unable to retrieve certain packages from bioconductor 3.15
2
1
Entering edit mode
Ashton ▴ 10
@6c1df597
Last seen 8 months ago
United States

Been failing to retrieve certain packages from bioconductor 3.15

instance 1

Retrieving 'https://cran.rstudio.com/src/contrib/Archive/GEOquery/GEOquery_2.64.2.tar.gz' ...
Warning: failed to find source for 'GEOquery 2.64.2' in package repositories
Warning: failed to retrieve 'https://cran.rstudio.com/src/contrib/Archive/GEOquery/GEOquery_2.64.2.tar.gz' [error code 22]
Error: failed to retrieve package 'GEOquery@2.64.2'
In addition: Warning messages:
1: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib' 
2: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib' 
3: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib' 
4: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/bioc/src/contrib' 
5: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/workflows/src/contrib' 
6: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib' 
7: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/bioc/src/contrib' 
8: curl: (22) The requested URL returned error: 404  
Traceback (most recent calls last):
9: renv::restore(clean = TRUE)
8: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
7: retrieve(packages)
6: handler(package, renv_retrieve_impl(package))
5: renv_retrieve_impl(package)
4: renv_retrieve_bioconductor(record)
3: renv_retrieve_repos(record)
2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
1: stop(sprintf(fmt, ...), call. = call.)
Execution halted

instance 2

Retrieving 'https://cran.rstudio.com/src/contrib/Archive/BiocManager/BiocManager_1.30.18.tar.gz' ...
    OK [downloaded 282.8 Kb in 0.1 secs]
Retrieving 'https://cran.rstudio.com/src/contrib/Archive/MASS/MASS_7.3-58.tar.gz' ...
    OK [downloaded 492 Kb in 0.2 secs]
Retrieving 'https://cran.rstudio.com/src/contrib/Archive/nlme/nlme_3.1-158.tar.gz' ...
    OK [downloaded 825.6 Kb in 0.3 secs]
* Querying repositories for available source packages ... Done!
Retrieving 'https://cran.rstudio.com/src/contrib/Archive/AnnotationDbi/AnnotationDbi_1.58.0.tar.gz' ...
Warning: failed to find source for 'AnnotationDbi 1.58.0' in package repositories
Warning: failed to retrieve 'https://cran.rstudio.com/src/contrib/Archive/AnnotationDbi/AnnotationDbi_1.58.0.tar.gz' [error code 22]
Error: failed to retrieve package 'AnnotationDbi@1.58.0'
In addition: Warning messages:
1: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib' 
2: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib' 
3: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib' 
4: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/bioc/src/contrib' 
5: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/workflows/src/contrib' 
6: could not retrieve available packages for url 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib' 
7: could not retrieve available packages for url 'https://bioconductor.org/packages/3.15/bioc/src/contrib' 
8: curl: (22) The requested URL returned error: 404 
Traceback (most recent calls last):
9: renv::restore(clean = TRUE)
8: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
7: retrieve(packages)
6: handler(package, renv_retrieve_impl(package))
5: renv_retrieve_impl(package)
4: renv_retrieve_bioconductor(record)
3: renv_retrieve_repos(record)
2: stopf("failed to retrieve package '%s'", renv_record_format_remote(record))
1: stop(sprintf(fmt, ...), call. = call.)
Execution halted
Bioconductor biocondu • 651 views
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0
Entering edit mode
ATpoint ★ 4.0k
@atpoint-13662
Last seen 21 hours ago
Germany

It's a known issue -- I guess Bioc core team is working on it -- can't open mghp.osn.xsede.org

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0
Entering edit mode
@james-w-macdonald-5106
Last seen 15 hours ago
United States

In addition to what ATpoint said, this issue only affects archived versions of Bioconductor, which we do not support, and which you should not be using unless absolutely necessary. R-4.3.0 and Bioconductor 3.17 are unaffected.

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