Question: biocLite on R 3.2.0 stalls then vanishes
gravatar for Will Landau
3.2 years ago by
United States
Will Landau0 wrote:

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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> 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" 

ADD COMMENTlink modified 3.2 years ago by Dan Tenenbaum ♦♦ 8.2k • written 3.2 years ago by Will Landau0
gravatar for Dan Tenenbaum
3.2 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

Maybe try



ADD COMMENTlink written 3.2 years ago by Dan Tenenbaum ♦♦ 8.2k

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?

ADD REPLYlink written 3.2 years ago by Will Landau0

BiocInstaller updates itself when it's out-of-date.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.

ADD REPLYlink written 3.2 years ago by Martin Morgan ♦♦ 22k
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