All three of the sites where genomeinfodbdata R packages are stored appear to be down.
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15753563659 ▴ 50
@558fa874
Last seen 8 months ago
United States

All three of the sites where genomeinfodbdata R packages are stored appear to be down. package: name: bioconductor-genomeinfodbdata version: 1.2.9 source: md5: 7cc138cfb74665fdfa8d1c244eac4879 url:

- https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz
- https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
- https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz
GenomeInfoDbData • 1.1k views
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larrycai ▴ 20
@9b7b1d4a
Last seen 8 months ago
Australia

I can't seem to install ANYTHING from bioconductor today. Not sure if related?

Example from one package:

BiocManager::install("ropls")

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31 ucrt)
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES'
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I can confirm that installation of Bioconductor 3.16 packages is not working today (5pm 13 August 2023 AEST). However installation of Bioconductor 3.17, which is the current version of Bioconductor, is working fine.

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May I ask when Bioconductor 3.16 packages will resume work?

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I do not work for Bioconductor and I have no information other than what I have given you. I am just a 3rd party giving my time free of charge to try to help you as far as I can.

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Thank you very much for your kind reply!

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Thanks, upgrading to 3.17 indeed fixed it for me.

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@gordon-smyth
Last seen 22 minutes ago
WEHI, Melbourne, Australia

See https://www.bioconductor.org/install/ for instructions on how to install Bioconductor packages.

The URLs you show in your email are neither up-to-date nor necessary for you to access. Just follow the instructions using the BiocManager package.

A few hours later

There does indeed seem to be a problem with Bioconductor 3.16 installation today (5pm 13 August 2023 AEST). However installation of Bioconductor 3.17 is working fine.
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Thank you very much for your reply. But I still want to install bioconductor-genomeinfodbdata via conda. However, the installation of conda has been failing. The reason is that the source code cannot be downloaded from the three links provided. Or can you open one of the links so that I can download bioconductor-genomeinfodbdata version 1.2.9 via conda

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I really, really need the 1.2.9 version of bioconductor-genomeinfodbdata because this version matches the other R packages I want to install. There are some lower versions of bioconductor-genomeinfodbdata, can you put 1.2.9 in it https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/

Looking forward to your reply very much

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