[BioC] makecdfenv

[Martin Morgan]

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
>>
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>
> -- 
> Martin T. Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>
>

-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org