bioc_version() now points to the most recent (2021-10-27) Bioconductor
release, v3.14 (@stufield, #664).git_remote, add regression tests (@achimgaedke, #646).remote_package_name.git2r_remote now passes credentials when looking up the package DESCRIPTION (#633, @rnorberg)remote_package_name.git2r_remote and remote_package_name.xgit_remote, http responses returning an invalid DESCRIPTION or that redirect to another page will now fallback to return NA instead of throwing an error when trying to parse the unexpected content (#628, @dgkf).git_remote (@niheaven #630).github_pull() documentation (@ms609 #640).Re-license as MIT. (#551)
Fix bug in install_bioc() when using version='devel'. The code will now pull from the git HEAD, not a branch named 'HEAD' (@bbimber, #612).
skip tests for download.file(method = "internal"), on R > 4.1, since that method is now defunct on those versions.
system_requirements() now works as intended if only the os argument is used (@mdneuzerling, #609)
remote_package_name.git2r_remote and remote_package_name.xgit_remote now get correct package name from HTTP(S) git repo's DESCRIPTION file, and thus package's DESCRIPTION file's Remotes field could have git::http(s)://<host>/<username>/<repo>[.git][@ref] items that install remote packages using git via HTTP(S) protocol (@niheaven, #603).
install_*() functions will no longer fail by default if there warnings from install.packages(). Concretely the default value of R_REMOTES_NO_ERRORS_FROM_WARNINGS has changed to true from the previous value of false. (#403)install_bioc() now respects the environment variable R_BIOC_VERSION, and will use the git branch corresponding to this Bioconductor version (@bbimber, #580).
remotes without package names are now unconditionally installed (#532, @jakubkovac)
It is now possible to specify a custom host for dependencies listed in the DESCRIPTION file with Remotes: <type>[@host]::<username>/<repo>[@ref]. The ref now supports / in it for GitLab repositories as it did for GitHubrepositories. (@dagola, #448)
Internal package2remote() function now supports local remotes created by pak.
github_pat() will now check if GITHUB_TOKEN is set if it cannot find GITHUB_PAT. (@coatless)
system_requirements() now supports querying released packages as well as development dependencies (#545)
system_requirements() now supports OS name + version in the os argument (#549, @krlmlr).
New system_requirements() function to query the Public RStudio Package Manager for system requirements for a package (and its dependencies)
Remotes functions can now install dependencies from additional DESCRIPTION fields, e.g. passing dependencies = "Config/Needs/website" will install the dependencies listed in the Config/Needs/website: field in the package's DESCRIPTION.
Prefixing fields with Config/Needs allows them to pass R CMD check without a NOTE, so it is the recommended format for these extra dependencies.
install_*() family of functions now use the default branch in the repository, not the master branch (@MyKo101,#508).
Internal functions remote_download(), remote_metadata(), remote_package_name() and remote_sha() are now exported, so 3rd party packages could provide methods for new remote types (#509, #56)
Internal functions add_metadata(), github_remote() are now exported. They are mainly for 3rd party extensions and should not be used by most users (#485).
install_version() now keeps searching subsequent repositories for the requested version, rather than failing if the version it finds in an early repository is unsuitable. (#305, @kenahoo)
install_version() now understands specifications like '>= 1.0' or '>= 1.12.0, < 1.14' to install the first version of the package it can find that satisfies the criteria. (#305, @kenahoo)
install_version() now avoids use of base::url(), as prior to R 3.6.2 it had a bug when downloading large files (#463)
parse_submodules() internal regular expression is now PCRE 2 compatible (#502, @jan-glx)
update_packages() argument force has been deprecated and no longer has any effect (#521)
Another fix for the mixed binary and source dependency issue, it should hopefully be fully squashed now (#296)
The upgrade menu is now interruptible in RStudio (#489).
Internal GitHub functions now correctly handle cases when characters are not representable in the default locale, but are representable in UTF-8 (#492).
Installing mixed binary and source dependencies when the latest versions of some packages do not have binaries yet should now install dependencies in the correct order to prevent load failures (#296)
github_error() now also works when a GitHub (Enterprise) server does not
return information about the rate limit (@dpprdan, #396, #413).
install_gitlab passes the quiet argument on to gitlab_pat (@michaelchirico, #437)
remotes is now resilient against installed packages that declare
RemoteType: standard but do not include a RemoteRepos or RemotePkgType
field. In such a case, the values for getOption("repos") and
getOption("pkgType") will be used (respectively).
install_gitlab() now installs from repositories in subgroups and with dots
in their name. subdir is now an explicit argument instead of implicit in
repo (@robertdj, #259, #420).
install() now passes the ellipsis ... to install_deps() (@Neil-Schneider, #411)
The tests have been updated to work with newer versions of callr and R 4.0
install_*() functions gain build_manual and build_vignette arguments
that previously existed in devtools versions < 2.0 (#353).
The interactive menu has been modified to provide more clear instructions on the skipping behavior (#207)
Credentials are now passed via HTTP headers, to reduce exposure when requests fail (#391).
download() with the external curl download method now always uses -L to
follow redirects. (#350)
update_packages() now has a more informative error message when the update
fails (#223, #232)
install_git() now can take credentials from the global option
remotes.git_credentials (#378).
install_git() now works with SHA references and external git (#389).
GitHub remotes that point to branches no longer fail when the branch is later deleted (#274).
Local remotes whose original location has been moved will no longer error when updating (#370).
update_deps() no longer sorts the dependencies alphabetically (#296, #301)
github_resolve_ref() now takes a host parameter (#284)
Remotes specific environment variables now accept 0 and 1 as valid values (#238)
remotes now uses locking by default when installing binary packages, which avoids issues when installing binaries that are already open in other R processes (#368)
update_deps() no longer fails if a local package no longer exists (#289)
install_version() now errors with a more informative message when type is
not 'source' (#323)
Bioc remote_sha() now always returns a character result (#379)
Fix API call for private repositories in install_gitlab
(@aornugent, #359, #363)
git submodules now work if the submodule file is empty (@muschellij2, #234)
git submodules now work if the R package is stored in a subfolder (@pommedeterresautee, #233)
install_gitlab() no longer adds the access token twice to the request
(@aornugent, #363).
Bitbucket dependencies now actually use the BITBUCKET_USER and
BITBUCKET_PASSWORD environment variables (@antoine-sachet, #347).
parse_deps() now ignores trailing whitespaces around comparison operators
in DESCRIPTION fields (@LiNk-NY, #366)
update.package_dependencies() now uses the pkg_type for the cran remote
rather than a global type attribute, fixing errors when this global attribute
is lost (#291, #304).
Credentials are no longer passed to dependencies, as this breaks dependencies
which use different credentials or hosts. If you have relied on this behavior
a more robust way to provide the credentials is using the appropriate
environment variables, e.g. GITHUB_PAT, BITBUCKET_USER etc.
(@antoine-sachet, #345).
The hash of bitbucket hosts is now correctly retrieved (@antoine-sachet, #344)
Fix parsing of Additional_Repositories which have a leading newline (@tmelliott, #251).
The order of choices for upgrade = "ask" now puts the stable ones 'All',
'CRAN only', 'none' first, so they always have the same numbers (#287).
update_submodules() now works with empty .gitmodules files (@jsilve24, #329).
remotes now understands the "standard" remote type, as produced by packages
installed from CRAN using pak (#309)
install_dev() now supports ref/pull format, e.g.
install_dev('[email protected]') (@mkearney, #279).
Fix return type of install_remote() when there is a circular dependency (#225)
remote_package_name.github_remote() now works properly on Windows (#248)
install_bioc() repositories now updated for the Bioconductor 3.8 release.
(#239)
install_* functions now set the R_LIBS* environment variables for
child processes correctly on Windows (@HenrikBengtsson, #253)
install_* functions now support the R_REMOTES_UPGRADE environment
variable, to set the default for the upgrade argument. See README for
details (@kevinushey, #240).
install_* functions perform basic HTTP authentication using HTTP
headers now. This fixes an issue with install_bitbucket() and private
repos (#255).
install_* functions now respect the download.file.method option,
if download_file() is used for HTTP.
install_* functions now use the libcurl method, if the
download.file.method option is not set to a different one, and libcurl
is available. Before, the wininet method was preferred on Windows.
If you rely on the proxy configuration of wininet, then you might
want to set the download.file.method option, or use another way to
set up proxies, see ?download.file.
Remotes without package names are now unconditionally installed (#246).
install_github() now includes a more informative error message when the
status code is 404, asking the user to check that they have spelled the
repo owner and repo correctly (included in the error message), and that
they have the required permissions to access the repository.
install_* functions (via the underlying private install function) now set
RGL_USE_NULL="TRUE" in order to avoid errors when running headless
and installing any package using rgl (@jefferis, ##333)
install_deps() now installs un-installed remotes packages even when
upgrade = "never" (@ankane, #227)
install_version() now removes metadata added as a byproduct of using
install_url() internally() (#224)
install() now avoids converting warnings to errors if
R_REMOTES_NO_ERRORS_FROM_WARNINGS is unset and
_R_CHECK_FORCE_SUGGESTS_=false. This avoids failures due to Suggested
packages potentially being missing.
install_bitbucket() now works properly with packages in subdirectories
(#220)
install_deps() now installs un-installed packages even when upgrade = "never" (#218)
install_github() now bundles a GitHub PAT which is used on Travis to avoid
hitting the rate limit too frequently. It also contains a more informative
error message when the rate limit is hit on how to setup a GitHub personal
access token.
The dialog when upgrade = "ask" now has a 'CRAN only' option, to update
only CRAN packages.
No longer include project specific .Rprofile code in the temporary .Rprofile when
R_REMOTES_NO_ERRORS_FROM_WARNINGS=false (the default).
update.package_deps() no longer prompts to install uninstalled
dependencies, they are always installed (#203).
available_packages(), available_packages_set() and
available_packges_reset() added to allow caching of the
available.packages() database.
install_github()'s previously deprecated username argument has been
removed. (#142)
install_deps()'s threads argument has been removed, use the Ncpus
argument instead (#153, #154)
install_git()'s branch argument has been renamed to ref and branch
has been deprecated.
remotes now builds packages by default before installing them. This step
uses the pkgbuild package, if available. If not, it calls R CMD build
directly.
New install_dev() to install the development version of a CRAN package,
based on the URL and BugReports fields in the DESCRIPTION file (#144).
install_()* functions now temporally put Rtools on the PATH when necessary,
as long as the pkgbuild package is installed.
remotes can be forced to use only its internal code by setting the
environment variable R_REMOTES_STANDALONE = "true". This is useful when
installing optional dependencies of remotes on Windows, such as curl or git2r
(#147)
When installing, remotes now errors on warnings, to catch cases where packages are only partially installed. This often happens on windows when the package dll is opened in another R process (#113).
install_() functions now pass arguments, including authentication
information and upgrade down to dependencies (#53, #86, #87).
install_() functions allow the selection of a subset of packages to
upgrade, in interactive mode, when upgrade = "ask".
install_git() now supports passing credentials, when it is used with
git = "git2r" (#106)
install_() functions now return the name of the package(s) which were
installed (#55).
git submodules are now installed if they exist and a git client is available (#138, #133, #103, #82).
New install_gitlab() and install_bioc() functions, to install
gitlab and bioc remote types.
remotes now uses the same SHA updating logic for remotes as devtools, including checking if the SHA of the remote has changed since the last installation. (#135)
install_url() can now install package binaries on windows
(r-lib/devtools#1765)
install_deps() et al. now do not rewrite the type argument from both
to binary to allow falling back to source. This fixes various
installation failures.
remotes now looks up GitHub package names locally, if possible, and uses the GitHub REST API (if the curl package is available, and not in standalone mode). This makes the remote lookup about 10x faster when the remote package has not changed since the last install.
Using a GITHUB_PAT no longer prints diagnostic messages by default (r-lib/devtools#1752).
remotes now always uses https URLs for R versions that support them (@ankane, #139)
Do not include the BioCextra repository in versions after it was deprecated (R 3.5+, Bioc 3.6+).
install_() functions now download tarballs (.tar.gz) files rather than zip
archives (.zip). This results in generally smaller files and avoids issues
with script permissions being lost and strange behavior of some external
unzip programs on Windows (#96).
Dependency parsing is now more robust to whitespace around the dependency specifications (#73).
standardise_dep() exported, for use in devtools.
install_local() now defaults to the current directory.
install_bitbucket() now correctly supports authentication, and the
subdir argument.
install_() functions give a helpful warning when the package has long
path names, on Windows. In this case building the package usually fails.
(#84, #178).
install_() functions have now a more robust way of handling various
tar programs on Windows (#172).
install_() functions now give a helpful warning on older R versions,
on Windows, if R.home() contains a space character. Installation
usually fails in this case.
GitHub API errors now give better error messages, including data about the API rate limits.
URL encode GitHub references, to allow installing from non-alphanumeric branch or tags, @krlmlr #38
Better cooperation with proxy servers, and better download method selection on Windows, @cderv, #45, #46
install_deps() supports tar balls, #47
Allow training slash in GitHub repo specification, #54
Work around on some Linux systems, where unzip is set to the empty string, @HenrikBengtsson, #57
Check for circular dependencies while installing, #31
Updated Bioconductor repo URLs for newer BioC versions
First public release.