[med-svn] [r-bioc-biocinstaller] 01/05: New upstream version 1.28.0
Andreas Tille
tille at debian.org
Fri Nov 10 07:47:59 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-biocinstaller.
commit 7375908edad57b51da9690e5c32432b9d74f96de
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 8 10:37:31 2017 +0100
New upstream version 1.28.0
---
DESCRIPTION | 4 ++--
NEWS | 10 ++++++++++
R/biocLite.R | 15 +++++++++++----
R/biocinstallRepos.R | 3 +--
R/zzz.R | 20 ++++++++++++--------
inst/scripts/BiocInstaller.dcf | 20 ++++++++++++++++----
inst/unitTests/test_biocLite.R | 13 +++++++++++++
inst/unitTests/test_biocinstallRepos.R | 2 +-
man/useDevel.Rd | 11 ++++++-----
9 files changed, 72 insertions(+), 26 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b09ab18..75b748f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: BiocInstaller
Title: Install/Update Bioconductor, CRAN, and github Packages
Description: This package is used to install and update Bioconductor,
CRAN, and (some) github packages.
-Version: 1.26.1
+Version: 1.28.0
Author: Dan Tenenbaum and Biocore Team
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Infrastructure
@@ -10,4 +10,4 @@ Depends: R (>= 3.4.0)
Suggests: devtools, RUnit, BiocGenerics
License: Artistic-2.0
NeedsCompilation: no
-Packaged: 2017-08-31 23:08:27 UTC; biocbuild
+Packaged: 2017-10-30 23:14:14 UTC; biocbuild
diff --git a/NEWS b/NEWS
index 2dba0f9..6f578c4 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,13 @@
+CHANGES IN VERSION 1.28.0
+-------------------------
+
+NEW FEATURES
+
+ o biocLite() supports full URLs, e.g., to archived Bioconductor
+ packages.
+
+ o Support MRAN (Microsoft R) archives.
+
CHANGES IN VERSION 1.24.0
-------------------------
diff --git a/R/biocLite.R b/R/biocLite.R
index df871d4..f567b29 100644
--- a/R/biocLite.R
+++ b/R/biocLite.R
@@ -19,11 +19,18 @@
setdiff(pkgs, doing)
}
+.rRepos <- function(pkgs, invert = FALSE)
+ grep("^(https?://.*|[^/]+)$", pkgs, invert = invert, value=TRUE)
+
+.githubRepos <- function(pkgs) {
+ pkgs <- .rRepos(pkgs, invert = TRUE)
+ grep("^[^/]+/.+", pkgs, value=TRUE)
+}
+
.reposInstall <-
function(pkgs, lib, ...)
{
- ## non-'github' packages
- doing <- grep("/", pkgs, invert=TRUE, value=TRUE)
+ doing <- .rRepos(pkgs)
if (length(doing)) {
pkgNames <- paste(sQuote(doing), collapse=", ")
.message("Installing package(s) %s", pkgNames)
@@ -35,7 +42,7 @@
.githubInstall <-
function(pkgs, ..., lib.loc=NULL)
{
- doing <- grep("/", pkgs, value=TRUE)
+ doing <- .githubRepos(pkgs)
if (length(doing)) {
pkgNames <- paste(sQuote(doing), collapse=", ")
.message("Installing github package(s) %s", pkgNames)
@@ -116,7 +123,7 @@
instlib=instlib),
s = update.packages(lib.loc, oldPkgs=oldPkgs, ask=TRUE,
instlib=instlib),
- n = invisible(pkgs))
+ n = invisible(pkgs))
} else {
.message("Updating packages '%s'", pkgList)
update.packages(lib.loc, oldPkgs=oldPkgs, ask=ask, instlib=instlib)
diff --git a/R/biocinstallRepos.R b/R/biocinstallRepos.R
index 859fd36..e007daf 100644
--- a/R/biocinstallRepos.R
+++ b/R/biocinstallRepos.R
@@ -43,7 +43,7 @@ biocinstallRepos <-
biocMirror <- getOption("BioC_mirror",
sprintf("%s//bioconductor.org", .protocol()))
biocPaths <- c(BioCsoft="bioc", BioCann="data/annotation",
- BioCexp="data/experiment", BioCextra="extra")
+ BioCexp="data/experiment")
biocRepos <- paste(biocMirror, "packages", biocVersion,
biocPaths, sep="/")
repos[names(biocPaths)] <- biocRepos
@@ -65,7 +65,6 @@ biocinstallRepos <-
## comment repos here as they become available.
inactive <- c(
## "BioCsoft"
- ## , "BioCextra"
## , "BioCann"
## , "BioCexp"
)
diff --git a/R/zzz.R b/R/zzz.R
index fd348c9..70c74c3 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,9 +1,9 @@
-R_VERSION_MAX <- IS_USER <- IS_END_OF_LIFE <- IS_UPGRADEABLE <- UPGRADE_IS_DEVEL <-
- IS_DOWNGRADEABLE <- UPGRADE_VERSION <- DOWNGRADE_VERSION <-
- NEXT_R_DEVEL_VERSION <- NULL
+R_VERSION_MAX <- IS_USER <- IS_END_OF_LIFE <- IS_UPGRADEABLE <-
+ UPGRADE_IS_DEVEL <- IS_DOWNGRADEABLE <- UPGRADE_VERSION <-
+ DOWNGRADE_VERSION <- NEXT_R_DEVEL_VERSION <- NULL
## The following values are updated with each Bioc release; see .onLoad
-BIOC_VERSION <- package_version("3.5") # Bioc version for this package
+BIOC_VERSION <- package_version("3.6") # Bioc version for this package
# R_VERSION_MAX <- package_version("3.3.0") # Maximum version of R for
# # this version of BiocInstaller
# IS_USER <- FALSE # TRUE if this version of
@@ -72,13 +72,17 @@ globalVariables("repos") # used in 'bootstrap' functions
function(libname, pkgname)
{
fl <- system.file(package="BiocInstaller", "scripts",
- "BiocInstaller.dcf")
+ "BiocInstaller.dcf")
dcf <- read.dcf(fl)
- opt <- getOption("BIOCINSTALLER_ONLINE_DCF",
- Sys.getenv("BIOCINSTALLER_ONLINE_DCF", TRUE))
+ opt <- getOption(
+ "BIOCINSTALLER_ONLINE_DCF",
+ Sys.getenv("BIOCINSTALLER_ONLINE_DCF", TRUE)
+ )
if (opt) {
tryCatch({
- con <- url(paste0(.protocol(), "//bioconductor.org/BiocInstaller.dcf"))
+ con <- url(paste0(
+ .protocol(), "//bioconductor.org/BiocInstaller.dcf"
+ ))
on.exit(close(con))
dcf <- read.dcf(con)
}, error=function(e) {})
diff --git a/inst/scripts/BiocInstaller.dcf b/inst/scripts/BiocInstaller.dcf
index 53d6f6b..fed3ea0 100644
--- a/inst/scripts/BiocInstaller.dcf
+++ b/inst/scripts/BiocInstaller.dcf
@@ -1,11 +1,23 @@
Comment: update NEXT_R_DEVEL_VERSION in all entries
Comment: Accurate as of release day
-BIOC_VERSION: 3.5
-R_VERSION_MAX: 3.4.0
+BIOC_VERSION: 3.6
+R_VERSION_MAX: 3.4.4
IS_USER: FALSE
IS_END_OF_LIFE: FALSE
IS_UPGRADEABLE: FALSE
UPGRADE_IS_DEVEL: FALSE
+IS_DOWNGRADEABLE: TRUE
+UPGRADE_VERSION: 3.7
+DOWNGRADE_VERSION: 3.5
+NEXT_R_DEVEL_VERSION: 3.5.0
+
+Comment: Accurate as of release day
+BIOC_VERSION: 3.5
+R_VERSION_MAX: 3.4.2
+IS_USER: TRUE
+IS_END_OF_LIFE: FALSE
+IS_UPGRADEABLE: TRUE
+UPGRADE_IS_DEVEL: TRUE
IS_DOWNGRADEABLE: FALSE
UPGRADE_VERSION: 3.6
DOWNGRADE_VERSION: 3.4
@@ -14,8 +26,8 @@ NEXT_R_DEVEL_VERSION: 3.5.0
Comment: Accurate as of release day
BIOC_VERSION: 3.4
R_VERSION_MAX: 3.3.3
-IS_USER: TRUE
-IS_END_OF_LIFE: FALSE
+IS_USER: FALSE
+IS_END_OF_LIFE: TRUE
IS_UPGRADEABLE: FALSE
UPGRADE_IS_DEVEL: FALSE
IS_DOWNGRADEABLE: FALSE
diff --git a/inst/unitTests/test_biocLite.R b/inst/unitTests/test_biocLite.R
new file mode 100644
index 0000000..18b4699
--- /dev/null
+++ b/inst/unitTests/test_biocLite.R
@@ -0,0 +1,13 @@
+test_reposType <- function()
+{
+ .rRepos <- BiocInstaller:::.rRepos
+ .githubRepos <- BiocInstaller:::.githubRepos
+
+ r <- "foo"
+ http <- c("http://foo.bar/baz", "https://foo.bar/baz")
+ github <- c("foo/bar", "foo/bar at baz")
+ all <- c(r, http, github)
+
+ checkIdentical(c(r, http), .rRepos(all))
+ checkIdentical(github, .githubRepos(all))
+}
diff --git a/inst/unitTests/test_biocinstallRepos.R b/inst/unitTests/test_biocinstallRepos.R
index e6fb520..7645e4f 100644
--- a/inst/unitTests/test_biocinstallRepos.R
+++ b/inst/unitTests/test_biocinstallRepos.R
@@ -3,7 +3,7 @@ repos <- biocinstallRepos()
test_biocinstallRepos_named_repositories <- function()
{
- allOS <- c("BioCsoft", "CRAN", "BioCann", "BioCexp", "BioCextra")
+ allOS <- c("BioCsoft", "CRAN", "BioCann", "BioCexp")
windowsOnly <- "CRANextra"
checkTrue(all(allOS %in% names(repos)))
diff --git a/man/useDevel.Rd b/man/useDevel.Rd
index 77ec46e..9a30fa9 100644
--- a/man/useDevel.Rd
+++ b/man/useDevel.Rd
@@ -58,11 +58,12 @@ useDevel(devel=TRUE)
be from the devel repository. You should run \code{\link{useDevel}}
only once.
- It is possible to use release and devel versions of Bioconductor with
- the same installation of R. To do this, use the \code{R_LIBS_USER}
- environment variable. First, create two separate directories for your
- BioC release and devel packages. Suggested directory names are as
- follows:
+ During release cycles where both the release and devel version of
+ Bioconductor use the same version of R, it is possible to use release
+ and devel versions of Bioconductor with the same installation of R.
+ To do this, use the \code{R_LIBS_USER} environment variable. First,
+ create two separate directories for your BioC release and devel
+ packages. Suggested directory names are as follows:
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