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Question: Trouble with GO.db - installation of package GO.db had non-zero exit status
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gravatar for christin.berlin
19 months ago by
christin.berlin0 wrote:

Hello everyone,

 

I am trying to install GO.db in R studio, but I keep failing... The installations fails telling me "installation of package ‘GO.db’ had non-zero exit status". I tried uninstalling R/R studio and reinstalling, but that didn't help.

I run: 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.1), ?biocLite for help

> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.1), R 3.3.0 (2016-05-03).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/GO.db_3.3.0.tar.gz'
Content type 'application/x-gzip' length 32027913 bytes (30.5 MB)
downloaded 30.5 MB

'C:\Program' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
    ‘C:\Users\cstottme\AppData\Local\Temp\RtmpIFZf3C\downloaded_packages’
Old packages: 'survival', 'survival'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
         binary source needs_compilation
survival 2.39-3 2.39-4              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/survival_2.39-3.zip'
Content type 'application/zip' length 4935511 bytes (4.7 MB)
downloaded 4.7 MB

package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\cstottme\AppData\Local\Temp\RtmpIFZf3C\downloaded_packages

  There is a binary version available but the source version is later:
         binary source needs_compilation
survival 2.39-3 2.39-4              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/survival_2.39-3.zip'
Content type 'application/zip' length 4935511 bytes (4.7 MB)
downloaded 4.7 MB

package ‘survival’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\cstottme\AppData\Local\Temp\RtmpIFZf3C\downloaded_packages
Warning messages:
1: running command '"C:/Program Files/R/R-3.3.0/bin/x64/R" CMD INSTALL -l "C:\Users\cstottme\Documents\R\win-library\3.3" C:\Users\cstottme\AppData\Local\Temp\RtmpIFZf3C/downloaded_packages/GO.db_3.3.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

 

Session Info

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] BiocInstaller_1.22.1       SummarizedExperiment_1.2.0 Biobase_2.32.0            
[4] GenomicRanges_1.24.0       GenomeInfoDb_1.8.0         IRanges_2.6.0             
[7] S4Vectors_0.10.0           BiocGenerics_0.18.0       

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 'git2r' is missing or broken

 

Thanks a lot,


Christin

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