Error in Forge the target package (BSgenome)

General
1

This error has been fixed by slicing the reference genome file into multiple .fas files per scaffold/chromossome.

Hi,

I am trying to forge a BSgenome according to the instruction https://www.bioconductor.org/packages/devel/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf. But I have error in checking the package with:

R CMD check <tarball>
where <tarball> is the path to the tarball produced by R CMD build.
  • installing source package ‘BSgenome.Rhinella.marina.UNSW.RM170330’ ...

** using staged installation

** R

** inst

** byte-compile and prepare package for lazy loading

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded from temporary location

Warning in .seqlengths_TwoBitFile(x) :

/Users/jiazhou/Box/methylation_analysis/msgbsR/BSgenome.Rhinella.marina/BSgenome.Rhinella.marina.UNSW.RM170330.Rcheck/00LOCK-BSgenome.Rhinella.marina.UNSW.RM170330/00new/BSgenome.Rhinella.marina.UNSW.RM170330/extdata/single_sequences.2bit doesn't have a valid twoBitSig

Error: package or namespace load failed for ‘BSgenome.Rhinella.marina.UNSW.RM170330’:

.onLoad failed in loadNamespace() for 'BSgenome.Rhinella.marina.UNSW.RM170330', details:

call: h(simpleError(msg, call))

error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': UCSC library operation failed

Error: loading failed

Execution halted

ERROR: loading failed

  • removing ‘/Users/jiazhou/Box/methylation_analysis/msgbsR/BSgenome.Rhinella.marina/BSgenome.Rhinella.marina.UNSW.RM170330.Rcheck/BSgenome.Rhinella.marina.UNSW.RM170330’

00install.out (END)

Just wondering whether anyone have suggestions for it.

Thanks,

Jia

2

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