Error in biocLite("BiocUpgrade") when trying to update to latest release
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@stephanie-m-gogarten-5121
Last seen 6 days ago
University of Washington

I'm getting an error trying to use biocLite("BiocUpgrade") to go from Bioconductor 3.1 to 3.2 with R 3.2.2. It's telling me the only update option is to devel. On another machine I had been using devel and the update was seamless, BiocInstaller updated itself to 1.20.0 upon first use of biocLite().

> source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
> biocLite("BiocUpgrade")
Bioconductor version 3.1 (BiocInstaller 1.18.4), ?biocLite for help
Error: Bioconductor version 3.1 can be upgraded, but only to 'devel'; see ?useDevel.
  Use biocLite() without any arguments to update installed packages
In addition: Warning message:
'BiocInstaller' update failed, using version 1.18.4
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BiocInstaller_1.18.4

loaded via a namespace (and not attached):
[1] tools_3.2.2
biocinstaller bioclite • 5.7k views
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What if you do 

useDevel()

On the machine where you're having problems, and then 

biocLite()

to update all installed packages?

I realize this is not what we suggest to do, but it may work. I'll look into the issue with BiocUpgrade. 

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This worked, thanks!

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 23 months ago
United States

So I think a better answer for you is that it appears that the BiocInstaller package is installed in a location where you (the user your're running R as) do not have permission to overwrite it. 

The biocLite("BiocUpgrade") command is trying to upgrade the BiocInstaller package so it is failing because of this.

So one approach would be to remove the package:

remove.packages("BiocInstaller")

You may need to be running R as root or another admin user in order for that to work.

Then as the user you normally run R as, do:

source("https://bioconductor.org/biocLite.R")

That should install the 3.2 version of BiocInstaller (in a location where it can later be auto-updated) and then you can just run

biocLite()

to upgrade all your installed packages.

 

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I actually have two versions of BiocInstaller, one installed by the sysadmin in a location I can't write to (this machine is a shared department server), and one in my local R library. I have my R_LIBS environment variable set so R knows to look in the local library first when installing/using packages, but maybe this situation is confusing BiocInstaller.

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