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Question: Loading BSgenome.Hsapiens.UCSC.hg19 package
0
gravatar for Sushant Pawar
20 months ago by
Nashik
Sushant Pawar0 wrote:

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
>
ADD COMMENTlink modified 20 months ago by Martin Morgan ♦♦ 20k • written 20 months ago by Sushant Pawar0
1

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 REPLYlink written 20 months ago by Martin Morgan ♦♦ 20k
1

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

ADD REPLYlink written 20 months ago by b.nota290
0
gravatar for Sushant Pawar
20 months ago by
Nashik
Sushant Pawar0 wrote:

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

problem solve.

ADD COMMENTlink written 20 months ago by Sushant Pawar0
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