GO.db will not download
0
0
Entering edit mode
MOD • 0
@mod-12330
Last seen 4.6 years ago
Teagasc Dublin

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?

 

GO.db • 948 views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 434 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6