R/makePkgSourceDir-methods.R

In switchr: Installing, Managing, and Switching Between Distinct Sets of Installed Packages

# setMethod('makePkgSourceDir', c(name = 'ANY', source = 'SVNSource'),
# function(name, source, path, repo) {
##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,SVNSource
##' @return logical scalar indicating success (\code{TRUE}) or failure of
##' the operation.
setMethod("makePkgDir", c(name = "ANY", source = "SVNSource"), function(name, source,
    path, latest_only = FALSE, param, forceRefresh = FALSE) {
    lfun = logfun(param)
    if (!file.exists(path))
        dir.create(path, recursive = TRUE)
    oldwd = setwd(path)
    on.exit(setwd(oldwd))
    if (missing(name))
        name = basename(location(source))

    opts = character()
    if (length(source@user) && nchar(source@user))
        opts = paste0(opts, " --username=", source@user)
    if (length(source@password) && nchar(source@password))
        opts = paste0(opts, " --password=", source@password)

    # did we already check it out?
    if (file.exists(name) && file.exists(name, ".svn") && !forceRefresh) {
        lfun(name, "Existing temporary checkout found at this location. Updating")
        up = updateSVN(file.path(path, name), source, param = param)
    } else {
        ## clean up the directory if it was created from some other type of source
        if (file.exists(name))
            unlink(name, recursive = TRUE)
        cmd = "svn"
        args = c("co", location(source), name, opts)
        lfun(name, paste("Attempting to create temporary source", "directory from SVN repo",
            location(source), "(branch", source@branch, "; cmd", cmd, ")"))
        out = tryCatch(system_w_init(cmd, args = args, param = param), error = function(x) x)
        if (is(out, "error")) {
            msg = c(paste("Temporary SVN checkout failed. cmd:", cmd), out$message)
            logfun(param)(name, msg, type = "error")
            return(FALSE)
        }
    }
    rtdir = file.path(path, name)

    ret = !is.null(findPkgDir(rtdir, branch(source), source@subdir, param = param))

    # success log
    if (ret) {
        logfun(param)(name, paste("Temporary source directory successfully created:",
            ret))
    }
    ret
})

##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,GithubSource
##' @importFrom utils unzip
setMethod("makePkgDir", c(name = "ANY", source = "GithubSource"), function(name,
    source, path, latest_only = FALSE, param, forceRefresh = FALSE) {
    if (latest_only) {
        ## https://github.com/gmbecker/ProteinVis/archive/IndelsOverlay.zip for
        ## IndelsOverlay branch

        reponm = gsub("\\.git", "", location(source))
        reponm = gsub(".*/([^/]+)/{0,1}$", "\\1", reponm)
        zipUrl = paste(gsub("\\.git", "", location(source)), "/archive/", branch(source),
            ".zip", sep = "")
        zipUrl = gsub("git://", "http://", zipUrl, fixed = TRUE)
        zpfile = normalizePath(file.path(path, paste(name, "-", branch(source), ".zip",
            sep = "")))
        if (!file.exists(zpfile) || forceRefresh)
            success = download.file2(zipUrl, zpfile) else success = 0
        if (success > 0)
            stop("Unable to get package zip file from git")
        destdir = file.path(path, name)
        if (file.exists(destdir))
            unlink(destdir, recursive = TRUE)
        unzip(zpfile, exdir = path)
        file.rename(file.path(path, paste(reponm, branch(source), sep = "-")), destdir)
        # uzdir
    } else {
        # source = as(source, 'GitSource', strict = TRUE) makePkgDir(name, source, path,
        # latest_only, param = param, forceRefresh)
        callNextMethod()
    }
})

# setMethod('makePkgSourceDir', c(name = 'ANY', source = 'GitSource'),
# function(name, source, path, repo) {
##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,GitSource
setMethod("makePkgDir", c(name = "ANY", source = "GitSource"), function(name, source,
    path, latest_only = FALSE, param, forceRefresh = FALSE) {

    if (!file.exists(path))
        dir.create(path, recursive = TRUE)
    oldwd = setwd(path)
    if (!is.null(oldwd))
        on.exit(setwd(oldwd)) else warning("working directory returned as NULL, unable to reset it after creating pkg directory")
    sdir = location(source)
    if (file.exists(name) && file.exists(file.path(name, ".git"))
        && file.exists(file.path(name, source@subdir, "DESCRIPTION"))) {
        logfun(param)(name, "Existing temporary checkout found at this location. Updating")
        up = updateGit(file.path(path, name), source, param = param)
    } else {
        if (file.exists(name)) {
            logfun(param)(name, ".git dir & DESCRIPTION file missing. Deleting src dir")
            unlink(name, recursive = TRUE)
        }
        if (latest_only && (is.na(source@branch) || source@branch == "master")) {
            logfun(param)(name, "Cloning only latest commit for package")
            args = c("clone --depth 1", sdir, name)
        } else {
            args = c("clone", sdir, name)
        }
        res = tryCatch(system_w_init("git", args = args, intern = TRUE, param = param),
            error = function(x) x)
        if (is(res, "error") || (!is.null(attr(res, "status")) && attr(res, "status") >
            0)) {
            logfun(param)(name, paste("Failed to clone package source using", "git command with arguments:",
                args), type = "both")
            logfun(param)(name, res, type = "error")
            return(FALSE)
        }
        medwd = setwd(name)

        args2 = c("checkout", branch(source))
        res2 = tryCatch(system_w_init("git", args = args2, intern = TRUE, param = param),
            error = function(e) e)
        setwd(medwd)
        if (is(res, "error") || (!is.null(attr(res, "status")) && attr(res, "status") >
            0)) {
            logfun(param)(name, paste("Failed to check out package source", "using git command with arguments:",
                args2), type = "both")
            logfun(param)(name, res, type = "error")
            return(FALSE)
        }

        logfun(param)(name, paste0("Successfully checked out package source from ",
            sdir, " on branch ", branch(source)))
    }
    rtdir = file.path(path, name)
    ret = file.exists(rtdir)
    # success log
    if (ret) {
        logfun(param)(name, paste("Temporary source directory successfully created:",
            ret))
    }

    ret
})
## stub for everyone else
##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,ANY
setMethod("makePkgDir", c(name = "ANY", source = "ANY"), function(name, source, path,
    latest_only, param, forceRefresh = FALSE) {
    warning("Source type not supported yet.")
    FALSE
})
##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,CRANSource
##' @importFrom utils untar download.packages
setMethod("makePkgDir", c(name = "ANY", source = "CRANSource"), function(name, source,
    path, latest_only, param, forceRefresh = FALSE) {

    if (!file.exists(file.path(path, name)))
        dir.create(file.path(path, name), recursive = TRUE)

    pkg = download.packages2(name, destdir = path)[, 2]
    untar(pkg, exdir = path)
    TRUE

})

##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,BiocSource

setMethod("makePkgDir", c(name = "ANY", source = "BiocSource"), function(name, source,
    path, latest_only, param, forceRefresh = FALSE) {
    repos = biocBaseRepos()
    if (!file.exists(file.path(path, name)))
        dir.create(file.path(path, name), recursive = TRUE)

    pkg = download.packages2(name, destdir = path, repos = repos)[,
        2]
    untar(pkg, exdir = path)
    return(TRUE)


})

##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,TarballSource

setMethod("makePkgDir", c(name = "ANY", source = "TarballSource"), function(name,
    source, path, latest_only, param, forceRefresh = FALSE) {
    loc = location(source)
    if (grepl("://", loc)) {
        destfile = file.path(path, basename(loc))
        download.file2(loc, destfile = destfile)
        loc = destfile
    }
    untar(loc, exdir = path)
    file.exists(file.path(path, name))

})





##'@rdname makePkgDir
##' @aliases makePkgDir,ANY,LocalSource

setMethod("makePkgDir", c(name = "ANY", source = "LocalSource"), function(name, source,
    path, latest_only, param, forceRefresh = FALSE) {

    if (file.exists(file.path(path, name)))
        unlink(file.path(path, name), recursive = TRUE, force = TRUE)
    if (!file.exists(path))
        dir.create(path, recursive = TRUE)
    oldwd = setwd(path)
    on.exit(setwd(oldwd))

    if (missing(name))
        name = basename(location(source))
    if (file.exists(file.path(path, name)))
        unlink(file.path(path, name), recursive = TRUE, force = TRUE)
    logfun(param)(name, "Copying local source directory into temporary checkout directory.")

    # ok= file.copy(location(source), file.path(path, name), recursive = TRUE)
    ok = file.copy(normalizePath2(location(source)), file.path(path), recursive = TRUE)
    if (basename(location(source)) != name) {
        logfun(param)(name, "Renamed copied directory to package name.")
        ok = file.rename(file.path(path, basename(location(source))), file.path(path,
            name))
    }
    ret = normalizePath2(file.path(path, name, source@subdir))

    # success log
    if (ok) {
        logfun(param)(name,
               paste("Temporary source directory successfully created:", ret))
    }
    ok

})