NEWS.md

In Require: Installing and Loading R Packages for Reproducible Workflows

Known issues: https://github.com/PredictiveEcology/Require/issues

version 0.3.1

enhancements

• minor modifications for when internet is not available
• Issue 81: deal with more edge cases for package snapshots that are not internally consistent, i.e., violate package versions, or skip missing branches on GitHub, if not needed.

bugfixes

• updates to tests that have begun to fail

version 0.3.0

enhancements

• Moved from MRAN archives for binaries to posit.packagemanager.co
• because of the move from MRAN to posit package manager, attempts are made to use archived binary packages for Linux also.
• improved messaging in several places
• improved error catching in several places
• a number of cases that were annoying for users were identified and addressed.
• setupOff and setLibPaths enhanced to be fully functioning in a wide diversity of cases.
• When setting install = "force" in Require, now only the user-specified packages are forced to be installed; the rest are installed if required, mimicking install.packages
• small efficiency gains in many places
• (HEAD) is now more robust as a way to keep a package up to date.

advanced changes

• several functions now exported, .downloadFileMasterMainAuth, messageVerbose, messageDF as they were deemed useful enough for other packages.

bugfixes

• slow assessment of package dependencies on CRAN packages because of stale available.packagesCached() object. Now, catches this condition and refreshes available.packages()
• corrected support for multiple repos that each offer the same packages. Now works like install.packages, i.e., first one first.
• base packages can now be installed as previous issues about installing them were dealt with.

version 0.2.6

enhancements

• attempts to deal with more cases of failed installations
• Install did not have an install argument; this has now been introduced, allowing the (most likely) use case of Install(pkg, install = "force")
• examples now use Install more often than Require(..., require = FALSE) for simplicity.

improved messaging

• If non-interactive and no CRAN mirror is set, user gets more informative error.

bugfixes

• Cases of multiple user-specified .libPaths() were treated incorrectly; they are now all respected.
• when git repo was not installed because it was identical to the SHA already installed, it would not be loaded, thinking it failed to install; fixed
• can now deal with case when repos has multiple, non-binary CRAN-like repositories, when there is also at least one binary repository supplied e.g., the rstudio package manager, i.e., there are at least 3 repositories supplied, 1 of which is binary.
• other minor

version 0.2.5

enhancements

• several modifications to enable CRAN-policy violations all addressed, notably keeping all temporary and (package and personal) cache directories clean after examples and tests
• This is a major overhaul of the inner workings of Require. It now downloads and builds Archive and GitHub packages prior to installation, then installs all packages (CRAN, Archive, GitHub, MRAN on Windows) with one install.packages call (Linux-alikes) or up to two install.packages calls (binary and source), allowing efficient parallel installs. This results in very fast installs for all combinations of packages. new options("Require.offlineMode") can be set to FALSE to stop Require and pkgDep from checking the internet. This will fail, unless the cached packages are available locally (i.e., it was run once with all packages installed previously). If they are, then they will be installed without needing the internet. This option will also be set automatically on the first attempt to get a file from the internet, which fails, triggering a test of the internet. If that fails, then the option will be set to FALSE until next call to Require or pkgDep when it will be reset. This is experimental still.
• many more edge cases found and dealt with
• experimental use of (HEAD) to keep a package "up to date" with the HEAD of a GitHub branch. The behaviour still uses version numbering, so will not update based on SHA, but if the HEAD is ahead of the locally installed package and the (HEAD) is specified, then it will update. Specifically, use this instead of a version number, e.g., "PredictiveEcology/Require@development (HEAD)"
• modifyList2 now follows modifyList by adding the keep.null argument.
• setdiffNamed will compare 2 named lists or vectors and keep on those elements that are in the first list (or vector), keeping in mind the name as well as the element.
• package messaging is not sorted alphabetically during installation
• all message calls now messageVerbose, so verbosity can be fully controlled with the argument verbose or options("Require.verbose"). See ?RequireOptions.
• tests clean up more completely after themselves
• if options(Require.RPackageCache = FALSE) (or environment variable "R_REQUIRE_PKGCACHE"), then no cache folder will be created; previously a nearly empty folder was created by default. See ?RequireOptions
• Remove option Require.persistentPkgEnv as it was deemed superfluous.
• numerous enhancements for speed
• new function Install, which is Require(..., require = FALSE)
• (HEAD) has now been tested for CRAN repositories and works as expected.
• Updated README to show new functionality
• will attempt to use local cached packages from crancache if the user sets options(Require.useCranCache = TRUE). This is experimental and is still being tested.
• A new function, clearRequirePackageCache, for clearing the package cache.
• The cache has been developed to be able to be shared across Operating Systems, if there is a shared file system.
• GitHub packages require the SHA to be assessed; now this is Cached to disk as well as RAM, so that it persists even if there is an R restart.
• All non-package cache files (available.packages, pkgDep, GitHubSHA) will be refreshed (purged) every 1 hour.
• Much improved messaging, including identifying MRAN package installs explicitly (instead of just "Archive")

bugfixes

• pkgDep was using local DESCRIPTION file to establish package dependencies for a package, if it was available. When the local package is ahead of CRAN (a developer's case), then this is desirable. But, when the local installed version is behind CRAN (a common user's case), then this is not desirable. pkgDep now uses CRAN's version (using available.packages) as developers can handle this situation on their own.
• several minor
• bugfix for defaultCacheDir, which would default to runneradmin under some conditions and did not allow installing packages due to permissions.

deprecated

• setup and setupOff are now deprecated; messaging is supplied for what to do if these were being used
• several options are deprecated

version 0.1.6

enhancements

• pkgSnapshot examples brought up to present usage & simplified
• pkgSnapshot now uses a default filename that is an option Require.packageVersionFile.
• Require can now accept packageVersionFile = TRUE, meaning use the package version file that is set in the Require.packageVersionFile option.

bugfix

• minor bugfix only detected on submission to CRAN

version 0.1.5

enhancements

• package caching for packages that need sources installs (i.e., identified with sourcePkgs(), which tend to occur when R packages require idiosyncratic system dependencies) cache the binary version and reuse that on the same system with subsequent re-installs.

bugfix

• pkgDep was misidentifying the correct package dependencies. This would manifest when a user had a version of package "A" installed as well as all its dependencies, e.g., "B". When the user updated "A" to a new version that required a new version of "B", it would not correctly identify the new dependency requirement, and not update "B", causing "A" update to fail. This is fixed.

version 0.1.4

• Make corrections for 2 failing architectures on CRAN
• MUCH less verbose during automated testing

enhancement

• verbose argument is now widespread, with -1, 0, 1, 2 all valid and correctly inherited values. See argument description in e.g., ?Require
• improved warning handling

bugfixes

• more edge cases found and dealt with

version 0.1.2

dependencies

• drop support for R 3.6 (R >= 4.0 are supported)

enhancements

• The Require argument, require, can now be a character string, indicating which packages should be attached via require
• Now can use GITHUB_PAT environment variable, if set, when it accesses GitHub.com repositories (files or entire repository)
• Attempt to capture and correct cases where GitHub.com branches are incorrectly labelled master instead of main (or vice versa)
• much quieter messaging by default (can increase with verbose = 1)

• require argument in Require can now be a character vector indicating which packages should be attached, not just installed. Note: by default, all packages that are passed to packages are attached if require = TRUE

• much faster installations:

• When source packages, they are grouped and installed together using the internal parallelism of install.packages (setting Ncpus option to 4)

• when binary, passes vectors to install.packages so much faster.

• all packages are installed in install-safe groups for speed

• can use pak package under the hood when options("Require.usepak" = TRUE), though there are still many cases that pak cannot deal with. Users should try and determine if this option delivers as expected. pak installs tend to be slightly faster if they work correctly.

• binary package caching is turned in by default in a user-specific standard directory, making repeat installations (on same system, or shared drive systems) much faster.
• MRAN installs for Windows are now much more robust under many conditions.
• archived packages (ie no longer on CRAN) will now be found and installed (latest available version)
• more robust dependency identification even for archived or older packages or package versions (including their dependencies)
• MRAN binaries will be used in MacOSX.
• improved installation of older packages (e.g. when dependencies are removed from CRAN, or source versions can't be easily compiled)
• several other minor improvements in package dependency resolution and installation.

bugfixes

• fix issue with 'dot directories' in normPath().
• identified possible bug with install.packages when options(Ncpus = XX) where XX is a number > 1. Some packages are skipped. Require now captures this and attempts to install the ones that did not get correctly installed.
• multiple fixes for certain edge cases.

version 0.1.1

enhancements

• can now use pak if options("Require.usepak" = TRUE) and there are no version specifications (i.e., if a user specifies e.g., Require("reproducible (<= 1.2.9)), then the non-pak approach will be used)

bugfixes

• fixed an error installing certain GitHub packages

version 0.1.0

enhancements

• install CRAN packages using vectorized install.packages --> much faster
• now uses internal installGithubPackage instead of remotes::install_github
• this previous means that all installations use install.packages directly
• remove dependency on remotes

bugfixes

• Require would silently fail to install a GitHub package if there was a warning during the installation. These warnings are now correctly captured, without stopping the installation.
• bugfix where a package being installed from GitHub directly had a Remotes field for a package that was in Suggests (in its DESCRIPTION file). It would install this Remotes package even though it was only in Suggests
• bugfix when user supplies a non-CRAN repos argument to Require. It was not correctly using. Thanks to @CeresBarros for identifying issue #30
• bugfix "All packages appear to have installed correctly" was misreporting under some cases.
• repos argument not correctly passed into doInstalls from Require. This meant that installs would not respect a user supplied repos, but would use the options("repos") instead.
• extractPkgNames now allows GitHub packages that have the repository omitted, i.e., they only have @. This is useful if there is a default expectation for a github repository
• better handling of GitHub package install issues

version 0.0.13

• fix CRAN policy violation -- dealt with extraneous folder created during testing

version 0.0.12

Dependency changes

• with the release of R 4.1, we dropped support for R 3.5. R 3.6 (oldrel) and newer are supported.

New features

• setup: new function for creating a new project. See readme.md
• setLibPath and package caching (via options("RPackageCache")) now automatically create and use a subfolder of user-provided path with the R major & minor version number (as with normal R behaviour) to allow multiple R versions to coexist on the same machine.
• setLibPaths gains a new argument, updateRprofile, which allows a user's changes to .libPaths() to persist through an R restart. Set to getOption("Require.updateRprofile", FALSE), at start

Bug fixes

• several edge cases with complex loading of many packages
• was incorrectly (not) loading base packages, e.g., parallel
• small minor bugfixes
• In cases where a DESCRIPTION file had both a package with a minimum version (e.g., in Imports) and a REMOTES: for that package (without a minimum version, but with a branch, say), Require would use the REMOTES: entry. But since that means there is no minimum package version, and Require does not automatically install a package that is not violating a minimum version number, it would not install anything. Now, it harmonizes the 2 entries for a given package, and uses both the minimum version number and the git branch as the potential source to find that version number.
• allow either master or main branches to be installed from GitHub, without needing to specify (#26)
• fix use of options in setup()

version 0.0.10

Bug fixes

• CRAN error on one flavour of Linux
• erroneous checkPath error creating Specified path xxxx doesn't exist even though it does.

version 0.0.9

New features

• modifyList2, a generalization of utils::modifyList for >2 lists. Also, can handle NULL lists.
• slight improvements in speed for some internal functions
• detachAll now unloads reverse depends of the depends, if they are loaded

Bug fixes

• deals with more cases of installing arbitrary packages from a packageVersion.txt file
• Does not mistakenly create a new, empty directory of packages to accommodate 2 LibPaths from packageVersion.txt file, if the second (or more) LibPath is full of base packages.
• Handles better false positives (packages did not install properly when they did) and some false negatives (no error collected at end when there was an error in installing)
• better suggestion of what to do in some edge cases of failed package installs
• captures and deals with a bug in install.packages (argument "av2" is missing, with no default) on R-devel for Windows (on Sept 09, 2020). May be transient.
• Was, by default, installing from source on Windows. Fixed.

version 0.0.8

New features

• GitHub SHA is now stored during pkgSnapshot, meaning that a new system can be built with exact versions and SHAs of GitHub packages.
• For GitHub packages, now uses both DESCRIPTION and NAMESPACE files to determine dependencies. GitHub packages are generally for packages in some state of development. This may include missing declarations in DESCRIPTION. NAMESPACE is what R uses to actually determine package dependencies upon installation.
• Now keeps the binary/source package locally if options("Require.RPackageCache" = "someLocalDir") is set to a local folder. Currently defaults to NULL, meaning no local cache.
• Require and pkgSnapshot can now understand and work with GitHub SHAs and thus packages installed from GitHub, e.g., Require("PredictiveEcology/Require@development") will install the development version. When using pkgSnapshot, the exact SHA will be used to restore that package at the exact version with Require(packageVersionFile = "packageVersions.txt").
• If a package is already loaded prior to changing running setLibPaths, it is possible to create a version conflict. base::require will error if the version in the .libPaths() is older than the version whose namespace is already loaded. To accommodate this, there is a check for this error, and if the newer version (that is already loaded) does not violate the Require('package (versionSpecification)'), then it will install the newer version. If it does violate the version specification, it will error cleanly with a message describing the possible solutions.
• Much better messaging and reporting
• New function: detachAll that attempts to detach and unload packages and all their dependencies, in reverse topological order.
• Speed improvements, especially with pkgDep and pkgDepTopoSort
• New function pkgDepAlt which is an alternative to pkgDep, yet easier to maintain and still experimental. It is not yet the workhorse inside Require, but it may become that.
• Now correctly removes spaces and tab characters within a package version description -- this was creating an error such as Error: invalid version specification ' 3.3-13'

Bug fixes

• pkgDepTopoSort now appears to be correct for all types of package descriptions currently allowed by Require, namely, packages with no version specification, packages with version specification (including older versions), and GitHub packages.
• many minor edge cases

version 0.0.7

New features

• no longer sets CRAN repository to cloud.r-project.org even if non-interactive with no CRAN repository set. Now uses chooseCRANmirror(ind = 1)

Bug fixes

• fixes CRAN check issues on Fedora.

version 0.0.6

New features

• none

Bug fixes

• fixed CRAN check issues.
• default repo now uses option repos instead of specifying CRAN repo.

version 0.0.5

New features

• moved several functions that have to do with package loading and installing from reproducible to Require, including pkgDep, pkgDepTopoSort.

Bug fixes

• recursive pkgDep did not correctly resolve multiple instances of the same package, each with different minimum version numbering. Now it reports minimum version required for all package dependencies.
• minor changes in non-exported functions
• handling of bugs in base::available.packages for old Mac machines and R versions

version 0.0.4

Bug fixes

• remove installed.packages from test code, as per CRAN request

version 0.0.3

• Change title to Title Case in DESCRIPTION

version 0.0.2

• Change backticks to single quotes in DESCRIPTION

version 0.0.1

New features

• This is a rewrite of the function, Require (and helpers) which will be removed from package reproducible
• This function is intended to be a tool for package management used within a "reproducible" workflow
• It differs from all other attempts at achieving this goal by having the trait that the first and subsequent times the function Require is run, the result will be the same

Require documentation built on May 31, 2023, 7:06 p.m.