Question

Bioconductor version too old

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spevdo • 0

@spevdo-13478

Last seen 8.3 years ago

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?

software error • 3.7k views

ADD COMMENT • link 8.3 years ago spevdo • 0

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

ADD REPLY • link 8.3 years ago Lluís Revilla Sancho ▴ 760

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

ADD REPLY • link 8.3 years ago spevdo • 0

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

ADD REPLY • link 8.3 years ago Martin Morgan 25k

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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 REPLY • link 8.3 years ago spevdo • 0

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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 REPLY • link 8.0 years ago khandarius ▴ 20

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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 REPLY • link 8.0 years ago Martin Morgan 25k