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Question: TCGAbiolinks Installation Issues
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gravatar for natalie_stephenson
6 months ago by
natalie_stephenson0 wrote:

Hi,

I've been working with TCGAbiolinks for a while with no issue (R version 3.3.2). 2 days ago my computer updated R to version 3.4.0 and now I am getting errors when I try to install TCGAbiolinks. Below are the commands used:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("TCGAbiolinks")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘TCGAbiolinks’

  There is a binary version available but the source version is later:
             binary source needs_compilation
TCGAbiolinks 2.3.18  2.4.2             FALSE

installing the source package ‘TCGAbiolinks’

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/TCGAbiolinks_2.4.2.tar.gz'
Content type 'application/x-gzip' length 49242557 bytes (47.0 MB)
downloaded 47.0 MB

* installing *source* package 'TCGAbiolinks' ...
** R
Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
  cannot open file 'C:/Users/fbsnls/Documents/R/R-3.4.0/library/TCGAbiolinks/R/sysdata.rdb': Permission denied
ERROR: unable to build sysdata DB for package 'TCGAbiolinks'
* removing 'C:/Users/fbsnls/Documents/R/R-3.4.0/library/TCGAbiolinks'

The downloaded source packages are in
    ‘C:\Users\fbsnls\AppData\Local\Temp\Rtmp0c3XVL\downloaded_packages’
Old packages: 'GenomicRanges', 'irlba', 'knitr', 'readr', 'rlang', 'tibble'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
              binary source needs_compilation
GenomicRanges 1.28.1 1.28.2              TRUE
irlba          2.1.2  2.2.1              TRUE
knitr         1.15.1   1.16             FALSE
readr          1.1.0  1.1.1              TRUE
rlang            0.1  0.1.1              TRUE
tibble         1.3.0  1.3.1              TRUE

  Binaries will be installed
Warning: package ‘readr’ is in use and will not be installed
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/GenomicRanges_1.28.1.zip'
Content type 'application/zip' length 3000817 bytes (2.9 MB)
downloaded 2.9 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/irlba_2.1.2.zip'
Content type 'application/zip' length 257570 bytes (251 KB)
downloaded 251 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/rlang_0.1.zip'
Content type 'application/zip' length 460953 bytes (450 KB)
downloaded 450 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/tibble_1.3.0.zip'
Content type 'application/zip' length 627578 bytes (612 KB)
downloaded 612 KB

package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘irlba’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘tibble’

The downloaded binary packages are in
    C:\Users\fbsnls\AppData\Local\Temp\Rtmp0c3XVL\downloaded_packages
installing the source package ‘knitr’

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.16.tar.gz'
Content type 'application/x-gzip' length 1031259 bytes (1007 KB)
downloaded 1007 KB

* installing *source* package 'knitr' ...
** package 'knitr' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (knitr)

The downloaded source packages are in
    ‘C:\Users\fbsnls\AppData\Local\Temp\Rtmp0c3XVL\downloaded_packages’
Warning messages:
1: running command '"C:/Users/fbsnls/DOCUME~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\fbsnls\Documents\R\R-3.4.0\library" C:\Users\fbsnls\AppData\Local\Temp\Rtmp0c3XVL/downloaded_packages/TCGAbiolinks_2.4.2.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TCGAbiolinks’ had non-zero exit status
> sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.26.0 readr_1.1.0         

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'tibble' is missing or broken

 

I also tried installing 'tibble' in case this was the reason I'm getting the error - however, this still gives the same error when installing TCGAbiolinks.

 

Any help or advice would be greatly appreciated.

Natalie

ADD COMMENTlink written 6 months ago by natalie_stephenson0
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