I am using R 3.2, and Bioconductor 3.1. When I am running the command to install BSgenome.Hsapiens.UCSC.hg19.
source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Hsapiens.UCSC.hg19")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'http://bioconductor.org/packages/3.1/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 'BiocParallel'
Error : package 'rtracklayer' could not be loaded
ERROR: lazy loading failed for package 'BSgenome.Hsapiens.UCSC.hg19'
* removing 'C:/Users/Nabaneeta/Documents/R/win-library/3.2/BSgenome.Hsapiens.UCSC.hg19'
* restoring previous 'C:/Users/Nabaneeta/Documents/R/win-library/3.2/BSgenome.Hsapiens.UCSC.hg19'
The downloaded source packages are in
‘C:\Users\Nabaneeta\AppData\Local\Temp\RtmpCempLG\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-32~1.0/bin/i386/R" CMD INSTALL -l "C:\Users\Nabaneeta\Documents\R\win-library\3.2" C:\Users\NABANE~1\AppData\Local\Temp\RtmpCempLG/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
When I am using
library(BSgenome.Hsapiens.UCSC.hg19)I am getting this error:
Error in library(BSgenome.Hsapiens.UCSC.hg19) :
‘BSgenome.Hsapiens.UCSC.hg19’ is not a valid installed package
@James W. MacDonald
I tried. I got this error.
biocLite("BSgenome")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘BSgenome’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BSgenome_1.36.0.zip'
Content type 'application/zip' length 13082285 bytes (12.5 MB)
downloaded 12.5 MB
package ‘BSgenome’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Nabaneeta\AppData\Local\Temp\RtmpieWiz1\downloaded_packages
> biocLite("BSgenome.Hsapiens.UCSC.hg19")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0.
Installing package(s) ‘BSgenome.Hsapiens.UCSC.hg19’
installing the source package ‘BSgenome.Hsapiens.UCSC.hg19’
trying URL 'http://bioconductor.org/packages/3.1/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 'BiocParallel'
Error : package 'rtracklayer' could not be loaded
ERROR: lazy loading failed for package 'BSgenome.Hsapiens.UCSC.hg19'
* removing 'C:/Users/Nabaneeta/Documents/R/win-library/3.2/BSgenome.Hsapiens.UCSC.hg19'
The downloaded source packages are in
‘C:\Users\Nabaneeta\AppData\Local\Temp\RtmpieWiz1\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-32~1.0/bin/i386/R" CMD INSTALL -l "C:\Users\Nabaneeta\Documents\R\win-library\3.2" C:\Users\NABANE~1\AppData\Local\Temp\RtmpieWiz1/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