On 15 October 2024 at 13:21, James W. MacDonald wrote:
| Don't you have to load BiocManager before using it?
Correct. The most minimal 'proof' I can offer is that after
docker run --rm -ti rocker/r2u:noble
the one line 'two-command' wrapping both R CMD INSTALL for BiocManager plus
calling BiocManager::install() for ggbreak, ie
time (install.r BiocManager; installBioc.r ggbreak)
finishes in 16 seconds from my machine (on decent connectivity) installing 35
(binary) packages in total on Ubuntu 24.04 ending in
[... stuff omitted ...]
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'BiocVersion', 'ggbreak'
[... two screens full of logs omitted]
Setting up r-cran-ggbreak (0.1.2-1.ca2404.1) ...
real 0m16.012s
user 0m8.481s
sys 0m2.769s
This uses binaries thanks to r2u [1] but you can of course do it 'by hand'
from source too if you ensure you have all your ducks in a row as all
packages are in good standing at CRAN and BioConductor. Doing it
incrementally and carefully perusing your build logs should get you there.
Dirk
[1] More about r2u is at https://eddelbuettel.github.io/r2u/
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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