sysreqs_check_installed() ignores packages

[JosiahParry]

I am trying to use pkgdepends to check which system requirements are not installed for the packages listed in my renv.lock file on ubuntu 24.

It looks like it does not complete checking for all of the packages because they are not installed. Which is somewhat confusing to me—particularly because I want to check the system dependencies so that I can install them before trying to install the packages probably with the results of pak::pkg_sysreqs(deps, sysreqs_platform = "ubuntu-24") for the install scripts.

Is there a way to get pkgdepends to report the sysreq status for all of the packages input? Or is there a better approach to doing this in general

deps <- c("DBI", "KernSmooth", "MASS", "Matrix", "R6", "RColorBrewer",
"Rcpp", "askpass", "backports", "base64enc", "bit", "bit64",
"blob", "broom", "bslib", "cachem", "callr", "cellranger", "class",
"classInt", "cli", "clipr", "commonmark", "conflicted", "crayon",
"crosstalk", "curl", "data.table", "dbplyr", "digest", "dplyr",
"dtplyr", "e1071", "evaluate", "fansi", "farver", "fastmap",
"fontawesome", "forcats", "fs", "gargle", "generics", "ggplot2",
"glue", "googledrive", "googlesheets4", "gtable", "haven", "highr",
"hms", "htmltools", "htmlwidgets", "httpuv", "httr", "ids", "isoband",
"jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice",
"lazyeval", "leaflet", "leaflet.providers", "lifecycle", "lubridate",
"magrittr", "memoise", "mgcv", "mime", "modelr", "nlme", "openssl",
"pillar", "pkgconfig", "png", "processx", "promises", "proxy",
"ps", "purrr", "ragg", "rappdirs", "raster", "readr", "readxl",
"rematch", "rematch2", "renv", "reprex", "rlang", "rmarkdown",
"rstudioapi", "rvest", "s2", "sass", "scales", "selectr", "sf",
"shiny", "sourcetools", "sp", "stringi", "stringr", "sys", "systemfonts",
"terra", "textshaping", "tibble", "tidyr", "tidyselect", "tidyverse",
"timechange", "tinytex", "tzdb", "units", "utf8", "uuid", "vctrs",
"viridisLite", "vroom", "withr", "wk", "xfun", "xml2", "xtable",
"yaml")

pkgdepends::sysreqs_check_installed(deps)
#> system package       installed required by
#> --------------       --        -----------
#> libcurl4-openssl-dev ✔         curl
#> libpng-dev           ✔         png
#> libssl-dev           ✔         curl
#> libx11-dev           ✖         clipr
#> Warning message:
#> In async_parse_installed(library = library, packages = packages) :
#>   Ignored 99 packages that are not installed: DBI, KernSmooth, MASS, Matrix, RColorBrewer, Rcpp,
#> askpass, backports, base64enc, blob, broom, bslib, cachem, cellranger, class, classInt, commonmark,
#> conflicted, …, xtable, and yaml.

[gaborcsardi]

Well, it checks the installed packages, not the ones you want to install. If you want to see what's missing for an installation proposal, run this:

prop <- pkgdepends::new_pkg_installation_proposal(deps, config = list(library = tempfile()))
prop$solve()
prop$show_solution()

The raw data is in there:

prop$get_solution()$data$sysreqs_packages

Alternatively, use pak::pkg_sysreqs(), that's the main user facing function for this. Unfortunately it does not mark whether a package is installed or not, it could certainly do that. For now some extra work is needed from pkgdepends:

srq <- pak::pkg_sysreqs(deps)
srq$packages$system_packages
inst <- pkgdepends:::synchronize(pkgdepends:::async_system_list_packages())[]$package

[JosiahParry]

Thanks @gaborcsardi the below does a good enough job for me!

I think having a table similar to the one from sysreqs_check_installed() would be very nice!

srq <- pak::pkg_sysreqs(deps)

# required system requirements
required <- unique(unlist(srq$packages$system_packages))

# fetch the current system packages
cur_sysdeps <- pkgdepends:::synchronize(
    pkgdepends:::async_system_list_packages()
)

# check if any are missing
has_idx <- required %in% inst

# report an error otherwise
if (length(has_idx) > 0) {
    missing <- required[!has_idx]
    cli::cli_abort("Missing system requirements: {.pkg {missing}}")
}

Out of curiosity would you be able to explain why sysreqs_check_installed() checks system reqs for only installed packages? my understanding is that in most cases packages won't be able to be installed without the system requirements.

[gaborcsardi]

Out of curiosity would you be able to explain why sysreqs_check_installed() checks system reqs for only installed packages? my understanding is that in most cases packages won't be able to be installed without the system requirements.

That's the installed in the name, it is specifically for R packages that are already installed. You can install binary packages without the system requirements.

For installation, pak::pkg_install() etc. already print out the needed system packages and whether they are installed.

pkg_sysreqs() calculates the system packages without installing anything, and as I said above, it could also include whether they are already installed. It currently does not do that, because it is possible to run it non-natively.

[JosiahParry]

Thanks for the explanation! Much appreciated. This makes a lot of sense particularly when accounting for binary packages.