Avoid upgrading BiocManager to 1.30.13; fix proposed
0
6
Entering edit mode
@vincent-j-carey-jr-4
Last seen 1 day 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 • 1.8k views
ADD COMMENT
0
Entering edit mode

Thank you. It worked.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 251 users visited in the last hour
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