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

[Lluís Revilla]

Hi Matej,

Usually when I find this kind of message it indicates that the package
is installed in different libraries and you are updating in just one
library.

Have you checked that it is installed in multiple libraries? I usually
use something similar to this to identify those packages:

ip1 <- installed.packages(lib = .libPaths()[1])
ip2 <- installed.packages(lib = .libPaths()[2])
union(rownames(ip1), rownames(ip2))

I hope this helps.

Best,

Lluís

On Sat, 12 Nov 2022 at 17:37, Matej Lexa <lexa using fi.muni.cz> wrote:
>
> 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
> 'https://cloud.r-project.org/src/contrib/VennDiagram_1.7.3.tar.gz'
> 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
> path
> * DONE (VennDiagram)
>
> The downloaded source packages are in
>      ‘/tmp/RtmpaW1s0x/downloaded_packages’
> Old packages: 'VennDiagram'
> Update all/some/none? [a/s/n]: a
>
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