I am trying to install CODEX Bioconductor package. The package has dependency on BSgenome.Hsapiens.UCSC.hg19, and when this package is installed by
source("https://bioconductor.org/biocLite.R") biocLite("BSgenome.Hsapiens.UCSC.hg19")
I get the following error message:
* installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details:
call: parseURI("")
error: cannot parse URI
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/nfs/home/m/kong/lib/R-3.2.2/BSgenome.Hsapiens.UCSC.hg19’
The downloaded source packages are in
‘/tmp/Rtmpg79DtQ/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status
The library location has enough space. I am using a mounted disk space. Local space is only for root.
Additional information:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
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=en_US.UTF-8 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
other attached packages:
[1] BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] tools_3.2.2
As far as I can tell, parseURI is called from rtracklayer en route to parsing a TwoBit file. Can you check that you have
current rtracklayer and BSgenome packages installed