[BioC] Problem with Biostrings

[Martin Morgan]

On 08/29/2011 08:35 AM, Guido Leoni wrote:
> Dear List I'm trying to update Biostrings package but every time with the
> same error message.
>
> * installing *source* package ‘Biostrings’ ...
> ** libs
> gcc -I/usr/share/R/include
> -I"/home/guido/R/x86_64-pc-linux-gnu-library/2.13/IRanges/include"   -fpic
>   -std=gnu99 -O3 -pipe  -g -c BAB_class.c -o BAB_class.o
> gcc: error trying to exec 'as': execvp: File name too long
> make: *** [BAB_class.o] Error 2
> ERROR: compilation failed for package ‘Biostrings’

Weird. Do other packages requiring source build work, e.g., Biobase? If 
not, it sounds like a system configuration issue. If so, try updating 
IRanges, then Biostrings?

I'm not sure what else to suggest, perhaps downloading the Biostrings 
source (as tar.gz) and running from the command line

   CFLAGS="-v" R CMD INSTALL --libs-only Biostrings_2.20.3.tar.gz

and looking for a suspicious path name that might actually trigger the 
'File name too long' message.

Martin

> * removing ‘/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings’
> * restoring previous
> ‘/home/guido/R/x86_64-pc-linux-gnu-library/2.13/Biostrings’
> This is my sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=it_IT.UTF-8
>   [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.13.0 tools_2.13.0
>
>
> Any idea?
> Thank you very much
> Guido
>
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