Version 1.50
> >>>
> >>> Copyright (c) Microsoft Corp 1988-94. All rights reserved.
> >>>
> >>>
> >>>
> >>> NMAKE : fatal error U1065: invalid option '-' Stop.
> >>>
> >>> *** Installation of apopcdf failed ***
> >>>
> >>>
> >>>
> >>> Removing 'C:/PROGRA~1/R/R-24~1.0/library/apopcdf'
> >>>
> >>>
> >>>
> >>> I try to consult the help page for makecdfenv package, but all the
> > links
> >>> there are not working.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Could you help me to find the problems?
> >>>
> >>>
> >>>
> >>> It will be very helpful to make the help link for this package works.
> >>>
> >>>
> >>>
> >>> Thanks in advance,
> >>>
> >>>
> >>>
> >>> Regards,
> >>>
> >>>
> >>>
> >>> Weiyin Zhou
> >>>
> >>> Statistics and Data Analyst
> >>>
> >>> ExonHit Therapeutics, Inc.
> >>>
> >>> 217 Perry Parkway, Building # 5
> >>>
> >>> Gaithersburg, MD 20877
> >>>
> >>>
> >>>
> >>> email: Weiyin.zhou at exonhit-usa.com
> >>>
> >>> phone: 240.404.0184
> >>>
> >>> fax: 240.683.7060
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --
> > Martin T. Morgan
> > Bioconductor / Computational Biology
> > http://bioconductor.org
> >
> >
>
>--
>Martin T. Morgan
>Bioconductor / Computational Biology
>http://bioconductor.org
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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