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omran.allatif
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@omranallatif-15310
Last seen 6.7 years ago
package ‘Glimma’ still not available for R version 3.4.4, why?
Could this be because of a compatibility issue between the current release of Bioconductor (version 3.6) and R 3.4.4 (2018-03-15)?
>
source("https://bioconductor.org/biocLite.R")Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
>
biocLite()BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.4.4 (2018-03-15).
Does this mean that I can not update Bioconductor because, perhaps, the latest version of R is too recent?
Here is R's answer when I try to download 'Glimma':
>
biocLite("Glimma")BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.4.4 (2018-03-15).
Installing package(s) ‘Glimma’
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.4:
cannot open URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/data/annotation/bin/windows/contrib/3.4:
cannot open URL 'https://bioconductor.org/packages/3.2/data/annotation/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/data/experiment/bin/windows/contrib/3.4:
cannot open URL 'https://bioconductor.org/packages/3.2/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/extra/bin/windows/contrib/3.4:
cannot open URL 'https://bioconductor.org/packages/3.2/extra/bin/windows/contrib/3.4/PACKAGES'
Warning message:
package ‘Glimma’ is not available (for R version 3.4.4)
You have an older version of BiocInstaller on a new version of R. It should look like this:
> library(BiocInstaller) Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help > version _ platform x86_64-w64-mingw32 arch x86_64 os mingw32 system x86_64, mingw32 status major 3 minor 4.3 year 2017 month 11 day 30 svn rev 73796 language R version.string R version 3.4.3 (2017-11-30) nickname Kite-Eating Tree >I have no idea how you got such an old version of BiocInstaller, but you should probably start R again (in a directory without a .Rdata, or using the --vanilla flag), do
remove.packages("BiocInstaller")And then re-install using
source("https://www.bioconductor.org/biocLite.R")Then you probably want to do
and follow the instructions to fix your Bioconductor installation first.