[BioC] R crashes when using CDF package generated using makecdfenv

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Feb 19 17:42:24 CET 2013


What is your question?

You do not provide any information about how the cdf file was created.
 Was it an official one from Affymetrix, and just using a custom chip,
or is it something you or collegeaues have hacked together?  It is
pretty easy to mess up the cdf specification.

Anyway, the cdf file reads fine with affxparser (and makecdfenv), but
if you look at the first entry of the created cdf env from makecdfenv
you clearly see something is messed up:

> as.list(testcdf)[[1]]
          pm  mm
 [1,]  60275 NaN
 [2,] 484839 NaN
 [3,] 423468 NaN
 [4,]  14388 NaN
 [5,]  69256 NaN
 [6,] 134831 NaN
 [7,] 483140 NaN
 [8,] 105347 NaN
 [9,] 315273 NaN
[10,] 215246 NaN
[11,] 161557 NaN
[12,]    NaN NaN
[13,]    NaN NaN
[14,]    NaN NaN
[15,]    NaN NaN
[16,]    NaN NaN
[17,]    NaN NaN
[18,]    NaN NaN
[19,]    NaN NaN
[20,]    NaN NaN
[21,]    NaN NaN
[22,]    NaN NaN

I (and probably others as well) are unlikely to try to chase this down
without some additional information.  I understand if you don't want
to share details on your custom design / data, but it does make it
much less likely for someone to help you.

Kasper



On Tue, Feb 19, 2013 at 11:23 AM, Lars Rønn Olsen [guest]
<guest at bioconductor.org> wrote:
>
> Dear Bioconductor/makecdfenv experts,
>
> I am having issues using a cdf package compiled from a custom cdf file using makecdfenv. The code below works fine with other .cdf files, but when I compile a cdf package with the cdf file located here (https://dl.dropbox.com/u/2790735/test.cdf), R simply crashes when I attempt to run rma. Perhaps the cdf file is corrupt?
>
> #Generating cdf package in R
> library(makecdfenv)
> make.cdf.package("test.cdf", species = "Homo_sapiens")
>
> #Install in terminal
> R CMD INSTALL testcdf
>
> #Back in R, attempting to use cdf package
> library(testcdf)
> library(affy)
> matrix <- ReadAffy()
> matrix at cdfName = "testcdf"
> matrix.rma <- rma(matrix)
> #R crashes here (also on other comps)
>
> I'm not sure if/what info from the Mac OSX problem report is relevant, so I uploaded it her (https://dl.dropbox.com/u/2790735/R_error_message.txt).
>
> Any help is greatly appreciated!
>
> Best regards,
> Lars
>
>  -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] testcdf_1.36.0       AnnotationDbi_1.20.3 affy_1.36.1          Biobase_2.18.0       BiocGenerics_0.4.0   makecdfenv_1.36.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.26.0         BiocInstaller_1.8.3   DBI_0.2-5             IRanges_1.16.5        parallel_2.15.2
>  [6] preprocessCore_1.20.0 RSQLite_0.11.2        stats4_2.15.2         tools_2.15.2          zlibbioc_1.4.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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