Question: GO.db installation problems with BiocManager in R
0
gravatar for d.m.j.thorburn
7 months ago by
d.m.j.thorburn0 wrote:

I am trying to install the package GO.db using BiocManager, but I keep getting error messages. I have tried installing and reinstalling BiocManager, even updated my version of R from 3.5.2 to 3.5.3. I have other packages like AnnotationDBi and TopGO installed - the latter won't load because it requires GO.db.

The error message I keep getting is:

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2
  (2018-12-20)
Installing package(s) 'GO.db'
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz'
Content type 'application/x-gzip' length 31820876 bytes (30.3 MB)
downloaded 30.3 MB

* installing *source* package 'GO.db' ...
Warning in file.copy(f, instdir, TRUE) :
  problem copying .\NAMESPACE to C:\Users\Name\Documents\R\win-library\3.5\GO.db\NAMESPACE: Permission denied
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Name/Documents/R/win-library/3.5/GO.db/DESCRIPTION': Permission denied
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'GO.db'
* removing 'C:/Users/Name/Documents/R/win-library/3.5/GO.db'
In R CMD INSTALL

The downloaded source packages are in
        ‘C:\Users\Name\AppData\Local\Temp\RtmpEpb8dH\downloaded_packages’
installation path not writeable, unable to update packages:
  class, codetools, Matrix
Update old packages: 'assertthat', 'mgcv'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GO.db’ had non-zero exit status

I'm starting to run out of ideas short of deleting R and restarting my collection of libraries from scratch. I tried installing GO.db on the computing cluster I use too, but alas that came up with similar error messages. Running R as an administrator also didn't seem to garner any differences.

Any ideas on how to fix this?

R bioconductor • 388 views
ADD COMMENTlink written 7 months ago by d.m.j.thorburn0

For clarification are you are able to install other packages into "C:/Users/Name/Documents/R/win-library/3.5/"? What are the paths specified in .libPaths()?

ADD REPLYlink written 7 months ago by shepherl ♦♦ 1.6k

The paths are:

[1] "C:/Users/Name/Documents/R/win-library/3.5" [2] "C:/Program Files/R/R-3.5.2/library"

And yes, I have installed other packages today. I even updated a package using the BiocManager earlier too.

ADD REPLYlink written 7 months ago by d.m.j.thorburn0

Is there anything in C:/Users/Name/Documents/R/win-library/3.5/GO.db right now? Is there an OOLOCK-GO.db directory in that dir? If there is a lock file, delete that and try again. If there is already a GO.db dir, you could try deleting that and trying again.

ADD REPLYlink written 7 months ago by James W. MacDonald51k

Unfortunately, I've already tried deleting them and trying again several times. The directories are typically empty though.

ADD REPLYlink written 7 months ago by d.m.j.thorburn0

Try the two-step process of downloading the package

download.packages(
    "GO.db", "C:/Users/Name/Documents",
    repos = BiocManager::repositories()
)

and installing it locally

install.packages("C:/Users/Name/Documents/GO.db_3.7.0.tar.gz", repos = NULL)
ADD REPLYlink modified 7 months ago • written 7 months ago by Martin Morgan ♦♦ 23k

Thanks again for the help, but again it seems that didn't work. In the end it was my antivirus "protecting" certain files. I had to essentially un-protect certain files as R was already on a list allowing it to modify these files but for some reason only this package was stopped without an error message.

I'm confused why GO.db was targeted, but I'm happy this has finally been resolved.

ADD REPLYlink written 7 months ago by d.m.j.thorburn0

The 'annotation' packages are installed from 'source' so have a different extension (.tar.gz) than the usual Windows 'binary' packages (extension .zip); perhaps that is the reason? Thanks for replying with the diagnosis.

ADD REPLYlink written 7 months ago by Martin Morgan ♦♦ 23k
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