[Bioc-devel] BiocManager::install() behavior with available updates

Matej Lexa |ex@ @end|ng |rom ||@mun|@cz
Sat Nov 12 17:36:49 CET 2022

Dear all,

I encountered strange behavior of BiocManager::install(). When I ask it 
to install a package that is flagged as one with available updates, it 
gives me the option to upgrade immediately after I install the latest 
version. Not a big deal but thought it should not offer that 
possibility. See my latest test:


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

replacement repositories:
     CRAN: https://cloud.r-project.org

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Installing package(s) 'VennDiagram'
trying URL 
Content type 'application/x-gzip' length 78508 bytes (76 KB)
downloaded 76 KB

* installing *source* package ‘VennDiagram’ ...
** package ‘VennDiagram’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** 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 
* DONE (VennDiagram)

The downloaded source packages are in
Old packages: 'VennDiagram'
Update all/some/none? [a/s/n]: a

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