"cannot parse URI" Error for Installing BSgenome.Hsapiens.UCSC.hg19
0
0
Entering edit mode
Haiying.Kong ▴ 110
@haiyingkong-9254
Last seen 5.1 years ago
Germany

  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

bioconductor • 1.4k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 516 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6