pak seems to ignore pkg.include_linkingto option

[alexmic95]

I tried to install the anytime R package using pak with LinkingTo dependencies explicitly enabled:

options(pkg.include_linkingto = TRUE)
pak::pkg_install(
  "anytime",
  upgrade = TRUE,
  dependencies = TRUE
)

According to the package DESCRIPTION, BH is listed under the LinkingTo field (see screenshot below). My expectation was that, with pkg.include_linkingto = TRUE, the BH package would be installed as part of the dependency resolution.

However, after the installation completes, BH is not present:

find.package("BH")
Error in find.package("BH") : there is no package called ‘BH’

* pak version:
- 0.9.5
* Version information:
- pak platform: x86_64-pc-linux-gnu (current: x86_64-pc-linux-gnu, compatible)
- pak repository: - (local install?)
* Optional packages installed:
- pillar
* Library path:
- /nfs-data/rhome/qeq/R/x86_64-pc-linux-gnu-library/4.5
- /opt/R/4.5.2/lib/R/library
* pak is installed at /nfs-data/rhome/qeq/R/x86_64-pc-linux-gnu-library/4.5/pak.
* Dependency versions:
- callr      3.7.6     
- cli        3.6.6     
- curl       5.2.3     
- desc       1.4.3     
- filelock   1.0.3     
- jsonlite   2.0.0     
- keyring    1.4.1     
- lpSolve    5.6.23    
- pkgbuild   1.4.8     
- pkgcache   2.2.5.9000
- pkgdepends 0.9.1.9000
- pkgsearch  3.1.5     
- processx   3.8.7     
- ps         1.9.2     
- R6         2.5.1     
- yaml       2.3.12    
- zip        2.3.3     
* Dependencies can be loaded

[gaborcsardi]

Seems like a bug:

> options(pkg.include_linkingto = TRUE)
> pak::pkg_install("anytime", lib = "/tmp/anylib")

→ Will install 3 packages.
→ Will download 3 packages with unknown size.
+ anytime   0.3.13    🔧 ⬇
+ BH        1.90.0-1   ⬇
+ Rcpp      1.1.1-1.1 🔧 ⬇
ℹ Getting 3 pkgs with unknown sizes
✔ Got anytime 0.3.13 (aarch64-apple-darwin23) (1.14 MB)
✔ Got Rcpp 1.1.1-1.1 (aarch64-apple-darwin23) (3.56 MB)
✔ Got BH 1.90.0-1 (aarch64-apple-darwin23) (13.88 MB)
✔ Downloaded 3 packages (18.58 MB) in 13s
✔ Installed anytime 0.3.13  (34ms)
✔ Installed Rcpp 1.1.1-1.1  (146ms)
✔ Installed BH 1.90.0-1  (1.8s)
✔ 1 pkg + 2 deps: added 3, dld 3 (18.58 MB) [15.1s]

So far so good. But then:

> pak::pkg_remove("BH", lib = "/tmp/anylib/")
> pak::pkg_install("anytime", lib = "/tmp/anylib")

ℹ No downloads are needed
✔ 1 pkg + 1 dep: kept 2 [225ms]