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Question: Bioconductor version too old
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gravatar for spevdo
4 months ago by
spevdo0
spevdo0 wrote:

So I am trying to upgrade bioconductor and I get the error:

`Bioconductor version 3.4 is too old for R version 3.4.1; see https://bioconductor.org/install/#troubleshoot-biocinstaller`

I follow the suggested link and perform the following, as suggested:

  • Quit your R session
  • Start a new session with R --vanilla
  • Run the command remove.packages("BiocInstaller")
  • Repeat that command until R says there is no such package.
  • Run the command source("https://bioconductor.org/biocLite.R")
  • Run biocValid() to ensure your installed packages are valid for the current version of Bioconductor, and follow the instructions it gives you.

The problem seems to then be that R version 3.4 is again installed and I continue to get the same error. What am I missing?

ADD COMMENTlink written 4 months ago by spevdo0

Did you repeat the remove.packages("BiocInstaller") until you got an error (make sure you have privileges to remove the BiocInstaller package) ?

ADD REPLYlink written 4 months ago by Lluís R300

Exactly, I followed the instructions here and I did this until it errored.

ADD REPLYlink written 4 months ago by spevdo0

Show the output of the source("https://bioconductor.org/biocLite.R") command. Remember to provide the output of sessionInfo().

ADD REPLYlink modified 4 months ago • written 4 months ago by Martin Morgan ♦♦ 20k
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller

And sessionInfo:

R version 3.4.1 (2017-06-30)
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_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.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_3.4.1 tools_3.4.1    knitr_1.16

 

ADD REPLYlink written 3 months ago by spevdo0

Hi,

I have the exact same problem with R 3.4.2 on Ubuntu16.04 LTS. I've tried all suggested solutions. Any ideas for correcting this? My sessionInfo():

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fi_FI.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fi_FI.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fi_FI.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fi_FI.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_3.4.2
ADD REPLYlink written 12 days ago by khandarius0

Your BiocInstaller is too old and needs to be updated following these instructions. If that fails, please copy and paste your attempts at removal and installation into a comment.

ADD REPLYlink written 12 days ago by Martin Morgan ♦♦ 20k
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