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Question: Problem in BSgenome.Hsapiens.UCSC.hg19 Installation
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gravatar for nabaneeta85
2.5 years ago by
United Kingdom
nabaneeta850 wrote:

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

 

 

ADD COMMENTlink modified 2.5 years ago by Martin Morgan ♦♦ 20k • written 2.5 years ago by nabaneeta850
0
gravatar for James W. MacDonald
2.5 years ago by
United States
James W. MacDonald45k wrote:

Try

biocLite("BSgenome")
biocLite("BSgenome.Hsapiens.UCSC.hg19")
ADD COMMENTlink written 2.5 years ago by James W. MacDonald45k

@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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by nabaneeta850
0
gravatar for Martin Morgan
2.5 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

I guess some of your packages are out-of-date or too new. Try

BiocInstaller::biocValid()

and follow suggestions there.

ADD COMMENTlink written 2.5 years ago by Martin Morgan ♦♦ 20k

Martin Morgan

I tried that. In the R 3.1 version it is installing and returning the following.

[1] TRUE

But when I run 

 library(BSgenome.Hsapiens.UCSC.hg19)

 

It gives the following error:

 

Loading required package: BSgenome
Loading required package: rtracklayer
Error : .onLoad failed in loadNamespace() for 'BatchJobs', details:
  call: makeClusterFunctionsInteractive()
  error: cannot open file 'C:/Users/Nabaneeta/Documents/R/win-library/3.1/checkmate/R/checkmate.rdb': No such file or directory
In addition: Warning messages:
1: package ‘BSgenome’ was built under R version 3.1.2 
2: package ‘rtracklayer’ was built under R version 3.1.3 
Error: package ‘rtracklayer’ could not be loaded

 

 

ADD REPLYlink written 2.5 years ago by nabaneeta850

From the error message, a best guess is to try to reinstall 'checkmate', e.g., biocLite("checkmate").

Somehow the message you now report is completely different from the message you reported earlier, so I guess you are making progress...

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 20k
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