Problem installing biomaRt on mac
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@alfonsosaera-19747
Last seen 15 months ago
Spain

Hi all,

I am trying to install biomaRt on my macOS 12.6.1 (Apple M1 Pro just in case it is important) with the following code

BiocManager::install("biomaRt")

that returns this

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.2 (2021-11-01)
Installing package(s) 'biomaRt'
Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1:
 it was not possible to open the URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES'
trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/biomaRt_2.50.3.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  it was not possible to open the URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/biomaRt_2.50.3.tgz'
Además: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/biomaRt_2.50.3.tgz': HTTP status was '503 Service Unavailable'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘biomaRt’ failed

I understand the important part is that cannot find the URLs that it needs but I do not know how to solve it.

Thank you very much

Alfonso

biomaRt mac • 899 views
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@james-w-macdonald-5106
Last seen 10 hours ago
United States

We are currently on Bioconductor 3.16, and unfortunately cannot provide support for old versions. Please upgrade to R-4.2.2 and the current version of Bioconductor.

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I can't login to https://mghp.osn.xsede.org/ to download old packages now. Can you tell me why? Because I need to download version 2.1.7 of genomeinfodbdata.

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