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Question: GO.db install fails in Windows 10 on second drive
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gravatar for Robert Baer
3 months ago by
Robert Baer70
United States
Robert Baer70 wrote:

In installing and updating  bioconductor packages the dependency GO.db fails on widows on what looks like a parsing error brought about by a space in the path on E: drive.  I don't know if this is because the linux equivalent is "/e/program files/..." to the Windows "E:\progem Files\..."

But, whether it is something else, but I'd be grateful for a workaround or better yet a fix.

Here's the console output ...

 

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Old packages: 'AnnotationDbi', 'clusterProfiler', 'flowCore',
  'flowWorkspace', 'GenomicRanges', 'limma'
Update all/some/none? [a/s/n]: 

Update all/some/none? [a/s/n]: 
a
also installing the dependency ‘GO.db’

...

package ‘limma’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Rob Baer\AppData\Local\Temp\RtmpagJM0a\downloaded_packages
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB

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

The downloaded source packages are in
    ‘C:\Users\Rob Baer\AppData\Local\Temp\RtmpagJM0a\downloaded_packages’
Warning messages:
1: running command '"E:/Program Files/R/R-3.3.3/bin/x64/R" CMD INSTALL -l "C:\Users\Rob Baer\R\win-library\3.3" C:\Users\ROBBAE~1\AppData\Local\Temp\RtmpagJM0a/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1 
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘GO.db’ had non-zero exit status

=====================

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.3

 

> R.Version()
$platform
[1] "x86_64-w64-mingw32"
$arch
[1] "x86_64"
$os
[1] "mingw32"
$system
[1] "x86_64, mingw32"
$status
[1] ""
$major
[1] "3"
$minor
[1] "3.3"
$year
[1] "2017"
$month
[1] "03"
$day
[1] "06"
$`svn rev`
[1] "72310"
$language
[1] "R"
$version.string
[1] "R version 3.3.3 (2017-03-06)"
$nickname
[1] "Another Canoe"

 RStudio.Version()
$citation

To cite RStudio in publications use:

  RStudio Team (2016). RStudio: Integrated Development for R. RStudio, Inc.,
  Boston, MA URL http://www.rstudio.com/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {RStudio: Integrated Development Environment for R},
    author = {{RStudio Team}},
    organization = {RStudio, Inc.},
    address = {Boston, MA},
    year = {2016},
    url = {http://www.rstudio.com/},
  }


$mode
[1] "desktop"

$version
[1] ‘1.0.136’

 

 

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