Categorygithub.com/insightsengineering/scribe
modulepackage
1.0.8
Repository: https://github.com/insightsengineering/scribe.git
Documentation: pkg.go.dev
Overview
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Dependencies
1
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4 SLOC

# README

scribe

build

scribe (acronym for system compatibility report for install & build evaluation) is a project that creates complete build, check and install reports for a collection of R projects that are defined in an renv.lock file.

renv.lock file can be typically generated by the renv R package, but you may also want to take a look at locksmith which can generate such a file more efficiently.

scribe, based on the input renv.lock:

  • downloads R packages from package repositories or GitHub/GitLab repositories,
  • determines the order in which the packages should be built and installed,
  • builds packages from git repositories, and installs all of the packages (by running R CMD build and R CMD INSTALL respectively),
  • checks the specified subset of packages by running R CMD check,
  • generates an HTML report with the statuses of the above processes.

Report example

The statuses in the report shown above, when clicked, show the logs from the execution of R CMD build, R CMD INSTALL, or R CMD check.

Installing

Simply download the project for your distribution from the releases page. scribe is distributed as a single binary file and does not require any additional system requirements other than R, with which it integrates and interfaces externally.

Usage

scribe is a command line utility, so after installing the binary in your PATH, simply run the following command to view its capabilities:

scribe --help

Example usage with multiple flags:

  • scribe --config custom-config-file.yml --logLevel debug --maskedEnvVars 'password|key|regexForAnEnvVarThatShouldNotBeDisplayed' --renvLockFilename output-renv.lock --reportDir output-report-directory
  • Specifying for which packages R CMD check should be run. 
    scribe --checkPackage 'package*,*abc,a*b,someOtherPackage'
  • Changing the default number of concurrent goroutines for downloading packages, running R CMD check, and running package building and installation. 
    scribe --maxDownloadRoutines 40 --maxCheckRoutines 10 --numberOfWorkers 20
  • Passing additional options to R CMD build, R CMD INSTALL and R CMD check. 
    scribe --buildOptions '--no-manual --no-build-vignettes' --installOptions '--no-docs' --checkOptions '--ignore-vignettes'

To download packages from git repositories, scribe uses Personal Access Tokens defined in environment variables:

  • for GitLab, it reads the token from GITLAB_TOKEN variable,
  • for GitHub, it reads the token from GITHUB_TOKEN variable.

Configuration file

If you'd like to set the above options in a configuration file, by default scribe tries to read ~/.scribe, ~/.scribe.yaml and ~/.scribe.yml files. If any of these files exist, scribe uses options defined there, unless they are overridden by command line flags.

You can also specify a custom path to configuration file with --config <your-configuration-file>.yml command line flag. When using custom configuration file, if you specify command line flags, the latter will still take precedence.

Example contents of configuration file:

logLevel: debug
maskedEnvVars: secret-variable-name|another_variable_name
checkPackage: teal*,tern
renvLockFilename: custom-renv.lock
outputReport: output-report-directory
maxDownloadRoutines: 40
maxCheckRoutines: 10
numberOfWorkers: 20
buildOptions: --no-manual --no-build-vignettes
installOptions: --no-docs
checkOptions: --ignore-vignettes

Environment variables

scribe reads environment variables with SCRIBE_ prefix and tries to match them with CLI flags. For example, setting the following variables will override the respective values from configuration file: SCRIBE_LOGLEVEL, SCRIBE_CHECKPACKAGE, SCRIBE_RENVLOCKFILENAME, SCRIBE_OUTPUTREPORT etc.

The order of precedence is:

CLI flag → environment variable → configuration file → default value.

Package repositories

If scribe should use source packages, then the repository URLs in the renv.lock header should point to the location where the /src/contrib directory is located (without the trailing /), for example:

"R": {
  "Repositories": [
    {
      "Name": "CRAN",
      "URL": "https://packagemanager.posit.co/cran/latest"
    }
  ]
}

For scribe to use binary packages, it expects the renv.lock to contain the repository definitions pointing to the binary repositories.

Examples of expected format of binary repository URLs:

  • Linux:
    • https://packagemanager.posit.co/cran/__linux__/<distribution-name>/latest
  • Windows:
    • https://cloud.r-project.org/bin/windows/contrib/<r-version>
    • https://www.bioconductor.org/packages/release/bioc/bin/windows/contrib/<r-version>
    • https://packagemanager.posit.co/cran/latest/bin/windows/contrib/<r-version>
  • macOS:
    • https://cloud.r-project.org/bin/macosx/contrib/<r-version>
    • https://www.bioconductor.org/packages/release/bioc/bin/macosx/big-sur-arm64/contrib/<r-version>
    • https://www.bioconductor.org/packages/release/bioc/bin/macosx/big-sur-x86_64/contrib/<r-version>
    • https://packagemanager.posit.co/cran/latest/bin/macosx/big-sur-x86_64/contrib/<r-version>
    • https://packagemanager.posit.co/cran/latest/bin/macosx/big-sur-arm64/contrib/<r-version>

where <r-version> is e.g. 4.2, 4.3 etc.

In all cases the URL points to a directory where the PACKAGES file is located, without the trailing /.

Additionally, on Windows it might be required to tell scribe where the R executable is located by using flag: --rExecutablePath 'C:\Program Files\R\R-4.3.2\bin\R.exe'.

Cache

scribe uses cache stored in /tmp/scribe for various purposes.

The results of download, installation, build and check stages are stored in /tmp/scribe/cache. When scribe detects presence of files with such results, it skips respective stages.

In order to run the download, installation, build and check from scratch, the /tmp/scribe/cache directory should be removed manually. Removing whole /tmp/scribe directory is also possible - in that case, the packages will have to be downloaded again because cached tar.gz packages and git repositories are stored in this directory.

The cache can also be cleared with --clearCache flag.

Development

This project is built with the Go programming language.

Development Environment

It is recommended to use Go 1.22+ for developing this project. This project uses a pre-commit configuration and it is recommended to install and use pre-commit when you are developing this project.

Common Commands

Run make help to list all related targets that will aid local development.

Style

This project adopts the Uber styleguide.

License

scribe is licensed under the Apache 2.0 license. See LICENSE.md for details.

# Packages

Copyright 2023 F.