neurocLite.R
In neuroconductor/neurocInstall: 'Neuroconductor' Installer
# neurocInstall package version: 0.12.0
pkg_ver = '# neurocInstall package version: 0.12.0'
# source("https://bioconductor.org/biocLite.R")
# biocLite(suppressUpdates = TRUE,
# suppressAutoUpdate = TRUE,
# ask = FALSE)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(update = FALSE, ask = FALSE)
# if (!require("neurocInstall")) {
#########################################
# Checking devtools version
#########################################
get_devtools_version = function() {
ipacks = installed.packages()
dtools = ipacks[ ipacks[, "Package"] %in% "devtools", "Version"]
return(dtools)
}
# needed for bioc stuff
req_version = "1.12.0.9000"
dtools = get_devtools_version()
install_from_cran = FALSE
if (length(dtools) == 0 ) {
install_from_cran = TRUE
} else {
# too low of a version
install_from_cran = compareVersion(dtools, req_version) < 0
}
if (install_from_cran) {
install.packages("devtools")
}
# now we assume devtools is installed
dtools = get_devtools_version()
if (length(dtools) == 0 ) {
stop(paste0("devtools tried to install but could not ",
"- try to install devtools manually.",
"Version >= ", req_version, " required."
)
)
} else {
comparison = compareVersion(dtools, "1.12.0.9000")
if (comparison < 0) {
devtools::install_github("r-lib/devtools")
}
}
message(paste("Using neurocLite version:", pkg_ver))
#' @title Neuroconductor Installer
#' @description Install function for neuroconductor packages
#' @param repo Package name in neuroconductor
#' @param release Stable or current (development) versions/branches
#' @param release_repo Repository for release repository, passed to
#' \code{\link{install.packages}}. If \code{release_repo = "github"},
#' then it will install using GitHub. If you set this using
#' \code{\link{make_release_version}} or specify the URL directly,
#' it will override \code{release} option.
#'
#' @param type character, indicating the type of package to download and
#' install, passed to \code{\link{install.packages}}.
#'
#' @param upgrade_dependencies Should dependencies be updated?
#' passed to \code{\link[devtools]{install}} if using
#' \code{release_repo = "github"}
#' @param ... additional arguments passed to
#' \code{\link{install.packages}}
#' or \code{\link[devtools]{install_github}} if
#' \code{release_repo = "github"}
#'
#' @return Result from \code{\link{install.packages}} or
#' \code{\link[devtools]{install_github}}
#'
#' @export
#' @importFrom devtools install_github
#' @importFrom utils read.csv
#' @importFrom utils compareVersion install.packages installed.packages
#'
#' @examples
#' \donttest{
#' tlib = tempfile()
#' dir.create(tlib, showWarnings = FALSE)
#' system.time({
#' install.packages("oro.asl",
#' lib = tlib,
#' repos = "https://neuroconductor.org/releases/2019/12/")
#' })
#' repos = getOption("repos")
#' print(repos)
#' #if (repos["CRAN"] == "@CRAN@") {
#' # repos["CRAN"] = "https://cloud.r-project.org"
#' # options(repos = repos)
#' #}
#' options(repos = NULL)
#' print(getOption("repos"))
#' neuro_install("oro.asl", lib = tlib,
#' release_repo = "https://neuroconductor.org/releases/2019/12")
#' options(repos = repos)
#' }
#' \dontrun{
#' neuro_install("cifti", type = "source", lib = tlib)
#' neuro_install("cifti",
#' release_repo = latest_neuroc_release("stable"),
#' lib = tlib)
#'
#' neuro_install("cifti", release_repo = "github")
#' }
#'
neuro_install = function(
repo,
release = c("stable", "current"),
release_repo = latest_neuroc_release(),
upgrade_dependencies = FALSE,
type = getOption("pkgType"),
...){
#############################
# Create a data.frame for merging
#############################
release = match.arg(release)
l_repo = trimws(tolower(release_repo))
if (!l_repo %in% "github") {
args = list(...)
repos = args$repos
repos = c(Neuroconductor = release_repo,
getOption("repos"),
repos)
args$repos = repos
contriburl = utils::contrib.url(repos, type)
repos = c(Neuroconductor = release_repo,
getOption("repos"),
repos)
repos = repos[ repos != "@CRAN@" ]
if ("contriburl" %in% names(args)) {
args$contriburl = c(contriburl, args$contriburl)
}
repos = repos[!duplicated(repos)]
args$contriburl = unique(args$contriburl)
args$pkgs = repo
# args$repos = repos
args$type = type
x = do.call(utils::install.packages, args = args)
# x = install.packages(pkgs = repo,
# repos = c(Neuroconductor = release_repo,
# getOption("repos")),
# type = type,
#
# ...)
lib.loc = NULL
if (!is.null(args$lib)) {
lib.loc = args$lib
}
not_installed = repo[!repo %in% installed.packages(
lib.loc = lib.loc
)[, "Package"]]
if (length(not_installed) > 0) {
msg = paste0("Package(s): ", paste(not_installed, sep = ", "),
" released binaries/sources were not installed,",
" please try to install with release_repo = \"github\"")
warning(msg)
}
return(invisible(x))
}
df = data.frame(repo = repo, stringsAsFactors = FALSE)
tab = neuro_package_table(long = TRUE)
tab = tab[ tab$release %in% release, ]
## import list of packages
# error if pkg not in list of packages
check_install = df$repo %in% tab$repo
if (!all(check_install)) {
bad_pkgs = df$repo[!check_install]
bad_pkgs = paste(bad_pkgs, collapse = ", ")
message(paste0("Available Packages on neuroconductor are ",
paste(unique(tab$repo), collapse = ", ")))
stop(paste0("Package(s) ", bad_pkgs,
" are not in neuroconductor"))
}
tab = merge(df, tab, by = "repo", all.x = TRUE)
tab$version = numeric_version(tab$version)
# pkg = tab$pkg
# tab$commit_id = tab[, "commit_id"]
tab = split(tab, tab$repo)
tab = lapply(tab, function(x) {
x$version = x[, "version"]
max_version = max(x$version)
x = x[ x$version %in% max_version,, drop = FALSE]
return(x)
})
tab = do.call("rbind", tab)
tab = data.frame(tab, stringsAsFactors = FALSE)
tab$repo = paste0("neuroconductor/", tab$repo, "@", tab$commit_id)
args = list(tab$repo)
gh_func = devtools::install_github
if ("upgrade" %in% methods::formalArgs(gh_func)) {
args$upgrade = upgrade_dependencies
} else {
args$upgrade_dependencies = upgrade_dependencies
}
if (!upgrade_dependencies) {
res = try({
results = do.call(gh_func, args = args)
})
if (is.logical(results)) {
check = any(!results)
} else {
check = FALSE
}
if (inherits(res, "try-error") || check) {
stop("Installation failed, please try with upgrade_dependencies = TRUE")
}
} else {
results = do.call(gh_func, args = args)
}
}
#' @rdname neuro_install
#' @aliases neuroc_install
#' @aliases neuro_install
#' @export
neuroc_install = function(...) {
neuro_install(...)
}
#' @rdname neuro_install
#' @aliases neurocLite
#' @export
neurocLite = function(...) {
neuro_install(...)
}
#' @title Make Full Package Version
#' @description Makes a package version to have all the same length.
#' This is helpful when using \code{\link{compareVersion}}.
#'
#' @param x Character vector of package versions
#'
#' @return Character vector of versions, each with the same length.
#' @export
#'
#' @examples
#' x = c("1.6", "1.6.0")
#' compareVersion(x[1], x[2])
#' x2 = make_full_version(x)
#' compareVersion(x2[1], x2[2])
#' x = c("1.6", "1.6.0")
#' compareVersion(x2[1], x2[2])
make_full_version = function(x) {
nx = names(x)
x = as.character(x)
r <- lapply(strsplit(x, "[.-]"), as.integer)
lx = sapply(r, length)
mlx = max(lx)
r <- lapply(r, function(ver) {
c(ver, rep(0, length = mlx - length(ver)))
})
x = sapply(r, paste, collapse = ".")
names(x) = nx
return(x)
}
#' Latest Neuroconductor Release Location
#'
#' @param secure Should https vs. http be used
#' @param release Stable or current (development) versions
#' @return URL of release page
#' @export
#'
#' @examples
#' make_release_version("2018/02/", check = FALSE)
#' \donttest{
#' latest_neuroc_release()
#' }
latest_neuroc_release = function(secure = TRUE) {
make_release_version(
release_path = NULL,
secure = secure)
}
#' @rdname latest_neuroc_release
#' @export
binary_release_repo = function(
release = c("stable", "current"),
secure = TRUE) {
release = match.arg(release)
release_version = paste0("latest/", release, "/")
release_version = make_release_version(release_version, secure = secure)
return(release_version)
}
#' @rdname latest_neuroc_release
#' @param release_path path to the release on
#' \url{https://neuroconductor.org/releases/}
#' @param check should the `release_path` need to be checked against
#' all the releases?
#' @export
make_release_version = function(release_path = NULL, secure = TRUE,
check = TRUE) {
if (is.null(release_path)) {
check = TRUE
}
if (check) {
df = release_versions()
if (is.null(release_path)) {
release_path = df$release[1]
}
if (!all(release_path %in% df$release)) {
warning(paste0("Release path created, but not in the ",
"Neuroconductor set of releases"))
}
}
release_path = paste0(
"http", ifelse(secure, "s", ""), "://neuroconductor.org/releases/",
release_path)
release_path
}
#' @rdname latest_neuroc_release
#' @importFrom utils download.file
#' @export
release_versions = function(secure = TRUE) {
# read from the page Adi Makes
# currently fail
url = paste0("http", ifelse(secure, "s", ""),
"://neuroconductor.org/api/releases/")
destfile = tempfile(fileext = ".txt")
x = try({
download.file(url = url, destfile = destfile, quiet = TRUE)
}, silent = TRUE)
if (inherits(x, "try-error") || x != 0) {
warning(paste0(
"Releases did not download, may be error with downloading ",
url))
if (requireNamespace("httr", quietly = TRUE)) {
url = sub("https", "http", url)
res = httr::GET(url,
httr::write_disk(path = destfile, overwrite = TRUE),
config = httr::config(ssl_verifypeer = FALSE))
httr::warn_for_status(res)
}
}
releases = readLines(destfile, warn = FALSE)
releases = trimws(releases)
releases = gsub('"', "", releases)
releases = releases[grepl("releases/", releases)]
releases = gsub('"', "", releases)
releases = trimws(releases)
releases = sub(',$', "", releases)
releases = sub("^releases/", "", releases)
ss = t(sapply(strsplit(releases, "/"), rbind))
colnames(ss) = c("year", "month")
df = data.frame(release = releases, stringsAsFactors = FALSE)
df = cbind(df, ss, stringsAsFactors = FALSE)
df = df[ df$year != "latest", , drop = FALSE]
df$year = as.numeric(df$year)
df$date = paste0(df$year, "-", df$month, "-01")
df$date = as.Date(x = df$date, format = "%Y-%m-%d")
df = df[ order(df$date, decreasing = TRUE), , drop = FALSE]
return(df)
}
#' @title Neuroconductor Package Table
#' @description Returns the table of Neuroconductor packages
#' @return \code{data.frame} of packages with commit IDs
#' @param path Path to the table of package
#' @param long Should the data be "long" (with respect to stable/current)
#' @param deployment indicator if this is a release, not standard flag.
#' @export
#'
#' @note Package information is obtained from
#' \url{https://neuroconductor.org/neurocPackages}
#'
#' @importFrom stats reshape
#' @examples
#' neuro_package_table()
neuro_package_table = function(
path = "https://neuroconductor.org/neurocPackages",
long = FALSE,
deployment = FALSE
) {
#############################
## grab list of current neuroc packages
#############################
args = list(file = path,
stringsAsFactors = FALSE, header = TRUE,
na.strings = ifelse(deployment, "NA", ""))
suppressWarnings({
tab = try( {
do.call("read.csv", args)
} , silent = TRUE)
})
if (inherits(tab, "try-error")) {
args$file = gsub("^https", "http", args$file)
suppressWarnings({
tab = try( {
do.call("read.csv", args)
} , silent = TRUE)
})
if (inherits(tab, "try-error")) {
if (requireNamespace("httr", quietly = TRUE)) {
destfile = tempfile()
httr::GET(args$file,
httr::write_disk(path = destfile),
config = httr::config(ssl_verifypeer = FALSE))
args$file = destfile
tab = do.call("read.csv", args)
}
}
}
if (nrow(tab) == 0) {
return(NULL)
}
xcn = colnames(tab) = c("repo",
"version.stable",
"neuroc_version.stable",
"commit_id.stable",
"version.current",
"neuroc_version.current",
"commit_id.current")
bad_version = is.na(tab$version.stable) | tab$version.stable %in% ""
tab$v = "0.0.0"
tab$v[!bad_version] = package_version(tab$version.stable[!bad_version])
if (nrow(tab) == 0 & !long) {
return(tab)
}
ss = split(tab, tab$repo)
ss = lapply(ss, function(x) {
x = x[ order(x$v, decreasing = TRUE), ]
x = x[1,,drop = FALSE]
x$v = NULL
x
})
tab = do.call("rbind", ss)
tab = as.data.frame(tab, stringsAsFactors = FALSE)
rownames(tab) = NULL
if (long) {
cn = colnames(tab)
varying = cn[ cn != "repo"]
if (nrow(tab) == 0) {
cn = sapply(strsplit(xcn, "[.]"), function(x) x[1])
cn = unique(cn)
tab = matrix(NA, nrow = 0, ncol = length(cn))
tab = data.frame(tab)
colnames(tab) = cn
} else {
tab = reshape(
data = tab, direction = "long",
idvar = "repo", varying = varying,
times = c("current", "stable"), timevar = "release")
}
rownames(tab) = NULL
}
return(tab)
}
#' @title Neuroconductor Packages
#' @description Returns the vector of Neuroconductor packages
#' @return \code{vector} of packages available on Neuroconductor
#' @param ... Arguments passed to \code{\link{neuro_package_table}}
#'
#' @export
#'
#' @examples
#' neuro_packages()
neuro_packages = function(...) {
tab = neuro_package_table(...)
tab = tab$repo
tab = unique(tab)
return(tab)
}
# } else {
# require("neurocInstall")
# pkgs = devtools::session_info()
# pkgs = pkgs$packages
# pkg_ver = pkgs$version[ pkgs$package %in% "neurocInstall"]
# message(paste0("Using neurocInstall version: ", pkg_ver,
# ", using neurocInstall::neurocLite for installation.")
# )
# }
neuroconductor/neurocInstall documentation built on May 19, 2021, 5:24 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# neurocInstall package version: 0.12.0
pkg_ver = '# neurocInstall package version: 0.12.0'
# source("https://bioconductor.org/biocLite.R")
# biocLite(suppressUpdates = TRUE,
# suppressAutoUpdate = TRUE,
# ask = FALSE)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(update = FALSE, ask = FALSE)
# if (!require("neurocInstall")) {
#########################################
# Checking devtools version
#########################################
get_devtools_version = function() {
ipacks = installed.packages()
dtools = ipacks[ ipacks[, "Package"] %in% "devtools", "Version"]
return(dtools)
}
# needed for bioc stuff
req_version = "1.12.0.9000"
dtools = get_devtools_version()
install_from_cran = FALSE
if (length(dtools) == 0 ) {
install_from_cran = TRUE
} else {
# too low of a version
install_from_cran = compareVersion(dtools, req_version) < 0
}
if (install_from_cran) {
install.packages("devtools")
}
# now we assume devtools is installed
dtools = get_devtools_version()
if (length(dtools) == 0 ) {
stop(paste0("devtools tried to install but could not ",
"- try to install devtools manually.",
"Version >= ", req_version, " required."
)
)
} else {
comparison = compareVersion(dtools, "1.12.0.9000")
if (comparison < 0) {
devtools::install_github("r-lib/devtools")
}
}
message(paste("Using neurocLite version:", pkg_ver))
#' @title Neuroconductor Installer
#' @description Install function for neuroconductor packages
#' @param repo Package name in neuroconductor
#' @param release Stable or current (development) versions/branches
#' @param release_repo Repository for release repository, passed to
#' \code{\link{install.packages}}. If \code{release_repo = "github"},
#' then it will install using GitHub. If you set this using
#' \code{\link{make_release_version}} or specify the URL directly,
#' it will override \code{release} option.
#'
#' @param type character, indicating the type of package to download and
#' install, passed to \code{\link{install.packages}}.
#'
#' @param upgrade_dependencies Should dependencies be updated?
#' passed to \code{\link[devtools]{install}} if using
#' \code{release_repo = "github"}
#' @param ... additional arguments passed to
#' \code{\link{install.packages}}
#' or \code{\link[devtools]{install_github}} if
#' \code{release_repo = "github"}
#'
#' @return Result from \code{\link{install.packages}} or
#' \code{\link[devtools]{install_github}}
#'
#' @export
#' @importFrom devtools install_github
#' @importFrom utils read.csv
#' @importFrom utils compareVersion install.packages installed.packages
#'
#' @examples
#' \donttest{
#' tlib = tempfile()
#' dir.create(tlib, showWarnings = FALSE)
#' system.time({
#' install.packages("oro.asl",
#' lib = tlib,
#' repos = "https://neuroconductor.org/releases/2019/12/")
#' })
#' repos = getOption("repos")
#' print(repos)
#' #if (repos["CRAN"] == "@CRAN@") {
#' # repos["CRAN"] = "https://cloud.r-project.org"
#' # options(repos = repos)
#' #}
#' options(repos = NULL)
#' print(getOption("repos"))
#' neuro_install("oro.asl", lib = tlib,
#' release_repo = "https://neuroconductor.org/releases/2019/12")
#' options(repos = repos)
#' }
#' \dontrun{
#' neuro_install("cifti", type = "source", lib = tlib)
#' neuro_install("cifti",
#' release_repo = latest_neuroc_release("stable"),
#' lib = tlib)
#'
#' neuro_install("cifti", release_repo = "github")
#' }
#'
neuro_install = function(
repo,
release = c("stable", "current"),
release_repo = latest_neuroc_release(),
upgrade_dependencies = FALSE,
type = getOption("pkgType"),
...){
#############################
# Create a data.frame for merging
#############################
release = match.arg(release)
l_repo = trimws(tolower(release_repo))
if (!l_repo %in% "github") {
args = list(...)
repos = args$repos
repos = c(Neuroconductor = release_repo,
getOption("repos"),
repos)
args$repos = repos
contriburl = utils::contrib.url(repos, type)
repos = c(Neuroconductor = release_repo,
getOption("repos"),
repos)
repos = repos[ repos != "@CRAN@" ]
if ("contriburl" %in% names(args)) {
args$contriburl = c(contriburl, args$contriburl)
}
repos = repos[!duplicated(repos)]
args$contriburl = unique(args$contriburl)
args$pkgs = repo
# args$repos = repos
args$type = type
x = do.call(utils::install.packages, args = args)
# x = install.packages(pkgs = repo,
# repos = c(Neuroconductor = release_repo,
# getOption("repos")),
# type = type,
#
# ...)
lib.loc = NULL
if (!is.null(args$lib)) {
lib.loc = args$lib
}
not_installed = repo[!repo %in% installed.packages(
lib.loc = lib.loc
)[, "Package"]]
if (length(not_installed) > 0) {
msg = paste0("Package(s): ", paste(not_installed, sep = ", "),
" released binaries/sources were not installed,",
" please try to install with release_repo = \"github\"")
warning(msg)
}
return(invisible(x))
}
df = data.frame(repo = repo, stringsAsFactors = FALSE)
tab = neuro_package_table(long = TRUE)
tab = tab[ tab$release %in% release, ]
## import list of packages
# error if pkg not in list of packages
check_install = df$repo %in% tab$repo
if (!all(check_install)) {
bad_pkgs = df$repo[!check_install]
bad_pkgs = paste(bad_pkgs, collapse = ", ")
message(paste0("Available Packages on neuroconductor are ",
paste(unique(tab$repo), collapse = ", ")))
stop(paste0("Package(s) ", bad_pkgs,
" are not in neuroconductor"))
}
tab = merge(df, tab, by = "repo", all.x = TRUE)
tab$version = numeric_version(tab$version)
# pkg = tab$pkg
# tab$commit_id = tab[, "commit_id"]
tab = split(tab, tab$repo)
tab = lapply(tab, function(x) {
x$version = x[, "version"]
max_version = max(x$version)
x = x[ x$version %in% max_version,, drop = FALSE]
return(x)
})
tab = do.call("rbind", tab)
tab = data.frame(tab, stringsAsFactors = FALSE)
tab$repo = paste0("neuroconductor/", tab$repo, "@", tab$commit_id)
args = list(tab$repo)
gh_func = devtools::install_github
if ("upgrade" %in% methods::formalArgs(gh_func)) {
args$upgrade = upgrade_dependencies
} else {
args$upgrade_dependencies = upgrade_dependencies
}
if (!upgrade_dependencies) {
res = try({
results = do.call(gh_func, args = args)
})
if (is.logical(results)) {
check = any(!results)
} else {
check = FALSE
}
if (inherits(res, "try-error") || check) {
stop("Installation failed, please try with upgrade_dependencies = TRUE")
}
} else {
results = do.call(gh_func, args = args)
}
}
#' @rdname neuro_install
#' @aliases neuroc_install
#' @aliases neuro_install
#' @export
neuroc_install = function(...) {
neuro_install(...)
}
#' @rdname neuro_install
#' @aliases neurocLite
#' @export
neurocLite = function(...) {
neuro_install(...)
}
#' @title Make Full Package Version
#' @description Makes a package version to have all the same length.
#' This is helpful when using \code{\link{compareVersion}}.
#'
#' @param x Character vector of package versions
#'
#' @return Character vector of versions, each with the same length.
#' @export
#'
#' @examples
#' x = c("1.6", "1.6.0")
#' compareVersion(x[1], x[2])
#' x2 = make_full_version(x)
#' compareVersion(x2[1], x2[2])
#' x = c("1.6", "1.6.0")
#' compareVersion(x2[1], x2[2])
make_full_version = function(x) {
nx = names(x)
x = as.character(x)
r <- lapply(strsplit(x, "[.-]"), as.integer)
lx = sapply(r, length)
mlx = max(lx)
r <- lapply(r, function(ver) {
c(ver, rep(0, length = mlx - length(ver)))
})
x = sapply(r, paste, collapse = ".")
names(x) = nx
return(x)
}
#' Latest Neuroconductor Release Location
#'
#' @param secure Should https vs. http be used
#' @param release Stable or current (development) versions
#' @return URL of release page
#' @export
#'
#' @examples
#' make_release_version("2018/02/", check = FALSE)
#' \donttest{
#' latest_neuroc_release()
#' }
latest_neuroc_release = function(secure = TRUE) {
make_release_version(
release_path = NULL,
secure = secure)
}
#' @rdname latest_neuroc_release
#' @export
binary_release_repo = function(
release = c("stable", "current"),
secure = TRUE) {
release = match.arg(release)
release_version = paste0("latest/", release, "/")
release_version = make_release_version(release_version, secure = secure)
return(release_version)
}
#' @rdname latest_neuroc_release
#' @param release_path path to the release on
#' \url{https://neuroconductor.org/releases/}
#' @param check should the `release_path` need to be checked against
#' all the releases?
#' @export
make_release_version = function(release_path = NULL, secure = TRUE,
check = TRUE) {
if (is.null(release_path)) {
check = TRUE
}
if (check) {
df = release_versions()
if (is.null(release_path)) {
release_path = df$release[1]
}
if (!all(release_path %in% df$release)) {
warning(paste0("Release path created, but not in the ",
"Neuroconductor set of releases"))
}
}
release_path = paste0(
"http", ifelse(secure, "s", ""), "://neuroconductor.org/releases/",
release_path)
release_path
}
#' @rdname latest_neuroc_release
#' @importFrom utils download.file
#' @export
release_versions = function(secure = TRUE) {
# read from the page Adi Makes
# currently fail
url = paste0("http", ifelse(secure, "s", ""),
"://neuroconductor.org/api/releases/")
destfile = tempfile(fileext = ".txt")
x = try({
download.file(url = url, destfile = destfile, quiet = TRUE)
}, silent = TRUE)
if (inherits(x, "try-error") || x != 0) {
warning(paste0(
"Releases did not download, may be error with downloading ",
url))
if (requireNamespace("httr", quietly = TRUE)) {
url = sub("https", "http", url)
res = httr::GET(url,
httr::write_disk(path = destfile, overwrite = TRUE),
config = httr::config(ssl_verifypeer = FALSE))
httr::warn_for_status(res)
}
}
releases = readLines(destfile, warn = FALSE)
releases = trimws(releases)
releases = gsub('"', "", releases)
releases = releases[grepl("releases/", releases)]
releases = gsub('"', "", releases)
releases = trimws(releases)
releases = sub(',$', "", releases)
releases = sub("^releases/", "", releases)
ss = t(sapply(strsplit(releases, "/"), rbind))
colnames(ss) = c("year", "month")
df = data.frame(release = releases, stringsAsFactors = FALSE)
df = cbind(df, ss, stringsAsFactors = FALSE)
df = df[ df$year != "latest", , drop = FALSE]
df$year = as.numeric(df$year)
df$date = paste0(df$year, "-", df$month, "-01")
df$date = as.Date(x = df$date, format = "%Y-%m-%d")
df = df[ order(df$date, decreasing = TRUE), , drop = FALSE]
return(df)
}
#' @title Neuroconductor Package Table
#' @description Returns the table of Neuroconductor packages
#' @return \code{data.frame} of packages with commit IDs
#' @param path Path to the table of package
#' @param long Should the data be "long" (with respect to stable/current)
#' @param deployment indicator if this is a release, not standard flag.
#' @export
#'
#' @note Package information is obtained from
#' \url{https://neuroconductor.org/neurocPackages}
#'
#' @importFrom stats reshape
#' @examples
#' neuro_package_table()
neuro_package_table = function(
path = "https://neuroconductor.org/neurocPackages",
long = FALSE,
deployment = FALSE
) {
#############################
## grab list of current neuroc packages
#############################
args = list(file = path,
stringsAsFactors = FALSE, header = TRUE,
na.strings = ifelse(deployment, "NA", ""))
suppressWarnings({
tab = try( {
do.call("read.csv", args)
} , silent = TRUE)
})
if (inherits(tab, "try-error")) {
args$file = gsub("^https", "http", args$file)
suppressWarnings({
tab = try( {
do.call("read.csv", args)
} , silent = TRUE)
})
if (inherits(tab, "try-error")) {
if (requireNamespace("httr", quietly = TRUE)) {
destfile = tempfile()
httr::GET(args$file,
httr::write_disk(path = destfile),
config = httr::config(ssl_verifypeer = FALSE))
args$file = destfile
tab = do.call("read.csv", args)
}
}
}
if (nrow(tab) == 0) {
return(NULL)
}
xcn = colnames(tab) = c("repo",
"version.stable",
"neuroc_version.stable",
"commit_id.stable",
"version.current",
"neuroc_version.current",
"commit_id.current")
bad_version = is.na(tab$version.stable) | tab$version.stable %in% ""
tab$v = "0.0.0"
tab$v[!bad_version] = package_version(tab$version.stable[!bad_version])
if (nrow(tab) == 0 & !long) {
return(tab)
}
ss = split(tab, tab$repo)
ss = lapply(ss, function(x) {
x = x[ order(x$v, decreasing = TRUE), ]
x = x[1,,drop = FALSE]
x$v = NULL
x
})
tab = do.call("rbind", ss)
tab = as.data.frame(tab, stringsAsFactors = FALSE)
rownames(tab) = NULL
if (long) {
cn = colnames(tab)
varying = cn[ cn != "repo"]
if (nrow(tab) == 0) {
cn = sapply(strsplit(xcn, "[.]"), function(x) x[1])
cn = unique(cn)
tab = matrix(NA, nrow = 0, ncol = length(cn))
tab = data.frame(tab)
colnames(tab) = cn
} else {
tab = reshape(
data = tab, direction = "long",
idvar = "repo", varying = varying,
times = c("current", "stable"), timevar = "release")
}
rownames(tab) = NULL
}
return(tab)
}
#' @title Neuroconductor Packages
#' @description Returns the vector of Neuroconductor packages
#' @return \code{vector} of packages available on Neuroconductor
#' @param ... Arguments passed to \code{\link{neuro_package_table}}
#'
#' @export
#'
#' @examples
#' neuro_packages()
neuro_packages = function(...) {
tab = neuro_package_table(...)
tab = tab$repo
tab = unique(tab)
return(tab)
}
# } else {
# require("neurocInstall")
# pkgs = devtools::session_info()
# pkgs = pkgs$packages
# pkg_ver = pkgs$version[ pkgs$package %in% "neurocInstall"]
# message(paste0("Using neurocInstall version: ", pkg_ver,
# ", using neurocInstall::neurocLite for installation.")
# )
# }
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