load binary packages ahead of use #1275
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I have a proof-of-concept which does not install a package into the primary library if it cannot be loaded, created by code-reading some of the package loading that R performs when installing from source. test_load_package.RR_runR <- function(cmd = NULL, Ropts = "", env = "",
stdout = TRUE, stderr = TRUE, stdin = NULL) {
# from tools/check.R; non-windows.
suppressWarnings(system2(file.path(R.home("bin"), "R"),
c(Ropts),
stdout, stderr, stdin, input = cmd, env = env))
}
setRlibs <- function() {
rlibs <- .libPaths()
rlibs <- paste(rlibs, collapse = .Platform$path.sep)
rlibs <- shQuote(rlibs)
c(paste0("R_LIBS=", rlibs),
"R_ENVIRON_USER=''",
"R_LIBS_USER='NULL'",
"R_LIBS_SITE='NULL'")
}
# This produces a (by default single) quoted string for use in a
# command sent to another R process.
# from tools::install.packages
quote_path <- function(path, quote = "'") {
path <- gsub("\\", "\\\\", path, fixed = TRUE)
path <- gsub(quote, paste0("\\", quote), path, fixed = TRUE)
paste0(quote, path, quote)
}
load_package <- function(pkg_name, tmplib) {
cat(paste0("trying to load: ", pkg_name, " from ", tmplib, "\n"))
# TODO: What versions of R contain this helper? Do we need our own?
cmd <- paste0("tools:::.test_load_package('", pkg_name, "', ", quote_path(tmplib), ")")
opts <- "--no-save --no-restore --no-echo"
env <- setRlibs()
out <- R_runR(cmd, Ropts = opts, env = env)
if (length(out)) {
cat(paste(c(out, ""), collapse = "\n"))
}
if (length(attr(out, "status"))) {
stop("loading failed", call. = FALSE, domain = NA)
}
cat("load successful.\n")
}
safe_install_impl <- function(pkg_name, lib) {
tmplib <- tempfile()
dir.create(tmplib)
on.exit(unlink(tmplib), add = TRUE)
cat(paste0("lib: ", lib, "\n"))
cat(paste0("tmplib: ", tmplib, "\n"))
old_paths <- .libPaths()
on.exit(.libPaths(old_paths), add = TRUE)
.libPaths(c(tmplib, lib, .libPaths()))
install.packages(pkg_name)
load_package(pkg_name, tmplib)
tmp_pkg_path <- file.path(tmplib, pkg_name)
pkg_path <- file.path(lib, pkg_name)
# FIXME: rename only works when within the same file-system.
# FIXME: handle when the target already exists.
cat(paste0("renaming: ", tmp_pkg_path, " => ", pkg_path, "\n"))
file.rename(tmp_pkg_path, pkg_path)
}
safe_install <- function(pkg_name, lib) {
tryCatch(
safe_install_impl(pkg_name, lib),
error = function(e) {
e$message <- paste0(
"Failed to install package ", pkg_name,
" into ", lib, ": ", e$message)
stop(e)
})
}
options(repos = c(CRAN = "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"))
# FIXME: Determine the target some other way.
lib <- .libPaths()[1L]
safe_install("coda", lib)
safe_install("rjags", lib)A similar FROM rstudio/r-base:4.3-jammy AS without-jags
RUN apt-get update && apt-get -y install pkg-config
FROM without-jags AS installation
COPY test_load_package.R /content/test_load_package.R
WORKDIR /content
RUN R -s -f test_load_package.RWhen run, the "install" errs, as we want: docker build \
--progress=plain \
--no-cache-filter installation \
-f Dockerfile.load-bad . |
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Re-tested this issue after the resolution of #1611 and the rjags load problem is still detected: Used a slightly different FROM rstudio/r-base:4.3-jammy
RUN apt-get update && apt-get -y install pkg-config
ARG REPOSITORY=https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
RUN mkdir /content && echo "library(rjags)" > /content/script.R
WORKDIR /content
RUN R -s -e "install.packages('remotes', repos=c(CRAN='${REPOSITORY}'))"
RUN R -s -e "remotes::install_github('rstudio/renv')"
RUN R -s -e "renv::init(bare = TRUE, repos=c(CRAN='${REPOSITORY}'))"
RUN R -s -e "renv::install('rjags', repos=c(CRAN='${REPOSITORY}'))"
RUN R -s -e "renv::snapshot()"
RUN R -s -f "script.R" |
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Installing binary packages can often hide problems with an environment until runtime.
Take, for example, the
Dockerfile:Building this image:
docker build \ --progress=plain \ --no-cache -f Dockerfile.renv .This example errs because the
librarystatement fails to load therjagspackage (becausejagsis missing).This same situation can be seen with renv:
The error:
Part of this is rooted in how R handles package installation: The
R CMD installcommand installs source and binary packages differently.R CMD install source/binary switch:
https://github.com/wch/r-source/blob/3a15e29d1b5a94e06b99cb9315c562fd8f71bc5b/src/library/tools/R/install.R#L419-L422
R CMD install package load test (inside do_install_source):
https://github.com/wch/r-source/blob/3a15e29d1b5a94e06b99cb9315c562fd8f71bc5b/src/library/tools/R/install.R#L1814-L1852
https://github.com/wch/r-source/blob/3a15e29d1b5a94e06b99cb9315c562fd8f71bc5b/src/library/tools/R/install.R#L1854-L1861
R CMD install do_install_binary does not attempt load:
https://github.com/wch/r-source/blob/3a15e29d1b5a94e06b99cb9315c562fd8f71bc5b/src/library/tools/R/install.R#L480-L502
When first added, only to the source path (and used library, not external process):
wch/r-source@7bc912f
Could renv attempt to validate binary packages by loading them before finalizing the installation? That would let us identify problems at restore-time rather than downstream when running the content.
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