Known issues: https://github.com/PredictiveEcology/Require/issues
- 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
GitHubpackages prior to installation, then installs all packages (
MRANon Windows) with one
install.packagescall (Linux-alikes) or up to two
install.packagescalls (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
pkgDepfrom 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
FALSEuntil next call to
pkgDepwhen 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.,
modifyListby adding the
setdiffNamedwill 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
messageVerbose, so verbosity can be fully controlled with the argument
- tests clean up more completely after themselves
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
- Remove option
Require.persistentPkgEnvas 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
crancacheif 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 (
GitHubSHA) will be refreshed (purged) every 1 hour.
- Much improved messaging, including identifying
MRANpackage installs explicitly (instead of just "Archive")
pkgDepwas using local
DESCRIPTIONfile 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.
pkgDepnow 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
runneradminunder some conditions and did not allow installing packages due to permissions.
setupOffare now deprecated; messaging is supplied for what to do if these were being used
- several options are deprecated
pkgSnapshotexamples brought up to present usage & simplified
pkgSnapshotnow uses a default filename that is an option
Requirecan now accept
packageVersionFile = TRUE, meaning use the package version file that is set in the
- minor bugfix only detected on submission to CRAN
- 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.
pkgDepwas 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.
- Make corrections for 2 failing architectures on CRAN
- MUCH less verbose during automated testing
verboseargument is now widespread, with -1, 0, 1, 2 all valid and correctly inherited values. See argument description in e.g.,
- improved warning handling
- more edge cases found and dealt with
- drop support for R 3.6 (R >= 4.0 are supported)
require, can now be a character string, indicating which packages should be attached via
Now can use
GITHUB_PATenvironment 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
main(or vice versa)
much quieter messaging by default (can increase with verbose = 1)
Requirecan now be a character vector indicating which packages should be attached, not just installed. Note: by default, all packages that are passed to
packagesare 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.
- fix issue with 'dot directories' in
- identified possible bug with
options(Ncpus = XX)where XX is a number > 1. Some packages are skipped.
Requirenow captures this and attempts to install the ones that did not get correctly installed.
- multiple fixes for certain edge cases.
- can now use
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-
pakapproach will be used)
- fixed an error installing certain GitHub packages
- install CRAN packages using vectorized
install.packages--> much faster
- now uses internal
- this previous means that all installations use
- remove dependency on
Requirewould 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
Remotesfield for a package that was in
Suggests(in its DESCRIPTION file). It would install this
Remotespackage even though it was only in
- bugfix when user supplies a non-CRAN
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.
reposargument not correctly passed into
Require. This meant that installs would not respect a user supplied repos, but would use the
extractPkgNamesnow 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
- fix CRAN policy violation -- dealt with extraneous folder created during testing
- with the release of R 4.1, we dropped support for R 3.5. R 3.6 (
oldrel) and newer are supported.
setup: new function for creating a new project. See
setLibPathand 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.
setLibPathsgains 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
- several edge cases with complex loading of many packages
- was incorrectly (not) loading base packages, e.g.,
- 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),
Requirewould use the REMOTES: entry. But since that means there is no minimum package version, and
Requiredoes 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
mainbranches to be installed from GitHub, without needing to specify (#26)
- fix use of options in
- CRAN error on one flavour of Linux
Specified path xxxx doesn't existeven though it does.
modifyList2, a generalization of
utils::modifyListfor >2 lists. Also, can handle NULL lists.
- slight improvements in speed for some internal functions
detachAllnow unloads reverse depends of the depends, if they are loaded
- deals with more cases of installing arbitrary packages from a
- Does not mistakenly create a new, empty directory of packages to accommodate 2
packageVersion.txtfile, if the second (or more)
LibPathis 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
argument "av2" is missing, with no default) on R-devel for Windows (on Sept 09, 2020). May be transient.
- Was, by default, installing from
sourceon Windows. Fixed.
- 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.
pkgSnapshotcan 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::requirewill 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:
detachAllthat attempts to detach and unload packages and all their dependencies, in reverse topological order.
- Speed improvements, especially with
- New function
pkgDepAltwhich 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'
pkgDepTopoSortnow 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
- no longer sets CRAN repository to cloud.r-project.org even if non-interactive with no CRAN repository set. Now uses
chooseCRANmirror(ind = 1)
- fixes CRAN check issues on Fedora.
- fixed CRAN check issues.
- default repo now uses option
reposinstead of specifying CRAN repo.
- moved several functions that have to do with package loading and installing from
pkgDepdid 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.packagesfor old Mac machines and R versions
installed.packagesfrom test code, as per CRAN request
- Change title to Title Case in DESCRIPTION
- Change backticks to single quotes in DESCRIPTION
- This is a rewrite of the function,
Require(and helpers) which will be removed from package
- 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
Requireis run, the result will be the same