[BioC] Error - BSgenomeForge function

[Hervé Pagès]

Hi Sara,

[also answering to the mailing list]

On 01/18/2013 03:44 AM, Sara Castelletti wrote:
> Dear Dr Pagès,
>
> I apologize for writing to you personally but since my post on the
> Bioconductor mailing list didn't receive any reply, I thought you might
> have overlooked it.
>
> I have been using the BSgenomeForge function to create a BSgenome data
> package for maize (as it is not available in the BSgenome package).
> I have prepared the seed file and downloaded the fasta sequences and
> then I proceeded to forge the genome. Then I quit R and followed the
> manual.
>
> R CMD build "~/projets/ZeaMays/ZmB73_5b_masked/BSgenome"
> * checking for file
> '~/projets/ZeaMays/ZmB73_5b_masked/BSgenome/DESCRIPTION' ... OK
> * preparing 'BSgenome':
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building 'BSgenome_1.27.1.tar.gz'

Ooops, it's not a good idea to name your BSgenome *data* package
"BSgenome", since this is the name of the BSgenome *software* package
that any BSgenome *data* package depends on. (The BSgenome *software*
package is also the place where you found the BSgenomeForge vignette.)

Using the name of an existing package for your own BSgenome *data*
package is guaranteed to create problems. In your case the problem
is probably due to the fact that, given its name, and according
to the Depends field in its DESCRIPTION file, your package seems to
depend on itself.

Why not follow the established convention for naming your package?
See the BSgenomeForge vignette and/or the man page for the
available.genomes function (?available.genomes) for the details.
In any case, you should definitely avoid using the name of an existing
Bioconductor or CRAN package (i.e. biocLite("myname") should fail).

Hope this helps,
H.

>
>
> R CMD check "~/projets/ZeaMays/ZmB73_5b_masked/BSgenome_1.27.1.tar.gz"
> * using log directory
> '/projets/gear/scastelletti/ZeaMays/ZmB73_5b_masked/BSgenome.Rcheck'
> * using R version 2.15.2 (2012-10-26)
> * using platform: x86_64-pc-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file 'BSgenome/DESCRIPTION' ... OK
> * this is package 'BSgenome' version '1.27.1'
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking whether package 'BSgenome' can be installed ... ERROR
> Installation failed.
> See
> '/projets/gear/scastelletti/ZeaMays/ZmB73_5b_masked/BSgenome.Rcheck/00install.out'
> for details.
>
>
> The error file goes like this
>
> * installing *source* package 'BSgenome'
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in match.fun(FUN) : pile de noeuds dborde vers le haut /*I think
> the translation of the error message is "node stack overflow"*/
> ERROR: lazy loading failed for package 'BSgenome'
> * removing
>
> I am, as you might have already guessed, not a computer scientist and
> have no clue whatsoever on what this means.
> I am attaching the seed file as well, if it is of any use.
> Thanks in advance for the reply,
>
> Sara

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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