biocLite on R 3.2.0 stalls then vanishes
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@will-landau-6891
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"

Copyright (C) 2015 The R Foundation for Statistical Computing

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

 

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

 

  Natural language support but running in an English locale

 

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

 

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

 

> source("http://bioconductor.org/biocLite.R")

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

> biocLite("limma")

^C

> 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)

 

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     

 

loaded via a namespace (and not attached):

[1] tools_3.2.0

.libPaths()

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

software error bioclite • 1.1k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 23 months ago
United States

Maybe try

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

again?

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Entering edit mode

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

I'm still wondering why rerunning source("http://bioconductor.org/biocLite.R") 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

~/R/x86_64-unknown-linux-gnu-library/3.2

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?

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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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