Entering edit mode
Hi,
I had some problems when installing BSgenome.Drerio.UCSC.danRer7. (Linux system)
source("https://bioconductor.org/biocLite.R")
biocLite("BSgenome.Drerio.UCSC.danRer7")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.1.
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
* installing *source* package 'BSgenome.Drerio.UCSC.danRer7' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
During startup - Warning message:
Setting LC_CTYPE failed, using "C"
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Error : .onLoad failed in loadNamespace() for 'BSgenome.Drerio.UCSC.danRer7', details:
call: parseURI("")
error: cannot parse URI
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/data4/bingjie/software/R-3.2.1/library/BSgenome.Drerio.UCSC.danRer7'
The downloaded source packages are in
'/tmp/RtmpCeGpTT/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 'BSgenome.Drerio.UCSC.danRer7' had non-zero exit status
It seems that I had the same problem as Problem installing BSgenome.Hsapiens.UCSC.hg19 but I am not that familiar with Linux, could someone show me how to "reset LD_LIBRARY_PATH to the bare minimum" ?
Thanks in advance!
It would be useful to get to the bottom of this. Create a text file '.Rprofile' in your home directory with the following lines
Then start a new R session (in a console, not RStudio or anything else) and try again
source("https://bioconductor.org/biocLite.R") biocLite("BSgenome.Drerio.UCSC.danRer7")Edit your question to include the output, and post a comment indicating that you've done this.