I used a Windows command line; I assumed the problem was related to 
the Windows OS because you have to go through a lot of steps to be 
able to compile and install a package. From what I know of R on unix 
(admittedly very little), you don't have this problem and I would 
assume you'd have no trouble making the documents there.

Jenny

At 01:15 PM 4/17/2008, Hamid Ashafi wrote:
>Hi Jenny,
>
>Thanks for the help. Did you use R CMD INSTALL in unix or windows 
>command line? I sent a message to BioC group but no response yet.
>
>Hamid
>
>
>From: Jenny Drnevich [mailto:drnevich@uiuc.edu]
>Sent: Thursday, April 17, 2008 11:08 AM
>To: Hamid Ashrafi; bioconductor@stat.math.ethz.ch
>Subject: Re: CDF Package installation
>
>Hi Hamid,
>
>It's good protocol to send your questions to the BioC list as well 
>as an individual person, so others in the future can find it. As I 
>recall, my computer wasn't able to make the documents for the 
>package and that's why it failed. You can turn off the documents 
>when you call R CMD INSTALL by setting docs="NONE". See R CMD 
>INSTALL --help to find out how. After doing this, I was able to 
>install the packages just fine.
>
>Cheers,
>Jenny
>
>At 08:14 PM 4/16/2008, you wrote:
>
>
>
>
>Hi
>Jenny,
>
>
>
>I am post doc at UC Davis
>and had the same problem as you had for installing the CDF package. I
>googled the error and I found your message that you had sent to Jim. I am
>assuming Jim is an expert. Did you find any
>solution?
>
>
>
>Thanks,
>
>
>
>Hamid
>
>
>
>
>
>
>
>
>
>Hi
>Jim,
>
>
>
>I'm in the process of
>trying to make a custom cdf package, and I got the
>
>warning
>below:
>
>
>
>
>  >make.cdf.package("lund-zfa530237N.cdf",species="song_bird",
>
>+
>maintainer="Jenny Drnevich
><<https://stat.ethz.ch/mailman/listinfo/bioconductor>drnevich
><https://stat.ethz.ch/mailman/listinfo/bioconductor>at
><https://stat.ethz.ch/mailman/listinfo/bioconductor>uiuc.edu>")
>
>Reading CDF
>file.
>
>Creating CDF
>environment
>
>Wait for about 231
>
>
>dots....................................................................................................................................................................................................................... 
>
>
>Creating package in
>C:/Statistics/Clayton/lundzfa530237ncdf
>
>[1]
>"lundzfa530237ncdf"
>
>Warning
>message:
>
>incomplete final line found
>by readLines on
>
>
>'C:/PROGRA~1/R/R-24~1.0/library/makecdfenv/Code/DESCRIPTION'
>
>  >
>
>
>
>I haven't been able to
>build the package yet - I thought I had gotten all
>
>the tools I needed, but
>I've been unsuccessful. I doubt this warning has
>
>anything to do with it, but
>I thought I should send it to you anyway.
>
>Actually, here's the error
>from the terminal, just in
>case:
>
>
>
>cp: cannot stat
>
>
>'C:/Statistics/Clayton/lundzfa530237ncdf/chm/lundzfa530237ncdf.chm: No
>such
>
>file or
>directory
>
>make[1]: ***
>[chm-lundzfa530237ncdf ] Error
>1
>
>make: ***
>[pkg-lundzfa530237ncdf ] Error
>2
>
>*** Installation of
>lundzfa530237ncdf failed
>***
>
>
>
>Removing
>'c:/PROGRA~1/R/R-24~1.0/library/lundzfa530237ncdf'
>
>
>
>The output was also saying
>'latex: not found' and 'hhc not found'. One of
>
>our IT guys is going to get
>my PC up to speed while I'm gone tomorrow &
>
>Monday, so if the problem
>is on my end, I'll be ready to go next
>week!
>
>
>
>Cheers,
>
>Jenny
>
>
>
>
>  >sessionInfo()
>
>R version 2.4.0
>(2006-10-03)
>
>i386-pc-mingw32
>
>
>
>locale:
>
>LC_COLLATE=English_United
>States.1252;LC_CTYPE=English_United
>
>
>States.1252;LC_MONETARY=English_United
>
>
>States.1252;LC_NUMERIC=C;LC_TIME=English_United
>States.1252
>
>
>
>attached base
>packages:
>
>[1]
>"splines"   "tools"
>"methods"   "stats"
>"graphics"
>"grDevices"
>
>[7]
>"utils"     "datasets"
>"base"
>
>
>
>other attached
>packages:
>
>
>makecdfenv  affyQCReport
>simpleaffy         made4
>scatterplot3d
>
>
>
>"1.12.0"
>"1.12.0"
>"2.8.0"
>"1.8.0"
>"0.3-24"
>
>
>
>ade4
>affyPLM         gcrma
>matchprobes
>affydata
>
>
>
>"1.4-2"
>"1.10.0"
>"2.6.0"
>"1.6.0"
>"1.10.0"
>
>
>affycoretools
>biomaRt
>RCurl
>XML
>GOstats
>
>
>
>"1.6.0"
>"1.8.0"
>"0.7-0"
>"0.99-93"
>"2.0.0"
>
>
>       Category
>genefilter
>survival
>KEGG
>RBGL
>
>
>
>"2.0.0"
>"1.12.0"
>"2.29"
>"1.14.0"
>"1.10.0"
>
>
>
>annotate
>GO
>graph
>limma
>affy
>
>
>
>"1.12.0"
>"1.14.0"
>"1.12.0"
>"2.9.1"
>"1.12.0"
>
>
>
>affyio
>Biobase
>RWinEdt
>
>
>
>"1.2.0"
>"1.12.2"
>"1.7-5"
>
>
>
>
>
>
>
>
>
>Cheers,
>
>Jenny
>
>
>
>
>
>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:
><https://stat.ethz.ch/mailman/listinfo/bioconductor>drnevich at
><https://stat.ethz.ch/mailman/listinfo/bioconductor>uiuc.edu
>
>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@uiuc.edu

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@uiuc.edu 
	[[alternative HTML version deleted]]

