biocLite on R 3.2.0 stalls then vanishes
Entering edit mode
Last seen 7.7 years ago
United States

I just upgraded to R 3.2.0, stashed all my old packages, and got ready to reinstall all my Bioconductor packages. I tried to run biocLite(), but the function just paused indefinitely. When I hit CTRL-C and tried again, R couldn't find biocLite anymore. Here's the whole session.


R version 3.2.0 (2015-04-16) -- "Full of Ingredients"

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Platform: x86_64-unknown-linux-gnu (64-bit)


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> source("")

Bioconductor version 3.1 (BiocInstaller 1.18.1), ?biocLite for help

> biocLite("limma")


> biocLite("limma")

Error: could not find function "biocLite"

> print(sessionInfo())

R version 3.2.0 (2015-04-16)

Platform: x86_64-unknown-linux-gnu (64-bit)

Running under: CentOS release 6.6 (Final)



 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    


 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            



attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     


loaded via a namespace (and not attached):

[1] tools_3.2.0


[1] "/home/landau/.R/library" "/apps/R-3.2.0/library" 

software error bioclite • 1.1k views
Entering edit mode
Dan Tenenbaum ★ 8.2k
Last seen 23 months ago
United States

Maybe try



Entering edit mode

That worked, so I guess I'm unstuck. Thanks.

I'm still wondering why rerunning source("") was necessary, though. Also, biocLite didn't initially pay attention to my .libPaths() (set in .Rprofile):

> .libPaths()

[1] "/home/landau/.R/library" "/apps/R-3.2.0/library" 

>  biocLite("limma")

The following objects are masked from biocBootstrapEnv (pos = 4):

    ask, bootstrap, dotArgs, pkgs, repos, suppressUpdates

Would you like to use a personal library instead?  (y/n) y

Would you like to create a personal library


to install packages into?  (y/n) n


The limma package did end up in ~/.R/library where I wanted it, but why didn't biocLite() just check .libPaths() and skip the dialogue?

Entering edit mode

BiocInstaller updates itself when it's out-of-date. It does this by creating a 'bootstrap' R environment that stores variables it needs to continue the installation (arguments to biocLite() provided explicitly or implicitly by the user), then removing the installed version of the package (including biocLite(), hence its disappearance), installing the new version of the package, and then using the bootstrapped environment to continue execution in the new version.

The 'following objects masked...' suggests that you somehow managed to get two versions of the bootstrap environment, maybe from the aborted stalled attempt and then re-attempting in the same session. 

I think the 'Would you like to use a personal library instead?' might be asking about where to install BiocInstaller.

Hope that at least partially addresses things; the reason for the initial stall that seemed to be at the root of the problem is not clear; a network error when trying to download the updated BiocInstaller sounds likely.


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