Description
The problem
Under certain conditions, installation of parsnip fails with the following error:
Error installing package 'parsnip':
===================================
* installing *source* package 'parsnip' ...
** package 'parsnip' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'parsnip'
finding HTML links ... done
C5.0_train html
C5_rules html
add_on_exports html
add_rowindex html
augment html
autoplot.model_fit html
bag_mars html
Error: bag_mars.Rd:36: there is no package called 'knitr'
* removing '/opt/R/4.2.1/lib/R/library/.renv/1/parsnip'
Error: install of package 'parsnip' failed [error code 1]
Traceback (most recent calls last):
12: renv::restore()
11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
10: renv_install_impl(records)
9: renv_install_staged(records)
8: renv_install_default(records)
7: handler(package, renv_install_package(record))
6: renv_install_package(record)
5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
vwritef("\tFAILED")
writef(e$output)
})
4: renv_install_package_impl(record)
3: r_cmd_install(package, path)
2: r_exec_error(package, output, "install", status)
1: stop(error)
Execution halted
executor failed running [/bin/sh -c Rscript -e "renv::restore()"]: exit code: 1
The error occurs for me when I install earth then parsnip, but I can only reproduce the error on CentOS 7. The error doesn't occur in Debian. If knitr is installed then the error goes away, of course, but I discovered this issue when using vetiver and renv, both of which have no way to automatically pick up on knitr as a dependency.
I believe the actual cause is as follows:
- install earth, and then attempt to install parsnip from source
- R attempts to convert the
.Rdfiles into help files - The following line is called during this conversion:
\Sexpr[stage=render,results=rd]{parsnip:::make_engine_list("bag_mars")}parsnip:::make_engine_list("bag_mars")picks up on the "earth" engine, and attempts to callknitr::combine_words.- knitr is only a suggested dependency of parsnip. If it's not already installed, R will error here.
Reproducible example
I'm afraid this reprex requires a Dockerfile. I've put up a minimal repository. The renv snapshot is produced by the below line, which is very similar to what vetiver would do:
renv::snapshot(packages = c("earth", "parsnip", "workflows"), prompt = FALSE)
Attempting to build the Docker image will error with the above, although because we're building from source the process may take 20 minutes. The alternative Debian-based Dockerfile doesn't error, and I just can't understand why.
Possible solutions
knitr::combine_words is a very small and self-contained component of knitr. Could this function be copied into parsnip?
I would be happy to contribute a PR, if you think this is a valid issue.