[BioC] make.cdf.package

[James W. MacDonald]

Hi Lana,

Lana Schaffer wrote:
> Hi,
> I am trying to create a cdf package in R2.3.1 and Bioconductor 1.8 and using
> the windows compiled version.
> I have previously created this cdf package in R2.2.0 with success.
> The package does not get compressed even though compress=TRUE
> is the directive so I have to compress it myself.

I think you are misunderstanding something here. The compress argument 
is TRUE if the cdf file you are reading is compressed. It doesn't have 
anything to do with the output.

> 
> glycov2a520086f = make.cdf.package("GLYCOv2a520086F.CDF",
> cdf.path=system.file("extdata", package="makecdfenv"),
> compress=TRUE, species = "Homo_sapiens",
> package.path = pkgpath)

Is your cdf file really in R_HOME/library/makecdfenv/extdata? That is 
sort of an odd place to put things. Anyway, I don't have the same 
problem with the example file in that directory:

 > make.cdf.package("hu6800.CDF.gz", cdf.path = system.file("extdata", 
package="makecdfenv"),compress=TRUE, species = "Homo_sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 71 
dots.........................................................................
Creating package in C:/rw2030beta/hu6800.cdf.gzcdf
[1] "hu6800.cdf.gzcdf"

I tried un-gzipping the cdf as well, and used compress = TRUE, and that 
still worked.

 > make.cdf.package("hu6800.CDF", cdf.path = system.file("extdata", 
package="makecdfenv"),compress=TRUE, species = "Homo_sapiens")
Reading CDF file.
Creating CDF environment
Wait for about 71 
dots...............................................................................
Creating package in C:/rw2030beta/hu6800cdf
[1] "hu6800cdf"

You should also always give your sessionInfo()!

 > sessionInfo()
Version 2.3.0 RC (2006-04-17 r37823)
i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
     "datasets"
[8] "base"

other attached packages:
makecdfenv       affy     affyio    Biobase
    "1.9.3"   "1.10.0"   "0.99.3"   "1.10.1"

What versions of makecdfenv, and more importantly, affyio are you using?

Also, if you download the Rtools and put them in your PATH, does the 
problem go away?

http://www.murdoch-sutherland.com/Rtools/tools.zip

Best,

Jim


> 
> Error in gzfile(file, "r") : unable to open connection
> In addition: Warning messages:
> 1: error -1 in extracting from zip file 
> 2: cannot open compressed file 'glycov2a520086fcdf/DESCRIPTION' 
> 
> I know this is a popular problem, so does anyone know the solution?
> Thanks.
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
> 
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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