updatePackages had 2 minor bugs that prevented some mixtures of necessary updates from being correctly identified.offlineMode, gained improved functionality; though it is still experimental. It can be set using options(Require.offlineMode = TRUE), but it will be automatically set if internet is not available, has now been widely tested. If packages are available in the local caches, and all elements of package versioning (e.g., available.packages() and github packages) have been previously run, then installations should occur as if the internet were available.sys package. This allows for more control over messaging during installations, and it also allows of installation of many packages that are already loaded (with a message that the session will need restarting). This can be turned off with This is turned on with option(Require.installPackagesSys = FALSE).pkgDep have been changed. The new algorithms are faster and more reliable, with far fewer lines of code.testit to using testthat. This change adds many dependencies to Suggests, but the benefits, e.g., using withr to control loading and unloading of options, packages etc., outweigh the drawbacks.packages argument for Require and Install can now be unquoted names length == 1 or if length > 1 using c() or list(), in addition to a character string, e.g., Install(ggplot2);GitHub.com package has a field Additional_repositories in the DESCRIPTION file, Require will search there for packages that it does not find in the repos argument. This does not affect CRAN packages, as this information is not contained within the available.packages() data base, which is what is used to identify dependencies, rather than reading each DESCRIPTION file individually;verbose now propagates better through all internal functions, so e.g., verbose = -2 will make installing very silent;pak as the backend installer of packages instead of install.packages. A user can attempt to use this backend with options(Require.usePak = TRUE). There are a number of cases (specifically when needing exact versions) that do not work; but for "normal" package installations it is widely tested. pak backend tends to be similar speed for first installations, but much slower for subsequent calls to Install/Require;Require.Rmd vignette for "Getting Started" is new;GitHub.com are done, Require now uses gitcreds to get git credentials and httr to download the files with the token;cache now start with cache, e.g., cacheClearPackages replaces clearRequirePackageCache. Previous names are kept for backwards compatibility.Require would incorrectly think it had successfully installed (#87);repos or getOption('repos'). The result was unaffected by the warning, but warning is now removed;pkgSnapshot() (#93);tests that previously would have hit errors;setupOff and setLibPaths enhanced to be fully functioning in a wide diversity of cases.install = "force" in Require, now only the user-specified packages are forced to be installed; the rest are installed if required, mimicking install.packages(HEAD) is now more robust as a way to keep a package up to date..downloadFileMasterMainAuth, messageVerbose, messageDF as they were deemed useful enough for other packages.available.packagesCached() object. Now, catches this condition and refreshes available.packages()install.packages, i.e., first one first.Install did not have an install argument; this has now been introduced, allowing the (most likely) use case of Install(pkg, install = "force")Install more often than Require(..., require = FALSE) for simplicity..libPaths() were treated incorrectly; they are now all respected.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.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.(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.message calls now messageVerbose, so verbosity can be fully controlled with the argument verbose or options("Require.verbose"). See ?RequireOptions.options(Require.cachePkgDir = FALSE) (or environment variable "R_REQUIRE_PKGCACHE"), then no cache folder will be created; previously a nearly empty folder was created by default. See ?RequireOptionsRequire.persistentPkgEnv as it was deemed superfluous.Install, which is Require(..., require = FALSE)(HEAD) has now been tested for CRAN repositories and works as expected.crancache if the user sets options(Require.useCranCache = TRUE). This is experimental and is still being tested.clearRequirePackageCache, for clearing the package cache.available.packages, pkgDep, GitHubSHA) will be refreshed (purged) every 1 hour.MRAN package installs explicitly (instead of just "Archive")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.defaultCacheDir, which would default to runneradmin under some conditions and did not allow installing packages due to permissions.setup and setupOff are now deprecated; messaging is supplied for what to do if these were being usedpkgSnapshot examples brought up to present usage & simplifiedpkgSnapshot 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.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.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.verbose argument is now widespread, with -1, 0, 1, 2 all valid and correctly inherited values. See argument description in e.g., ?RequireThe 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:
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.
normPath().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.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)install.packages --> much fasterinstallGithubPackage instead of remotes::install_githubinstall.packages directlyremotesRequire 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.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 Suggestsrepos argument to Require. It was not correctly using. Thanks to @CeresBarros for identifying issue #30repos 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 repositoryoldrel) and newer are supported.setup: new function for creating a new project. See readme.mdsetLibPath 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 startparallelRequire 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.master or main branches to be installed from GitHub, without needing to specify (#26)setup()checkPath error creating Specified path xxxx doesn't exist even though it does.modifyList2, a generalization of utils::modifyList for >2 lists. Also, can handle NULL lists.detachAll now unloads reverse depends of the depends, if they are loadedpackageVersion.txt fileLibPaths from packageVersion.txt file, if the second (or more) LibPath is full of base packages.install.packages (argument "av2" is missing, with no default) on R-devel for Windows (on Sept 09, 2020). May be transient.source on Windows. Fixed.pkgSnapshot, meaning that a new system can be built with exact versions and SHAs of GitHub packages.options("Require.cachePkgDir" = "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").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.detachAll that attempts to detach and unload packages and all their dependencies, in reverse topological order.pkgDep and pkgDepTopoSortpkgDepAlt 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.Error: invalid version specification ' 3.3-13'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.chooseCRANmirror(ind = 1)repos instead of specifying CRAN repo.reproducible to Require, including pkgDep, pkgDepTopoSort.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.base::available.packages for old Mac machines and R versionsinstalled.packages from test code, as per CRAN requestRequire (and helpers) which will be removed from package reproducibleRequire is run, the result will be the same