Question

Cannot install Bioconductor v3.9

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thkapell ▴ 10

@tkapell-14647

Last seen 22 months ago

Helmholtz Center Munich, Germany

Hi all,

I am trying to update a Bioconductor package (scran) which is a dependency for another one (cellassign) and so I had to update my Bioconductor version from 3.7 to 3.9 (I am using R 3.6.1). I got the following message and nothing was updated. Can somebody provide a quick fix?

Thanks in advance!

> BiocManager::install(version = "3.9")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/workflows/src/contrib/PACKAGES'
installation path not writeable, unable to update packages: boot, foreign, mgcv, nlme
Update old packages: 'Seurat'

scran cellassign bioconductor • 3.4k views

ADD COMMENT • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by thkapell ▴ 10

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Me too, in the same situation!!

> * checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES'

ADD REPLY • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by alaihd ▴ 10

Martin Morgan · Answer 1 · 2019-10-03

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christopherlhartl • 0

@christopherlhartl-10884

Last seen 5.1 years ago

This is an issue with the CA certificate of bioconductor.org expiring; and the fact that bioconductor does not use an http fallback for https.

In the meantime you can perform a manual installation, using the base R install.packages, and specifying the bioconductor repo directly, as in:

install.packages(libs, repos=c('http://bioconductor.org/packages/3.9/bioc',
   'http://cran.wustl.edu/', 
   'http://bioconductor.org/packages/release/data/annotation'))

Note the lack of "httpS" here.

ADD COMMENT • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by christopherlhartl • 0

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Thank you for the prompt answer

ADD REPLY • link 5.2 years ago thkapell ▴ 10

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A better solution, in case one needs http access, is to use chooseBioCmirror() to use a non-https mirror (it's on the second 'screen', choose 0-bioconductor). This will change BiocManager::repositories() to point to the http:// repositories.

Generally, http:// is less secure, especially for software installation, so it's worth thinking carefully about whether this is the right solution.

ADD REPLY • link 5.2 years ago Martin Morgan 25k

score 0 · Answer 2 · 2019-10-03

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shepherl 4.1k

@lshep

Last seen 3 hours ago

United States

I am in the process of fixing the credentials now. It issue should be fixed shortly

ADD COMMENT • link 5.2 years ago shepherl 4.1k