Question

Avoid upgrading BiocManager to 1.30.13; fix proposed

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Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 6 weeks ago

United States

A problem has been observed with the version of BiocManager currently available at CRAN. Do not upgrade to 1.30.13.

If you have already done so, please use

remotes::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo")

and restart R; this will provide BiocManager 1.30.13.1

If you run into problems with this please let me know.

BiocManager • 7.2k views

ADD COMMENT • link updated 3.2 years ago by Mengfei • 0 • written 3.5 years ago by Vincent J. Carey, Jr. 6.7k

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Thank you. It worked.

ADD REPLY • link 3.5 years ago san0016 • 0

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Important fix to consider for GitHub Actions - the above solution fixed failing jobs. Example

ADD REPLY • link 3.5 years ago Mikhail Dozmorov ▴ 30

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This new version did not help me download org.Hs.eg.db by calling BiocManager::install("org.Hs.eg.db"). it reports: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.12") The new version helped me downloaded pathview which had the same problem as this one. Anything I can do?

ADD REPLY • link 3.5 years ago lareinawjn • 0

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Please provide more information. Remember you have to restart R to take advantage of the updated BiocManager. Please give the full transcription of what happens as you run BiocManager::install('org.Hs.eg.db')

ADD REPLY • link 3.5 years ago Vincent J. Carey, Jr. 6.7k

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sorry, I copied the wrong thing. This is the report:

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

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

Bioconductor version 3.12 (BiocManager 1.30.13.1), R 4.0.5 (2021-03-31)

and this:

Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'org.Hs.eg.db'

I kept changing CRAN Mirror but it did not work. I did restart and I had download pathview successfully after I restarted it yesterday. I'm using a Macbook Pro with OS 10.13.6. I tried BiocManager::install("org.Dr.eg.db") is shows the same message but it was downloaded successfully like this:

BiocManager::install("org.Dr.eg.db")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: http://cran.wustl.edu/

Bioconductor version 3.12 (BiocManager 1.30.13.1), R 4.0.5 (2021-03-31)
Installing package(s) 'org.Dr.eg.db'
installing the source package ‘org.Dr.eg.db’

trying URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Dr.eg.db_3.12.0.tar.gz'
Content type 'application/x-gzip' length 32776131 bytes (31.3 MB)
==================================================
downloaded 31.3 MB

* installing *source* package ‘org.Dr.eg.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (org.Dr.eg.db)

The downloaded source packages are in
    ‘/private/var/folders/h6/rmxc4hyn3t108nv5_h3g448h0000gn/T/RtmpnBUCLO/downloaded_packages’

I tried the new version 1.30.13.14, the results were same.

ADD REPLY • link 3.5 years ago lareinawjn • 0

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Hi lareinawjn, I got the same problem (as below), have you found a resolution? Thank you.

BiocManager::install("singscore") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://repo.miserver.it.umich.edu/cran

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.0/library packages: Matrix, mgcv Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'singscore'

ADD REPLY • link 3.2 years ago Mengfei • 0