Question: Windows fails to install package from source 'tar.gz', e.g., "GO.db"
0
gravatar for s3462450
23 months ago by
s34624500
Australia
s34624500 wrote:

Hi, 

I can't download WGCNA on Windows. 

When I use command:

source("http://bioconductor.org/biocLite.R")
biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore"))
install.packages("WGCNA")

I get following error:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see
  http://bioconductor.org/install
> biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore"))
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) ‘AnnotationDbi’, ‘impute’, ‘GO.db’, ‘preprocessCore’
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/AnnotationDbi_1.32.3.zip'
Content type 'application/zip' length 9460389 bytes (9.0 MB)
downloaded 9.0 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/impute_1.44.0.zip'
Content type 'application/zip' length 1339240 bytes (1.3 MB)
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/preprocessCore_1.32.0.zip'
Content type 'application/zip' length 413020 bytes (403 KB)
downloaded 403 KB

package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
package ‘impute’ successfully unpacked and MD5 sums checked
package ‘preprocessCore’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\s3462450\AppData\Local\Temp\RtmpMvHhUc\downloaded_packages
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/GO.db_3.2.2.tar.gz'
Content type 'application/x-gzip' length 31248918 bytes (29.8 MB)
downloaded 29.8 MB

'\\ntapprdfs01n02.rmit.internal\sh0\s3462450'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\ntapprdfs01n02.rmit.internal\sh0\s3462450\R\R-32~1.3' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
        ‘C:\Users\s3462450\AppData\Local\Temp\RtmpMvHhUc\downloaded_packages’
Warning messages:
1: running command '"//ntapprdfs01n02.rmit.internal/sh0/s3462450/R/R-3.2.3/bin/i386/R" CMD INSTALL -l "\\ntapprdfs01n02.rmit.internal\sh0\s3462450\R\win-library\3.2" C:\Users\s3462450\AppData\Local\Temp\RtmpMvHhUc/downloaded_packages/GO.db_3.2.2.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status
> install.packages("WGCNA")
Installing package into ‘\\ntapprdfs01n02.rmit.internal/sh0/s3462450/R/win-library/3.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning: dependency ‘GO.db’ is not available
trying URL 'https://cran.ms.unimelb.edu.au/bin/windows/contrib/3.2/WGCNA_1.51.zip'
Content type 'application/zip' length 2204728 bytes (2.1 MB)
downloaded 2.1 MB

package ‘WGCNA’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\s3462450\AppData\Local\Temp\RtmpMvHhUc\downloaded_packages

Please advice. Thanks for your help!

wgcna go.db • 713 views
ADD COMMENTlink modified 23 months ago by Martin Morgan ♦♦ 22k • written 23 months ago by s34624500
Answer: Can't download WGCNA
0
gravatar for Martin Morgan
23 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

I'm not exactly sure of the details, but I think you could map the network drive (google led me to here, but there might be better instructions) where R is installed, and launch R from the mounted drive rather than the network location. Then try the problematic command

BiocInstaller::biocLite("GO.db")
ADD COMMENTlink written 23 months ago by Martin Morgan ♦♦ 22k
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