[BioC] makecdfenv

Tue Dec 12 22:24:23 CET 2006

Hi,

instead of using the default Windows Command prompt, I have got a
RCMDPrompt.bat script which I use to setup my Command prompt.  If you
use a Windows Shortcut to call

  "%ProgramFiles%\R\RCMDPrompt" "C:\foo\bar\" R-2.4.0

the identified R version is reported, and you will get a prompt with
C:\foo\bar\ as the current working direction.  Example:

R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License.  For more information about
these matters, see http://www.gnu.org/copyleft/gpl.html.

C:\foo\bar\>

When you type Rterm, you will in this case launch R-2.4.0.  This
prompt will also be good for building package etc.

The script assumes default installation paths on R, R tools,
ActivePerl, Microsoft HTML Help Compiler, MikTeX etc, but you may
modify the script for other setting.  The script also sets environment
variables R_HOME, TEXINPUTS etc.  You can find the script at:

  http://www.braju.com/R/RCMDPrompt.bat

Hope this helps

Henrik

On 12/12/06, Martin Morgan <mtmorgan at fhcrc.org> 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
>
> _______________________________________________
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