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I am trying to read my mogenest2.0 CEL files into R with oligo. But pd.mogene.2.0st appears to not work for my release of R (says it is not available for R 3.1.2). This seems odd to me since pd.mogene.2.0st is listed as part of the Bioconductor 3.0 release (which works in my version of R). Does anyone know what I can do to fix this or otherwise work with my files?
> celFiles <- list.celfiles()
> affyRaw <- read.celfiles(celFiles)
Loading required package: pd.mogene.2.0.st
Attempting to obtain 'pd.mogene.2.0.st' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.mogene.2.0.st' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in read.celfiles(celFiles) :
The annotation package, pd.mogene.2.0.st, could not be loaded.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘pd.mogene.2.0.st’
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> biocLite("pd.mogene.2.0.st")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'pd.mogene.2.0.st'
package ‘pd.mogene.2.0.st’ is available as a source package but not as a binary
Warning message:
package ‘pd.mogene.2.0.st’ is not available (for R version 3.1.2)
It looks like oligo downloads annotation packages using biocLite() (or maybe install.packages()). Just any case any oligo folks are reading this, it should perhaps be updated (in release) to add the type="source" argument. In devel this won't be necessary due to recent changes in R.
Hi Dan,
This is an issue at the repository level, as far as I can tell:
> biocLite("pd.mogene.1.0.st.v1") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1. Installing package(s) 'pd.mogene.1.0.st.v1' trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.1/pd.mogene.1.0.st.v1_3.10.0.zip' Content type 'application/zip' length 75389629 bytes (71.9 Mb) opened URL downloaded 71.9 Mb The downloaded binary packages are in C:\Users\BioinfAdmin\AppData\Local\Temp\RtmpCQiZJu\downloaded_packages > biocLite("pd.mogene.2.0.st") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1. Installing package(s) 'pd.mogene.2.0.st' package ‘pd.mogene.2.0.st’ is available as a source package but not as a binary > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.1 loaded via a namespace (and not attached): [1] tools_3.1.1Yes, the repository does not have binary packages. Marc is going to fix it. adding type="source" would also fix it.