[Bioc-sig-seq] problems installing ShortRead on Linux

[kristen.dang at syngenta.com]

Dear List Members,
I asked my sysadmin to install the ShortRead package on one of our Linux servers and he ran into a problem. He reports that all the dependencies for Shortread installed fine, but the install of ShortRead itself failed. The error message he receives is below:

"Error in mkScalar(FALSE) : no scalar class implemented for type: logical
Error : unable to load R code in package 'ShortRead'"

I have included the output of sessionInfo at the bottom of this message.

We have previously successfully installed ShortRead on another Linux machine that is running the same version of R, so it seems as though there is a machine-specific difference, perhaps something to do with the R installation. However from the error message, I cannot guess what the problem might be.

If anyone has any suggestions, I would greatly appreciate it.

> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

Best regards,

Kristen Dang
Computational Biologist
Syngenta Biotechnology
3054 E. Cornwallis Rd.
Research Triangle Park, NC 27709
www.syngenta.com




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