[BioC] readCelFile function in Starr is crashing R

[Kasper Daniel Hansen]

Hi Noah

Re-download the R binary from CRAN and re-install it (what is
available now is different from what was available a week ago).

Afterwards you need to re-install affxparser and possibly every other
package.  You may have to use type = "source", or Bioconductor might
have been re-build using the new CRAN binary.  See recent post on
bioc-devel from me.

Kasper

On Tue, Nov 15, 2011 at 10:46 PM, Noah Dowell [guest]
<guest at bioconductor.org> wrote:
>
> Hello All,
>
> I could find any solutions searching the archives so I throw this out there.  I think my packages are all updated.
>
> I have been trying to analyze some old data using the excellent Starr package.  Everything in my old Starr workflow was working fine several months ago but now when I try to read in cel files using the readCelFile function my R session crashes.  I went to the running the examples provides in the vignette and the same thing is happening.
>
> Hopefully someone can help with this.
>
> Best,
>
> Noah
>
>
> Here is my code from the vignette (I typed sessionInfo() before the readCelFile line so it is provided before my session crashes):
>
>> dataPath <- system.file("extdata", package="Starr")
>
>> dataPath
> [1] "/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Starr/extdata"
>> bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))
>> cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"),
> +       file.path(dataPath,"Rpb3_IP2_chr1.cel"))
>> names <- c("rpb3_1", "wt_1","rpb3_2")
>> type <- c("IP", "CONTROL", "IP")
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Starr_1.10.0       affxparser_1.26.1  affy_1.32.0        Ringo_1.18.0       Matrix_1.0-1       lattice_0.20-0
> [7] limma_3.10.0       RColorBrewer_1.0-5 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.2  BiocInstaller_1.2.1   DBI_0.2-5
>  [6] genefilter_1.36.0     IRanges_1.12.1        MASS_7.3-16           preprocessCore_1.16.0 pspline_1.0-14
> [11] RSQLite_0.10.0        splines_2.14.0        survival_2.36-10      xtable_1.6-0          zlibbioc_1.0.0
>> rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T)
>
>  -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Starr_1.10.0       affxparser_1.26.1  affy_1.32.0        Ringo_1.18.0       Matrix_1.0-1       lattice_0.20-0
> [7] limma_3.10.0       RColorBrewer_1.0-5 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.2  BiocInstaller_1.2.1   DBI_0.2-5
>  [6] genefilter_1.36.0     IRanges_1.12.1        MASS_7.3-16           preprocessCore_1.16.0 pspline_1.0-14
> [11] RSQLite_0.10.0        splines_2.14.0        survival_2.36-10      xtable_1.6-0          zlibbioc_1.0.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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