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

[Vincent Carey]

The current version of R is 2.11.1 and an upgrade is advisable.  If
the installation was attempted using biocLite() which is the most
recommended approach, a full transcript of the installation messages
would be useful.  I believe your Biobase may be out of date.

> getAnywhere("mkScalar")
A single object matching 'mkScalar' was found
It was found in the following places
  package:Biobase
  namespace:Biobase
with value

function (obj)
{
    switch(typeof(obj), character = new("ScalarCharacter", obj),
        logical = new("ScalarLogical", obj), integer = new("ScalarInteger",
            obj), double = new("ScalarNumeric", obj), stop("no scalar
class implemented for type: ",
            typeof(obj)))
}
<environment: namespace:Biobase>

> mkScalar(FALSE)
FALSE
> class(.Last.value)
[1] "ScalarLogical"
attr(,"package")
[1] "Biobase"
> sessionInfo()
R version 2.11.1 Patched (2010-06-08 r52234)
x86_64-apple-darwin10.3.0

locale:
[1] C

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

other attached packages:
 [1] ShortRead_1.6.2     Rsamtools_1.0.5     lattice_0.18-5
 [4] Biostrings_2.16.0   GenomicRanges_1.0.3 IRanges_1.6.14
 [7] Biobase_2.8.0       weaver_1.14.0       codetools_0.2-2
[10] digest_0.4.2

loaded via a namespace (and not attached):
[1] grid_2.11.1 hwriter_1.2


On Wed, Sep 1, 2010 at 10:55 AM,  <kristen.dang at syngenta.com> wrote:
> 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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