Loading BSgenome.Hsapiens.UCSC.hg19 package
1
0
Entering edit mode
@sushant-pawar-9287
Last seen 7.8 years ago
Nashik

Hello friends,
unable to load this library. please help me to load this package.

source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("BSgenome.Hsapiens.UCSC.hg19")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz'
Content type 'application/x-gzip' length 688190187 bytes (656.3 MB)
downloaded 656.3 MB

* installing *source* package 'BSgenome.Hsapiens.UCSC.hg19' ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  there is no package called 'XML'
Error : package 'rtracklayer' could not be loaded
ERROR: lazy loading failed for package 'BSgenome.Hsapiens.UCSC.hg19'
* removing 'D:/User Profiles/Documents/R/win-library/3.2/BSgenome.Hsapiens.UCSC.hg19'

The downloaded source packages are in
‘C:\TEMP\RtmpQJx0PD\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-32~1.3/bin/x64/R" CMD INSTALL -l "D:\User Profiles\Documents\R\win-library\3.2" C:\TEMP\RtmpQJx0PD/downloaded_packages/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘BSgenome.Hsapiens.UCSC.hg19’ had non-zero exit status
>
ucsc bsgenome.hsapiens.ucsc.hg19 • 2.6k views
ADD COMMENT
1
Entering edit mode

The proximal cause can likely be solved with biocLite("XML"). It could be that you / your administrator has set .libPaths when they should have set R_LIBS / R_LIBS_USER, as in this post.

ADD REPLY
1
Entering edit mode

Looks like you have to install the package 'XML' and/or 'rtracklayer' first.

ADD REPLY
0
Entering edit mode
@sushant-pawar-9287
Last seen 7.8 years ago
Nashik

thank you "Martin Morgan" and  "b.nota"

problem solve.

ADD COMMENT

Login before adding your answer.

Traffic: 361 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