object ‘geneInCategory’ is not exported by 'namespace:DOSE' when attempting to install package

[VictQuad]

Hey all, I am trying to install the package using both pak::pak() and devtools::install_github() and both methods provide the same error message. I am currently on R version 4.6.0.

The following are the errors provided by both methods

devtools::install_github("PNNL-Comp-Mass-Spec/MSnSet.utils", build_vignettes = TRUE)

Downloading GitHub repo PNNL-Comp-Mass-Spec/MSnSet.utils@HEAD
Skipping 1 packages ahead of CRAN: MSnbase
Installing 2 packages: msmsEDA, msmsTests
trying URL 'https://bioconductor.org/packages/3.23/bioc/bin/macosx/sonoma-arm64/contrib/4.6/msmsEDA_1.50.0.tgz'
trying URL 'https://bioconductor.org/packages/3.23/bioc/bin/macosx/sonoma-arm64/contrib/4.6/msmsTests_1.50.0.tgz'

The downloaded binary packages are in
/var/folders/ml/9f6kds_92bs11c0qlshlppgr0000gn/T//Rtmp1gTCey/downloaded_packages
── R CMD build ───────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/ml/9f6kds_92bs11c0qlshlppgr0000gn/T/Rtmp1gTCey/remotes7186621d53/PNNL-Comp-Mass-Spec-MSnSet.utils-43e4612/DESCRIPTION’ ...
─ preparing ‘MSnSet.utils’:
✔ checking DESCRIPTION meta-information ...
─ installing the package (it is needed to build vignettes)
-----------------------------------
─ installing source package ‘MSnSet.utils’ ...
** this is package ‘MSnSet.utils’ version ‘0.2.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘geneInCategory’ is not exported by 'namespace:DOSE'
Execution halted
ERROR: lazy loading failed for package ‘MSnSet.utils’
─ removing ‘/private/var/folders/ml/9f6kds_92bs11c0qlshlppgr0000gn/T/RtmpC7zELV/Rinst1688458eeb37/MSnSet.utils’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'MSnSet.utils' from GitHub:
! System command 'R' failed

pak::pak("PNNL-Comp-Mass-Spec/MSnSet.utils")

! error in pak subprocess
Caused by error in stop_task_build(state, worker):
! Failed to build source package MSnSet.utils.
Full installation output:

• installing source package ‘MSnSet.utils’ ...
  ** this is package ‘MSnSet.utils’ version ‘0.2.0’
  staged installation is only possible with locking
  ** using non-staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object ‘geneInCategory’ is not exported by 'namespace:DOSE'
  Execution halted
  ERROR: lazy loading failed for package ‘MSnSet.utils’
• removing ‘/private/var/folders/ml/9f6kds_92bs11c0qlshlppgr0000gn/T/RtmpmnsWeR/pkg-lib142066d09d71/MSnSet.utils’
  Type .Last.error to see the more details.

.Last.error details output

<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in stop_task_build(state, worker):
! Failed to build source package MSnSet.utils.
Full installation output:

• installing source package ‘MSnSet.utils’ ...
  ** this is package ‘MSnSet.utils’ version ‘0.2.0’
  staged installation is only possible with locking
  ** using non-staged installation
  ** R
  ** data
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object ‘geneInCategory’ is not exported by 'namespace:DOSE'
  Execution halted
  ERROR: lazy loading failed for package ‘MSnSet.utils’
• removing ‘/private/var/folders/ml/9f6kds_92bs11c0qlshlppgr0000gn/T/RtmpmnsWeR/pkg-lib1420184f5a5f/MSnSet.utils’

---

Backtrace:

1. pak::pak("PNNL-Comp-Mass-Spec/MSnSet.utils")
2. pak::pkg_install(pkg, ...)
3. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
4. err$throw(res$error)

---

Subprocess backtrace:

1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_do_plan", asNamespace("pak"))(...)
3. proposal$install()
4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
5. base::withCallingHandlers({ …
6. pkgdepends:::handle_events(state, events)
7. pkgdepends:::handle_event(state, i)
8. pkgdepends:::stop_task(state, worker)
9. pkgdepends:::stop_task_build(state, worker)
10. base::throw(pkg_error("Failed to build source package {.pkg {pkg}}.", …
11. | base::signalCondition(cond)
12. global (function (e) …

[VictQuad]

After reverting back to R version 4.5.0, the package is able to be installed as directed on the main page (additionally, pak::pak() works as well). It seems one of the export functions or files needs to be updated for 4.6.0.