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