diff --git a/com.oracle.truffle.r.test.packages/r/install.packages.R b/com.oracle.truffle.r.test.packages/r/install.packages.R
index 798ee89b0ec8a8e1432a1004f8b645b9fdac397b..01facbd88a767347d392589cdeaedb117e837654 100644
--- a/com.oracle.truffle.r.test.packages/r/install.packages.R
+++ b/com.oracle.truffle.r.test.packages/r/install.packages.R
@@ -42,8 +42,10 @@
# BioConductor has it's own install mechanism but it is layered on the CRAN model.
-# By default, we use the CRAN mirror specified by --cran-mirror or env var CRAN_MIRROR.
-# If unset, it defaults to "http://cran.cnr.berkeley.edu/"
+# A list of repos can be provided with the --repos argument, which ia comma separated string of name=value pairs.
+# The names "CRAN", "BIOC" and "FASTR" are understood and have default values.
+# By default, we use the CRAN mirror specified in the --repos argument or env var CRAN_MIRROR.
+# The default value for --repos is "CRAN=http://cran.cnr.berkeley.edu"
# Packages are installed into the directory specified by the --lib arg (or R_LIBS_USER env var)
@@ -102,7 +104,8 @@
args <- commandArgs(TRUE)
usage <- function() {
- cat(paste("usage: Rscript [--cran-mirror url] ",
+ cat(paste("usage: Rscript ",
+ "[--repos name=value,...]",
"[--verbose | -v] [-V] [--dryrun]",
"[--no-install | -n] ",
"[--create-blacklist] [--blacklist-file file] [--ignore-blacklist]",
@@ -258,26 +261,35 @@ set.repos <- function() {
# Based on the value of repos.list we set the "repos" option
# which is used by available.packages etc.
repos <- character()
- needCran <- F
- if ("BIOC" %in% repo.list) {
- # source("http://bioconductor.org/biocLite.R")
- # repos["BIOC"] <- biocinstallRepos()[1]
- # above is correct but provokes bug:
- # Error in read.table(): more columns than column names
- repos["BIOC"] <- "https://bioconductor.org/packages/3.4/bioc"
- needCran <- T
- }
- if (needCran || "CRAN" %in% repo.list) {
- # set from the cran-mirror value
- if (is.na(cran.mirror)) {
- # not set on command line
- cran.mirror <<- Sys.getenv("CRAN_MIRROR", unset = "http://cran.cnr.berkeley.edu/")
+ for (repo in repo.list) {
+ parts <- strsplit(repo, "=", fixed=T)[[1]]
+ name <- parts[[1]]
+ if (length(parts) > 1) {
+ uri <- parts[[2]]
+ } else {
+ uri <- NA_character_
+ }
+ if (name == "BIOC") {
+ # source("http://bioconductor.org/biocLite.R")
+ # repos["BIOC"] <- biocinstallRepos()[1]
+ # above is correct but provokes bug:
+ # Error in read.table(): more columns than column names
+ repos[["BIOC"]] <- "https://bioconductor.org/packages/3.4/bioc"
+ } else if (name == "CRAN") {
+ if (is.na(uri)) {
+ # not set on command line
+ cran.mirror <<- Sys.getenv("CRAN_MIRROR", unset = "http://cran.cnr.berkeley.edu/")
+ } else {
+ cran.mirror <- uri
+ }
+ repos[["CRAN"]] <- cran.mirror
+ } else if (name == "FASTR") {
+ # set the FastR internal repo
+ repos[["FASTR"]] <- paste0("file://", normalizePath("com.oracle.truffle.r.test.native/packages/repo"))
+ } else {
+ # User defined
+ repos[[name]] <- uri
}
- repos["CRAN"] <- cran.mirror
- }
- if ("FASTR" %in% repo.list) {
- # set the FastR internal repo
- repos["FASTR"] <- paste0("file://", normalizePath("com.oracle.truffle.r.test.native/packages/repo"))
}
options(repos = repos)
}
@@ -833,8 +845,6 @@ parse.args <- function() {
initial.blacklist.file <<- get.argvalue()
} else if (a == "--repos") {
repo.list <<- strsplit(get.argvalue(), ",")[[1]]
- } else if (a == "--cran-mirror") {
- cran.mirror <<- get.argvalue()
} else if (a == "--random") {
random.count <<- as.integer(get.argvalue())
if (is.na(random.count)) {
diff --git a/documentation/dev/testing.md b/documentation/dev/testing.md
index 9d7e514bda36279d8287feec74a4611809412ee7..45c3893fa88ea26b2006ced2ac56bb560bbe110a 100644
--- a/documentation/dev/testing.md
+++ b/documentation/dev/testing.md
@@ -63,7 +63,7 @@ The command has a rather daunting set of options but, for normal use, most of th
##### Usage
- mx installpkgs [--repos list] [--cran-mirror url]
+ mx installpkgs [--repos list]
[--verbose | -v] [-V]
[--dryrun]
[--no-install | -n]
@@ -100,7 +100,7 @@ There are many packages that cannot be installed due to either missing functiona
3. TODO
##### CRAN Mirror
-Packages are downloaded and installed from the repos given by the `repos` argument, a comma-separated list, that defaults to `CRAN`. CRAN packages are downloaded from a CRAN mirror. When the standard `utils::install_packages` function is run interactively, the user is prompted for a mirror. To avoid such interaction, `install.packages` has two ways for specifying a mirror. The default CRAN mirror is `http://cran.cnr.berkeley.edu/` but this can be changed either with the command line argument `--cran-mirror` or the environment variable `CRAN_MIRROR`. The `FASTR` repo is internal to the source base and contains FastR-specific test packages. The BioConductor repo can be added by setting `--repos BIOC`. It also implies `CRAN`.
+Packages are downloaded and installed from the repos given by the `repos` argument, a comma-separated list of `name[=value]` pairs, that defaults to `CRAN`. CRAN packages are downloaded from a CRAN mirror. When the standard `utils::install_packages` function is run interactively, the user is prompted for a mirror. To avoid such interaction, `install.packages` has two ways for specifying a mirror. The default CRAN mirror is `http://cran.cnr.berkeley.edu/` but this can be changed either with `CRAN=url` or the environment variable `CRAN_MIRROR`. The `FASTR` repo is internal to the source base and contains FastR-specific test packages. The BioConductor repo can be added by setting `--repos BIOC`. User defined repos can be specified by `USERNAME=url`. N.B. For file system paths this must be a `file:` URL.
##### Installation Directory
The directory in which to install the package can be specified either by setting the `R_LIBS_USER` environment variable or with the `--lib` command line argument. The former is recommended and indeed required for running tests after installation (the testing system does not honor the `--lib` argument).
@@ -160,6 +160,10 @@ Testing packages requires that they are first installed, so all of the above is
Install the `A3` package (and its dependents) in `$R_LIBS_USER`, creating the `package.blacklist` file first if it does not exist. The dependents (`xtable`, `pbapply`) will be installed implicitly by the underlying R install.packages function
+ $ mx installpkgs --repos CRAN=file://path-to-local-cran-mirror --pkg-pattern '^A3$'
+
+Similar to above but uses a local CRAN mirror stored in `path-to-local-cran-mirror`.
+
$ mx installpkgs --install-dependents-first--pkg-pattern '^A3$'
Similar to the above but the dependents of A3 are explicitly installed first. This is equivalent to using `--pkg-filelist` file, where file would contain xtable, pbapply and A3 in that order.