when installing via renv or pak, it sometimes will try to pull treeio from github.com (not from bioconductor)

[idavydov]

Summary

DESCRIPTION file has the following line:

Remotes:
    GuangchuangYu/treeio

This line forces tools like renv (or pak, I think) to gather the latest treeio from github.com, instead of using the Bioconductor release.

This was probably useful to have before treeio was on bioc; and is probably useful for installing the latest versions from github; but this breaks renv, when it's trying to update packages within a Bioconductor release.

Example

$ cat ggtree.R
library(ggtree)
$ R -q
> renv::init(bioconductor=TRUE)
The following package(s) will be installed:
- BiocManager [1.30.22]
These packages will be installed into "~/myR/tmp_treeio/renv/library/R-4.3/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]:
# Installing packages --------------------------------------------------------
- Installing BiocManager ...                    OK [linked from cache]
Successfully installed 1 package in 8.2 milliseconds.

The following loaded package(s) have been updated:
- BiocManager
Restart your R session to use the new versions.

- Using Bioconductor version '3.17'.
- Linking packages into the project library ... Done!
The following package(s) will be updated in the lockfile:

# Bioconductor ---------------------------------------------------------------
- BiocVersion    [* -> 3.17.1]
- ggtree         [* -> 3.8.2]
- treeio         [* -> 1.24.3]

# CRAN -----------------------------------------------------------------------
- ape            [* -> 5.7-1]
- aplot          [* -> 0.2.0]
- BiocManager    [* -> 1.30.22]
- cachem         [* -> 1.0.8]
- cli            [* -> 3.6.1]
- colorspace     [* -> 2.1-0]
- cpp11          [* -> 0.4.4]
- digest         [* -> 0.6.33]
- dplyr          [* -> 1.1.2]
- fansi          [* -> 1.0.4]
- farver         [* -> 2.1.1]
- fastmap        [* -> 1.1.1]
- generics       [* -> 0.1.3]
- ggfun          [* -> 0.1.2]
- ggplot2        [* -> 3.4.2]
- ggplotify      [* -> 0.1.2]
- glue           [* -> 1.6.2]
- gridGraphics   [* -> 0.5-1]
- gtable         [* -> 0.3.3]
- isoband        [* -> 0.2.7]
- jsonlite       [* -> 1.8.7]
- labeling       [* -> 0.4.2]
- lattice        [* -> 0.21-8]
- lazyeval       [* -> 0.2.2]
- lifecycle      [* -> 1.0.3]
- magrittr       [* -> 2.0.3]
- MASS           [* -> 7.3-60]
- Matrix         [* -> 1.6-0]
- memoise        [* -> 2.0.1]
- mgcv           [* -> 1.9-0]
- munsell        [* -> 0.5.0]
- nlme           [* -> 3.1-163]
- patchwork      [* -> 1.1.3]
- pillar         [* -> 1.9.0]
- pkgconfig      [* -> 2.0.3]
- purrr          [* -> 1.0.1]
- R6             [* -> 2.5.1]
- RColorBrewer   [* -> 1.1-3]
- Rcpp           [* -> 1.0.11]
- renv           [* -> 1.0.2]
- rlang          [* -> 1.1.1]
- scales         [* -> 1.2.1]
- stringi        [* -> 1.7.12]
- stringr        [* -> 1.5.0]
- tibble         [* -> 3.2.1]
- tidyr          [* -> 1.3.0]
- tidyselect     [* -> 1.2.0]
- tidytree       [* -> 0.4.5]
- utf8           [* -> 1.2.3]
- vctrs          [* -> 0.6.3]
- viridisLite    [* -> 0.4.2]
- withr          [* -> 2.5.0]
- yulab.utils    [* -> 0.0.7]

The version of R recorded in the lockfile will be updated:
- R              [* -> 4.3.0]

- Lockfile written to "~/myR/tmp_treeio/renv.lock".
- renv activated -- please restart the R session.
>
Save workspace image? [y/n/c]: n
$ R -q
- Project '~/myR/tmp_treeio' loaded. [renv 1.0.2]
R-4.3.0-foss-> renv::install()
The following package(s) will be installed:
- treeio [GuangchuangYu/treeio@devel]
These packages will be installed into "~/myR/tmp_treeio/renv/library/R-4.3/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: - Operation canceled.

CC @klmr