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Question: Problem with upgrading Bioconductor from 3.4 to 3.5
0
gravatar for michal.combik
11 months ago by
michal.combik0 wrote:

I'm trying to ugrade Bioconductor 3.5 to 3.5 using:

biocLite("BiocUpgrade")
Error: Bioconductor version 3.4 cannot be upgraded with R version 3.4.0


Why? I have R 3.4.0

 sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.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] compiler_3.4.0 tools_3.4.0    RCurl_1.95-4.8 h2o_3.10.4.6   jsonlite_1.5  
[6] bitops_1.0-6  

 

 

ADD COMMENTlink modified 11 months ago • written 11 months ago by michal.combik0
0
gravatar for Martin Morgan
11 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

Remove (all copies of) BiocInstaller and source("https://bioconductor.org/biocLite.R"). This should provide you with BiocInstaller version 1.26.0; use biocValid() and biocLite(ask=FALSE) to update packages.

ADD COMMENTlink written 11 months ago by Martin Morgan ♦♦ 21k
0
gravatar for michal.combik
11 months ago by
michal.combik0 wrote:

Thanks for answer, I removed all R and all libraries and I installed everything from beginning. Now I have Bioconductor 3.5.

Thanks, problem solved!

ADD COMMENTlink written 11 months ago by michal.combik0

It was only necessary to remove the BiocInstaller package, not all R / all packages, but I'm glad you got it working.

ADD REPLYlink written 11 months ago by Martin Morgan ♦♦ 21k
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