Upgrade to Bioconductor 3.4 - problems with R
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Entering edit mode
Lna • 0
@lna-10651
Last seen 4.2 years ago

Hi,

I was trying to upgrade to Bioconductor 3.4 and in order to do so I had to make an R upgrade (3.2.2 to 3.3.2). When running biocLite("BiocUpgrade") I get the error:

Bioconductor version 3.4 cannot be upgraded with R version 3.3.2

I already tried to remove BiocInstaller with

remove.packages("BiocInstaller",lib="/home/f/R/x86_64-pc-linux-gnu-library/3.3")
from all paths listed with

.libPaths()

[1] "/home/f/R/x86_64-pc-linux-gnu-library/3.3"
[2] "/usr/local/lib/R/site-library"                    
[3] "/usr/lib/R/site-library"                          
[4] "/usr/lib/R/library"

Didn't work. I came across a post asking for a similar solution and a comment saying the problem might be caused by installing the new R version over the old one. I think this might be the problem in my case, but I don't no how to clean up the mess...

Does the existence of both "/usr/local/lib/R/site-library" AND "/usr/lib/R/site-library" mean, that I made the installation of the two R versions in two different ways does the old library interfere with the new installation? If this is true, do I have to remove R completely or what should I do? Just deleting old libraries or will that cause additional problems?

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

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

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

Thank you for any suggestions.

r update upgrade bioclite • 4.2k views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

If you already have BiocInstaller 1.24.0, then I am not sure you want to use biocLite("biocUpgrade"). Instead I think you just want to do biocLite(ask = FALSE).
 

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