Diagnosing failed R package installations

When the preflight check did not happen

Sometimes preflight checks do not happen. A user runs install.packages(), a package compiles from source, and the installation fails. The useful next step is to turn the error into a small list of likely system packages, not to ask the user to read a long compiler log alone.

sysreqr has two diagnosis paths:

Direct log patterns, for common missing headers, linker errors, and pkg-config failures.
Failed R package lookup, where the failed R package names are matched against the bundled or optional live system requirement database.

Both paths return a regular sysreqr_plan, so the output can be passed to the same command, report, script, Dockerfile, GitHub Actions, and administrator helpers used for preflight checks.

Check the last error

After a failed install in the current R session:

install.packages("xml2")
check_error(platform = "ubuntu-22.04")

check_error() reads geterrmessage() by default. You can also pass text explicitly:

check_error(
  text = "ERROR: configuration failed for package 'xml2'",
  platform = "ubuntu-22.04",
  backend = "bundled"
)
#> System requirement preflight
#> 
#> Platform: Ubuntu 22.04
#> Package manager: apt
#> Backend: diagnose-log
#> 
#> R packages checked:
#>   xml2
#> 
#> System packages to install: 
#>   libxml2-dev  needed by: xml2  status: unknown
#> 
#> Run:
#>   sudo apt-get update
#>   sudo apt-get install -y libxml2-dev

Diagnose a log file

Use diagnose_log() for an install log on disk:

plan <- diagnose_log("install.log", platform = "ubuntu-22.04")

Use the text argument when the log text is already in R:

diagnose_log(
  text = "fatal error: libxml/parser.h: No such file or directory",
  platform = "ubuntu-22.04"
)
#> System requirement preflight
#> 
#> Platform: Ubuntu 22.04
#> Package manager: apt
#> Backend: diagnose-log
#> 
#> System packages to install: 
#>   libxml2-dev  needed by:   status: unknown
#> 
#> Run:
#>   sudo apt-get update
#>   sudo apt-get install -y libxml2-dev

diagnose_install_log() is an alias for diagnose_log().

Start from failed package names

If the user already knows which R packages failed, skip log parsing:

diagnose_failed_packages(
  c("xml2", "curl"),
  platform = "ubuntu-22.04",
  backend = "bundled"
)
#> System requirement preflight
#> 
#> Platform: Ubuntu 22.04
#> Package manager: apt
#> Backend: failed-package-lookup
#> 
#> R packages checked:
#>   curl, xml2
#> 
#> System packages to install: 
#>   libcurl4-openssl-dev  needed by: curl  status: unknown
#>   libssl-dev  needed by: curl  status: unknown
#>   libxml2-dev  needed by: xml2  status: unknown
#> 
#> Run:
#>   sudo apt-get update
#>   sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev

This is useful when the log only says that an R package had non-zero exit status. It is a medium-confidence result, because package installation can fail for reasons unrelated to system libraries.

Turn diagnosis into action

Diagnosis returns a sysreqr_plan. Use the same helpers as in the preflight workflow:

plan <- diagnose_log("install.log", platform = "ubuntu-22.04")
install_command(plan)
write_install_script(plan, "install-sysreqs.sh")
admin_request(plan)
write_report(plan, "SYSREQS.md")

For automation:

dockerfile(plan)
github_actions(plan)
write_json(plan, "sysreqs.json")

For explanation:

explain(plan)
as_data_frame(plan)

Check a whole project

When one package fails, dependencies nearby in the project may fail next. check_project() scans a project before the next installation attempt. It reads renv.lock, then DESCRIPTION, then source files.

project_plan <- check_project(".")

Include Suggests when preparing a development or testing environment:

project_plan <- check_project(".", include_suggests = TRUE)

To inspect only package detection:

detect_project_packages(".")
detect_project_packages(".", include_suggests = TRUE)

Check an installed library

check_library() checks installed packages in an R library. This is useful when a machine already has many packages installed and you want to see whether their common external requirements are present.

check_library()
check_library(c("xml2", "curl"))

Interpret confidence

sysreqr uses conservative confidence labels:

high: a direct missing-header or linker pattern, or structured upstream requirement data.
medium: a likely tool failure, or a failed package lookup against the bundled fallback.
low: reserved for future broader heuristics.

A medium-confidence result is still useful, but it is not proof that a missing system library caused the failure. R version mismatches, network problems, locked libraries, compiler bugs, unsupported package versions, and permission problems can all produce failed installs that are outside the system requirement database.

When setup advice is the better answer

If repeated installs fail, run setup_advice() instead of chasing one error at a time:

setup_advice(
  packages = c("xml2", "curl"),
  platform = "ubuntu-22.04",
  script = "setup-sysreqr.sh"
)

That gives the user a broader checklist: binary R packages, source build tools, optional R Project operating system repositories, and package-specific system requirements.