All three of the sites where genomeinfodbdata R packages are stored appear to be down.
2
2
Entering edit mode
15753563659 ▴ 60
@558fa874
Last seen 15 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 • 1.5k views
ADD COMMENT •
2
Entering edit mode
larrycai ▴ 20
@9b7b1d4a
Last seen 15 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'
ADD COMMENT •
2
Entering edit mode

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.

ADD REPLY •
1
Entering edit mode

May I ask when Bioconductor 3.16 packages will resume work?

ADD REPLY •
0
Entering edit mode

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.

ADD REPLY •
0
Entering edit mode

Thank you very much for your kind reply!

ADD REPLY •
0
Entering edit mode

Thanks, upgrading to 3.17 indeed fixed it for me.

ADD REPLY •
1
Entering edit mode
@gordon-smyth
Last seen 2 hours 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.
ADD COMMENT •
0
Entering edit mode

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

ADD REPLY •
0
Entering edit mode

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

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 712 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6