installing GO.db on windows 64x
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Entering edit mode
nikka1691 • 0
@nikka1691-8887
Last seen 5.7 years ago
Philippines

Hi. I can't install GO.db. Whenever I try to, I always get this message:
 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("GO.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.4), R version 3.2.2.
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/GO.db_3.1.2.tar.gz'
Content type 'application/x-gzip' length 30192432 bytes (28.8 MB)
downloaded 28.8 MB

* installing *source* package 'GO.db' ...
** R
** inst
** preparing package for lazy loading
Error : package 'Biobase' required by 'AnnotationDbi' could not be found
ERROR: lazy loading failed for package 'GO.db'
* removing 'C:/Users/mGOMEZ/Documents/R/win-library/3.2/GO.db'

The downloaded source packages are in
        ‘C:\Users\mGOMEZ\AppData\Local\Temp\RtmpslIcBl\downloaded_packages’
Old packages: 'class', 'foreign', 'MASS', 'nlme', 'nnet', 'spatial'
Update all/some/none? [a/s/n]: a
Warning in install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  'lib = "C:/Program Files/R/R-3.2.2/library"' is not writable
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/class_7.3-14.zip'
Content type 'application/zip' length 100276 bytes (97 KB)
downloaded 97 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/foreign_0.8-66.zip'
Content type 'application/zip' length 288676 bytes (281 KB)
downloaded 281 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/MASS_7.3-44.zip'
Content type 'application/zip' length 1088035 bytes (1.0 MB)
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nlme_3.1-122.zip'
Content type 'application/zip' length 2140619 bytes (2.0 MB)
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/nnet_7.3-11.zip'
Content type 'application/zip' length 121054 bytes (118 KB)
downloaded 118 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/spatial_7.3-11.zip'
Content type 'application/zip' length 151838 bytes (148 KB)
downloaded 148 KB

package ‘class’ successfully unpacked and MD5 sums checked
package ‘foreign’ successfully unpacked and MD5 sums checked
package ‘MASS’ successfully unpacked and MD5 sums checked
package ‘nlme’ successfully unpacked and MD5 sums checked
package ‘nnet’ successfully unpacked and MD5 sums checked
package ‘spatial’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\mGOMEZ\AppData\Local\Temp\RtmpslIcBl\downloaded_packages
Warning messages:
1: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\mGOMEZ\Documents\R\win-library\3.2" C:\Users\mGOMEZ\AppData\Local\Temp\RtmpslIcBl/downloaded_packages/GO.db_3.1.2.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

go install • 2.2k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 9 minutes ago
United States

Yes, and the message has a message for you:

Error : package 'Biobase' required by 'AnnotationDbi' could not be found

Whenever you get an error that says a package cannot be found, you have to then install that package.

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