[BioC] readCelFile function in Starr is crashing R

Noah Dowell noahd at ucla.edu
Wed Nov 16 19:14:58 CET 2011 

Hello Kasper,

I have tried your suggestions but I am not having much luck.  It very well may be my fault but any additional help is appreciated.

1.  I  went to CRAN this morning and downloaded R but I am not seeing any updates past the 10-31-2011 version.  

Are you suggesting I move to a developer version? (I prefer to not do this but if it is the only solution...)

2.  I then tried to re-install affxparser alone using:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> update.packages("affxparser", repos=biocinstallRepos(), type= "source")


3. or all packages using:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> pkgs <- rownames(installed.packages())
> biocLite(pkgs)
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'affxparser' 'affy' 'affyio' 'annotate' 'AnnotationDbi' 'base' 'Biobase' 'BiocInstaller' 'boot' 'class' 'cluster'
  'codetools' 'compiler' 'datasets' 'DBI' 'foreign' 'genefilter' 'graphics' 'grDevices' 'grid' 'IRanges' 'KernSmooth' 'lattice' 'limma'
  'MASS' 'Matrix' 'methods' 'mgcv' 'nlme' 'nnet' 'parallel' 'preprocessCore' 'pspline' 'RColorBrewer' 'Ringo' 'rpart' 'RSQLite'
  'spatial' 'splines' 'Starr' 'stats' 'stats4' 'survival' 'tcltk' 'tools' 'utils' 'vsn' 'xtable' 'zlibbioc'
trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/macosx/leopard/contrib/2.14/affxparser_1.26.1.tgz'
Content type 'application/x-gzip' length 2724437 bytes (2.6 Mb)
opened URL
==================================================
downloaded 2.6 Mb

# Then a bunch more contacting the url and downloading happens
## It does throw this warning at the end:

The downloaded packages are in
	/var/folders/14/14lHU6sYHXWDo48Jc3Lq++lgIs+/-Tmp-//RtmpyoIISL/downloaded_packages
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  packages ‘base’, ‘compiler’, ‘datasets’, ‘graphics’, ‘grDevices’, ‘grid’, ‘methods’, ‘parallel’, ‘splines’, ‘stats’, ‘stats4’, ‘tcltk’, ‘tools’, ‘utils’ are not available (for R version 2.14.0)



When I run through the sample Starr code it still crashes:

dataPath <- system.file("extdata", package="Starr")
> bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))
> 
> 
> ###################################################
> ### code chunk number 3: Data read-in
> ###################################################
> 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")
> rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=T, log.it=T)




And my session Info output:

> 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      BiocInstaller_1.2.1

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         annotate_1.32.0       AnnotationDbi_1.16.2  DBI_0.2-5             genefilter_1.36.0     IRanges_1.12.1       
 [7] MASS_7.3-16           preprocessCore_1.16.0 pspline_1.0-14        RSQLite_0.10.0        splines_2.14.0        survival_2.36-10     
[13] tools_2.14.0          xtable_1.6-0          zlibbioc_1.0.0 


On Nov 16, 2011, at 9:18 AM, Kasper Daniel Hansen wrote:

> 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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>>

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