Question: Unable to install GO.db
0
gravatar for h.burke
13 months ago by
h.burke0
h.burke0 wrote:

I am unable to load GO.db... see code: Please can you advise a fix. Many thanks.

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz'
Content type 'application/x-gzip' length 31763273 bytes (30.3 MB)
downloaded 30.3 MB

'\\filestore.soton.ac.uk\users\hb6g13'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\filestore.soton.ac.uk\users\hb6g13\mydocuments\R\R-3.5.0' is not recognized as an internal or external command,
operable program or batch file.
In R CMD INSTALL

The downloaded source packages are in
	‘C:\Users\hb6g13\AppData\Local\Temp\Rtmp0MpTwm\downloaded_packages’
Old packages: 'bit', 'graph', 'MASS', 'mvtnorm', 'purrr', 'rlang', 'stringi', 'survival'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
> traceback()
No traceback available 
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0   
> .libPaths()
[1] "\\\\filestore.soton.ac.uk/users/hb6g13/mydocuments/R/R-3.5.0/library"
 

>

installation problem • 265 views
ADD COMMENTlink modified 13 months ago by Martin Morgan ♦♦ 23k • written 13 months ago by h.burke0
Answer: Unable to install GO.db
0
gravatar for Martin Morgan
13 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

The problem is that "\\filestore.soton.ac.uk\users\..." is a 'UNC' path, and you need to map this network drive to a Windows drive, so that you can reference, e.g., "W:\\..."). One would then usually start R using this mapped drive, rather than from the UNC path.

ADD COMMENTlink written 13 months ago by Martin Morgan ♦♦ 23k
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