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Question: GO.db will not download
0
gravatar for MOD
9 months ago by
MOD0
Teagasc Dublin
MOD0 wrote:

Hi,

I have been trying to download GO.db, but it keeps failing with the following message:

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘GO.db’
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

'\\nfvx341\homeshares3$\HOME.ODO'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\nfvx341\homeshares3$\HOME.ODO\R\R-3.3.2' is not recognized as an internal or external command,
operable program or batch file.

Warning messages:
1: running command '"//nfv/homeshares3$/HOME.ODO/R/R-3.3.2/bin/x64/R" CMD INSTALL -l "\\nfvx341\homeshares3$\HOME\R\R-3.3.2\library" C:\Users\HOME~1.ODO\AppData\Local\Temp\RtmpYtru21/downloaded_packages/GO.db_3.4.0.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:

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] AnnotationDbi_1.36.2 IRanges_2.8.1        S4Vectors_0.12.1    
[4] Biobase_2.34.0       BiocGenerics_0.20.0  RSQLite_1.1-2       
[7] BiocInstaller_1.24.0 limma_3.30.11       

loaded via a namespace (and not attached):
[1] DBI_0.5-1     tools_3.3.2   memoise_1.0.0 Rcpp_0.12.9   digest_0.6.12

 

My R and Bioconductor seems to be up-to-date (Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31)), as is my RSQLite (1.1-2) and AnnotationDbi (1.36.2).

I had seen in one group that biocValid(fix=TRUE) worked for them, but this was not the case for me.

Any ideas what I am doing wrong?

 

ADD COMMENTlink written 9 months ago by MOD0

It sounds like Windows fails to install package from source 'tar.gz', e.g., "GO.db" ; can you map the UNC network drive \\nfvfx... to a windows drive letter, launch R from there, and try again?

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 20k

Sorry for delay. I only just saw your message. For some reason the header had "0 answers". Yep, it seemed running R on the C drive worked and then transferring the file manually back to \\nfvfx . Thanks for you help Martin.

ADD REPLYlink written 9 months ago by MOD0
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