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) protocal (@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
GitHub
repositories. (@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('shiny@v1.2-rc')
(@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.