BiocManager test scripts

bad-BiocVersion.R

url <- Sys.getenv("BIOCVERSION_REPOS")

dir.create(tmp <- tempfile())
pkg <- file.path(tmp, "BiocVersion")

system2("git", c("-C", tmp, "clone", url))
system2("git", c("-C", pkg, "checkout", "RELEASE_3_9"))
install.packages(pkg, repos=NULL)
remotes:: install_git(url, ref = "RELEASE_3_9")

BiocManager_test.sh

export BIOCVERSION_REPOS=~/b/git/BiocVersion
export BIOCMANAGER_REPOS=~/b/git/BiocManager
export BIOCMANAGER_SANDBOX=/Users/ma38727/tmp/BiocManagerSandbox

#
# R-4.0
#

echo "R-4.0"
export R_LIBS_USER=$BIOCMANAGER_SANDBOX/R-4.0-Bioc-3.10
mkdir -p $R_LIBS_USER

rm -rf BiocManager_*tar.gz
~/bin/R-devel/bin/R \
    --vanilla --silent -e "source('install-dependencies.R', echo = TRUE)"
~/bin/R-devel/bin/R CMD build $BIOCMANAGER_REPOS
~/bin/R-devel/bin/R CMD check BiocManager_*tar.gz

echo "R-4.0 No BiocVersion"
~/bin/R-devel/bin/R \
    --vanilla --silent -e "source('remove-BiocVersion.R', echo=TRUE)"
~/bin/R-devel/bin/R CMD build $BIOCMANAGER_REPOS
_R_CHECK_FORCE_SUGGESTS_=0 \
    ~/bin/R-devel/bin/R CMD check BiocManager_*tar.gz

echo "R-4.0 wrong BiocVersion"
~/bin/R-3-6-branch/bin/R \
    --vanilla --silent -e "source('bad-BiocVersion.R', echo=TRUE)"
~/bin/R-devel/bin/R CMD build $BIOCMANAGER_REPOS
~/bin/R-devel/bin/R CMD check BiocManager_*tar.gz

echo "cleaning up R-4.0"
~/bin/R-devel/bin/R \
    --vanilla --silent -e "source('install-dependencies.R', echo = TRUE)"

#
# R-3.6
#

echo "R-3.6"
export R_LIBS_USER=$BIOCMANAGER_SANDBOX/R-3.6-Bioc-3.9
mkdir -p $R_LIBS_USER
rm -rf BiocManager_*tar.gz
~/bin/R-3-6-branch/bin/R \
    --vanilla --silent -e "source('install-dependencies.R')"
~/bin/R-3-6-branch/bin/R CMD build $BIOCMANAGER_REPOS
~/bin/R-3-6-branch/bin/R CMD check BiocManager_*tar.gz

#
# R-3.5
#

echo "R-3.5"
export R_LIBS_USER=$BIOCMANAGER_SANDBOX/R-3.5-Bioc-3.8
mkdir -p $R_LIBS_USER
rm -rf BiocManager_*tar.gz
~/bin/R-3-5-branch/bin/R \
    --vanilla --silent -e "source('install-dependencies.R')"
~/bin/R-3-5-branch/bin/R CMD build $BIOCMANAGER_REPOS
~/bin/R-3-5-branch/bin/R CMD check BiocManager_*tar.gz

install-dependencies.R

pkgpath <- Sys.getenv("BIOCMANAGER_REPOS")
stopifnot(dir.exists(pkgpath))

has_internet <-
    function()
{
    tryCatch({
        suppressWarnings(readChar("https://httpbin.org", 1L))
        TRUE
    }, error = function(e) {
        FALSE
    })
}

if (!has_internet())
    quit()

## make sure there are no left-over packages
pkgs0 <- c("BiocManager", "BiocVersion")
inst <- installed.packages()
idx <- which(rownames(inst) %in% pkgs0)
for (i in idx)
    remove.packages(inst[i, "Package"], inst[i, "LibPath"])

## install from R base configuration
setRepositories(ind = 1:4)
chooseCRANmirror(ind=1)
chooseBioCmirror(ind=1)

fields <- c("Depends", "Imports", "Suggests", "Enhances", "LinkingTo")
dcf <- read.dcf(file.path(pkgpath, "DESCRIPTION"), fields)
pkgs <- Filter(Negate(is.na), unlist(strsplit(dcf, "[[:punct:]|[:space:]]+")))

pkgs <- setdiff(pkgs, rownames(installed.packages()))
message(
    "installing packages:\n  ",
    paste(pkgs, collapse="\n  ")
)
install.packages(pkgs)

remove-BiocVersion.R

inst <- installed.packages()
idx <- which(inst[,"Package"] %in% "BiocVersion")
for (i in idx)
    remove.packages(inst[i, "Package"], inst[i, "LibPath"])