#  File src/library/tools/R/checktools.R
#  Part of the R package, http://www.R-project.org
#
#  Copyright (C) 2013-2013 The R Core Team
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  A copy of the GNU General Public License is available at
#  http://www.r-project.org/Licenses/

check_packages_in_dir <-
function(dir,
         check_args = character(), check_args_db = list(),
         reverse = NULL,
         check_env = character(),
         xvfb = FALSE,
         Ncpus = getOption("Ncpus", 1L),
         clean = TRUE,
         ...)
{
    owd <- getwd()
    dir <- normalizePath(dir)
    setwd(dir)
    on.exit(setwd(owd))

    pfiles <- Sys.glob("*.tar.gz")
    if(!length(pfiles)) {
        message("no packages to check")
        return(invisible())
    }
    pnames <- sub("_.*", "", pfiles)

    os_type <- .Platform$OS.type

    ## Xvfb usage and options.
    ## We do not use Xvfb on Windows.
    ## Otherwise, if argument 'xvfb' is
    ## * a logical, Xvfb is used only if identical to TRUE;
    ## * something else, then as.character(xvfb) gives the Xvfb options.
    xvfb_options <- "-screen 0 1280x1024x24"
    if(os_type == "windows")
        xvfb <- FALSE
    else if(is.logical(xvfb)) {
        if(!identical(xvfb, TRUE))
            xvfb <- FALSE
    } else {
        xvfb_options <- as.character(xvfb)
        xvfb <- TRUE
    }
    
    curl <- if(os_type == "windows") 
        sprintf("file:///%s", dir)
    else
        sprintf("file://%s", dir)

    libdir <- file.path(dir, "Library")
    dir.create(libdir, showWarnings = FALSE)
    outdir <- file.path(dir, "Outputs")
    dir.create(outdir, showWarnings = FALSE)

    ## Determine packages using fake/no install for checking.
    ## Handle these as follows:
    ## * For packages using '--install=no', forward dependencies do not
    ##   need to installed, and reverse dependencies do not need to be
    ##   checked.
    ## * For packages using '--install=fake', forward dependencies must
    ##   be available for checking, and checking reverse dependencies
    ##   makes sense (e.g, to spot missing Rd xrefs).
    pnames_using_install_no <- character()
    pnames_using_install_fake <- character()
    check_args_db <- as.list(check_args_db)
    if(length(check_args_db) &&
       !is.null(nms <- names(check_args_db))) {
        args <- lapply(check_args_db,
                       function(e)
                       scan(text = e, what = character(), quiet = TRUE))
        pnames_using_install_no <-
            nms[sapply(args, function(e) any(e == "--install=no"))]
        pnames_using_install_fake <-
            nms[sapply(args, function(e) any(e == "--install=fake"))]
    } else {
        ## If check_args_db has no names it is useless.
        ## Perhaps complain?
        check_args_db <- list()
    }

    ## Build a package db from the source packages in the working
    ## directory.
    write_PACKAGES(dir, type = "source")
    
    curls <- c(curl,
               utils::contrib.url(getOption("repos"), type = "source"))
    available <- utils::available.packages(contriburl = curls,
                                           type = "source")

    ## As of c52164, packages with OS_type different from the current
    ## one are *always* checked with '--install=no'.
    ## These packages are also filtered out by default (via the OS_type
    ## filter) from the repository package computations.
    ## Hence move packages in the install=fake list not listed by
    ## available.packages() to the install=no list.
    pnames_using_install_no <-
        c(pnames_using_install_no,
          setdiff(pnames_using_install_fake, available[, "Package"]))
    pnames_using_install_fake <-
        intersect(pnames_using_install_fake, available[, "Package"])
    
    if(!is.null(reverse) && !identical(reverse, FALSE)) {
        ## Determine and download reverse dependencies to be checked as
        ## well.
        
        reverse <- as.list(reverse)
        ## Merge with defaults, using partial name matching.
        defaults <- list(which = c("Depends", "Imports", "LinkingTo"),
                         recursive = FALSE,
                         repos = getOption("repos"))
        pos <- pmatch(names(reverse), names(defaults), nomatch = 0L)
        defaults[pos] <- reverse[pos > 0L]

        rnames <- if(is.list(defaults$which)) {
            ## No recycling of repos for now.
            defaults$recursive <- rep_len(as.list(defaults$recursive),
                                          length(defaults$which))
            unlist(Map(function(w, r)
                       package_dependencies(setdiff(pnames,
                                                    pnames_using_install_no),
                                            available,
                                            which = w,
                                            recursive = r,
                                            reverse = TRUE),
                       defaults$which,
                       defaults$recursive),
                   use.names = FALSE)
        } else {
            package_dependencies(setdiff(pnames,
                                         pnames_using_install_no),
                                 available,
                                 which = defaults$which,
                                 recursive = defaults$recursive,
                                 reverse = TRUE)
        }

        rnames <- intersect(unlist(rnames, use.names = FALSE),
                            available[, "Package"])
        rnames <- setdiff(rnames, pnames)

        pos <- match(rnames, available[, "Package"], nomatch = 0L)
        if(!identical(defaults$repos, getOption("repos"))) {
            pos <- split(pos[pos > 0L], available[pos, "Repository"])
            ## Only want the reverse dependencies for which Repository
            ## is pmatched by contrib.url(defaults$repos).
            nms <- names(pos)
            pos <- unlist(pos[unique(c(outer(defaults$repos, nms,
                                             pmatch, nomatch = 0L)))],
                          use.names = FALSE)
        }
        rnames <- available[pos, "Package"]
        rfiles <- sprintf("%s_%s.tar.gz",
                          rnames,
                          available[pos, "Version"])

        if(length(rfiles)) {
            message("downloading reverse dependencies ...")
            rfurls <- sprintf("%s/%s",
                              available[pos, "Repository"],
                              rfiles)
            for(i in seq_along(rfiles)) {
                message(sprintf("downloading %s ... ", rfiles[i]),
                        appendLF = FALSE)
                status <- if(!utils::download.file(rfurls[i], rfiles[i]))
                    "ok" else "failed"
                message(status)
            }
            message("")
        }

    } else {
        rfiles <- rnames <- character()
    }

    pnames <- c(pnames, rnames)

    ## Install what is needed.

    depends <-
        package_dependencies(pnames, available, which = "most")
    depends <- setdiff(unique(unlist(depends, use.names = FALSE)),
                       unlist(.get_standard_package_names(),
                              use.names = FALSE))

    ## Need to install depends which are not installed or installed but
    ## old.
    libs <- c(libdir, .libPaths())
    installed <- utils::installed.packages(libs)[, "Package"]
    depends <-
        c(setdiff(depends, installed),
          intersect(intersect(depends, installed),
                    utils::old.packages(libs, contriburl = curls)[, "Package"]))
    if(length(depends)) {
        message(paste(strwrap(sprintf("installing dependencies %s",
                                      paste(sQuote(depends),
                                            collapse = ", ")),
                              exdent = 2L),
                      collapse = "\n"))
        ## <NOTE>
        ## Ideally we would capture stdout and stderr in e.g.
        ##   outdir/install_stdout.txt
        ##   outdir/install_stderr.txt
        ## But using several CPUs uses Make to install, which seems to
        ## write to stdout/stderr "directly" ... so using sink() will
        ## not work.  Hence, use 'keep_outputs' to capture "outputs"
        ## (combining install stdout and stderr into one file).
        message("")
        iflags <- as.list(rep.int("--fake",
                                  length(pnames_using_install_fake)))
        names(iflags) <- pnames_using_install_fake
        tmpdir <- tempfile(tmpdir = outdir)
        dir.create(tmpdir)
        utils::install.packages(depends, lib = libdir,
                                contriburl = curls,
                                available = available,
                                dependencies = TRUE,
                                INSTALL_opts = iflags,
                                keep_outputs = tmpdir,
                                Ncpus = Ncpus, 
                                type = "source")
        outfiles <- Sys.glob(file.path(tmpdir, "*.out"))
        file.rename(outfiles,
                    file.path(outdir,
                              sprintf("install_%s",
                                      basename(outfiles))))
        unlink(tmpdir, recursive = TRUE)
        message("")
        ## </NOTE>
    }

    ## Merge check_args and check_args_db into check_args_db used for
    ## checking.
    check_args <- if(is.list(check_args)) {
        c(rep.int(list(check_args[[1L]]), length(pfiles)),
          rep.int(list(check_args[[2L]]), length(rfiles)))
    } else {
        rep.int(list(check_args), length(pnames))
    }
    check_args_db <- check_args_db[pnames]
    check_args_db <- Map(c, check_args, check_args_db)
    names(check_args_db) <- pnames

    check_env <- if(is.list(check_env)) {
        c(rep.int(list(check_env[[1L]]), length(pfiles)),
          rep.int(list(check_env[[2L]]), length(rfiles)))
    } else {
        rep.int(list(check_env), length(pnames))
    }
    ## No user level check_env_db for now.
    check_env_db <- as.list(check_env)
    names(check_env_db) <- pnames

    pfiles <- c(pfiles, rfiles)

    check_package <- function(pfile, args_db = NULL, env_db = NULL) {
        message(sprintf("checking %s ...", pfile))
        pname <- sub("_.*", "", basename(pfile))
        out <- file.path(outdir,
                         sprintf("check_%s_stdout.txt", pname))
        err <- file.path(outdir,
                         sprintf("check_%s_stderr.txt", pname))
        env <- c(check_env_db[[pname]],
                 sprintf("R_LIBS=%s", shQuote(libdir)))
        system.time(system2(file.path(R.home("bin"), "R"),
                            c("CMD",
                              "check",
                              "--timings",
                              args_db[[pname]],
                              pfile),
                            stdout = out,
                            stderr = err,
                            env = env))
    }


    if(xvfb) {
        pid <- start_virtual_X11_fb(xvfb_options)
        on.exit(close_virtual_X11_db(pid), add = TRUE)
    }

    if(Ncpus > 1L) {
        if(os_type != "windows") {
            timings <- parallel::mclapply(pfiles,
                                          check_package,
                                          check_args_db,
                                          check_env_db,
                                          mc.cores = Ncpus)
        } else {
            cl <- parallel::makeCluster(Ncpus)
            timings <- parallel::parLapply(cl,
                                           pfiles,
                                           check_package,
                                           check_args_db,
                                           check_env_db)
            parallel::stopCluster(cl)
        }
    } else {
        timings <- lapply(pfiles,
                          check_package,
                          check_args_db,
                          check_env_db)
    }

    timings <- do.call(rbind, lapply(timings, summary))
    rownames(timings) <- pnames
    write.table(timings, "timings.tab")

    file.rename(sprintf("%s.Rcheck", rnames),
                sprintf("rdepends_%s.Rcheck", rnames))

    if(clean) {
        file.remove(rfiles)
    } else {
        file.rename(rfiles, sprintf("rdepends_%s", rfiles))
    }

    invisible(pfiles)

}

start_virtual_X11_fb <-
function(options)
{
    ## Determine the display number from the options, or the PID of the
    ## current R process (alternatively, could mimic xvfb-run).
    args <- scan(text = options, what = character(), quiet = TRUE)
    ind <- grepl("^:[[:digit:]]+$", args)
    if(any(ind)) {
        num <- args[ind][1L]
    } else {
        num <- paste0(":", Sys.getpid())
        options <- c(num, options)
    }

    dis <- Sys.getenv("DISPLAY", unset = NA)

    ## We need to start Xvfb with the given options and obtain its pid
    ## so that we can terminate it when done checking.
    ## This could be done via
    ##   system2("Xvfb", options, stdout = FALSE, stderr = FALSE,
    ##           wait = FALSE)
    ## and then determine the pid as 
    ##   pid <- scan(text =
    ##               grep(sprintf("Xvfb %s", num),
    ##                    system2("ps", "auxw", stdout = TRUE),
    ##                    value = TRUE,
    ##                    fixed = TRUE),
    ##               what = character(),
    ##               quiet = TRUE)[2L]
    ## A better approach (suggested by BDR) is to create a shell script
    ## containing the call to start Xvfb in the background and display
    ## the pid of this as available in the shell's $! parameter.
    tf <- tempfile()
    on.exit(unlink(tf))
    writeLines(c(paste(c(shQuote("Xvfb"), options, ">/dev/null 2>&1 &"),
                       collapse = " "),
                 "echo ${!}"),
               tf)
    pid <- system2("sh", tf, stdout = TRUE)
    Sys.setenv("DISPLAY" = num)
    
    ## Propagate both pid and original setting of DISPLAY so that the
    ## latter can be restored when Xvfb is closed.
    attr(pid, "display") <- dis
    pid
}

close_virtual_X11_db <-
function(pid)
{
    pskill(pid)
    if(is.na(dis <- attr(pid, "display")))
        Sys.unsetenv("DISPLAY")
    else
        Sys.setenv("DISPLAY" = dis)
}

R_check_outdirs <-
function(dir, all = FALSE)
{
    dir <- normalizePath(dir)
    outdirs <- dir(dir, pattern = "\\.Rcheck")
    if(!all) outdirs <- outdirs[!grepl("^rdepends_", outdirs)]
    file.path(dir, outdirs)
}

summarize_check_packages_in_dir_depends <-
function(dir, all = FALSE)
{
    for(d in R_check_outdirs(dir, all = all)) {
        dfile <- Sys.glob(file.path(d, "00_pkg_src", "*",
                                    "DESCRIPTION"))[1L]
        if(file_test("-f", dfile)) {
            meta <- .read_description(dfile)
            has_depends <- !is.na(meta["Depends"])
            has_imports <- !is.na(meta["Imports"])
            if(has_depends || has_imports) {
                writeLines(c(sprintf("Package: %s",
                                     meta["Package"]),
                             if(has_depends)
                             strwrap(sprintf("Depends: %s",
                                             meta["Depends"]),
                                     indent = 2L,
                                     exdent = 4L),
                             if(has_imports)
                             strwrap(sprintf("Imports: %s",
                                             meta["Imports"]),
                                     indent = 2L,
                                     exdent = 4L)))
            }
        }
    }
}

summarize_check_packages_in_dir_results <-
function(dir, all = TRUE, full = FALSE)
{
    dir <- normalizePath(dir)
    outdirs <- R_check_outdirs(dir, all = all)
    ## Re-arrange to have reverse dependencies last.
    ind <- grepl("^rdepends_", basename(outdirs))
    outdirs <- c(outdirs[!ind], outdirs[ind])
    logs <- file.path(outdirs, "00check.log")
    logs <- logs[file_test("-f", logs)]
    
    results <- check_packages_in_dir_results(logs = logs)

    Map(function(p, r) {
        writeLines(c(sprintf("%s ... %s", p, r$status), r$lines))
    },
        names(results),
        results)

    if(full &&
       !all(as.character(unlist(lapply(results, `[[`, "status"))) ==
            "OK")) {
        writeLines("")
        details <- check_packages_in_dir_details(logs = logs)
        flags <- details$Flags
        out <- cbind(sprintf("Package: %s %s",
                             details$Package, details$Version),
                     ifelse(nzchar(flags),
                            sprintf("Flags: %s\n", flags),
                            ""),
                     sprintf("Check: %s, Result: %s",
                             details$Check, details$Status),
                     c(gsub("\n", "\n  ", details$Output,
                            perl = TRUE, useBytes = TRUE)))
        cat(t(out), sep = c("\n", "", "\n  ", "\n\n"))
    }

    invisible()
}

summarize_check_packages_in_dir_timings <-
function(dir, all = FALSE, full = FALSE)
{
    dir <- normalizePath(dir)
    tfile <- file.path(dir, "timings.tab")
    if(file_test("-f", tfile)) {
        timings <- utils::read.table(tfile)
        ## Should we store the information about reverse dependencies in
        ## some place (rather than rely on the naming convention)?
        if(!all) {
            rdepends <- Sys.glob(file.path(dir, "rdepends_*.Rcheck"))
            timings <- timings[is.na(match(rownames(timings),
                                           sub("rdepends_(.*).Rcheck",
                                               "\\1",
                                               basename(rdepends)))),
                               ]
        }
        print(timings)
    }
    if(full) {
        tfiles <- Sys.glob(file.path(R_check_outdirs(dir, all = all),
                                     "*-Ex.timings"))
        if(length(tfiles)) message("")
        timings <- lapply(tfiles, read.table, header = TRUE)
        ## Order by CPU time.
        timings <- lapply(timings,
                          function(x)
                          x[order(x$user, decreasing = TRUE), ])
        ## This looks silly, but we want a common alignment.
        timings <- split(as.data.frame(lapply(do.call(rbind, timings),
                                              format)),
                         rep.int(sub("\\.Rcheck$", "",
                                     basename(dirname(tfiles))),
                                 sapply(timings, nrow)))
        invisible(Map(function(x, y) {
            writeLines(sprintf("Example timings for package '%s':", x))
            cat(rbind(" ", t(as.matrix(y))),
                sep = c(" ", " ", " ", " ", "\n"))
        },
                      names(timings), timings))
    }
}

read_check_log <-
function(log)
{
    lines <- readLines(log, warn = FALSE)

    ## Drop CRAN check status footer.
    ## Ideally, we would have a more general mechanism to detect footer
    ## information to be skipped (e.g., a line consisting of a single
    ## non-printing control character?)
    pos <- grep("^Current CRAN status:", lines,
                perl = TRUE, useBytes = TRUE)
    if(length(pos) && lines[pos <- (pos[1L] - 1L)] == "") {
        lines <- lines[seq_len(pos - 1L)]
    }

    lines
}


check_packages_in_dir_results <-
function(dir, logs = NULL)
{
    if(is.null(logs))
        logs <- Sys.glob(file.path(dir, "*.Rcheck", "00check.log"))

    results <- lapply(logs, function(log) {
        lines <- read_check_log(log)
        m <- regexpr("^\\*.*\\.\\.\\. *(\\[.*\\])? *(NOTE|WARN|ERROR)", 
                     lines, perl = TRUE, useBytes = TRUE)
        ind <- (m > 0L)
        status <- if(any(ind)) {
            if(all(grepl("NOTE$", regmatches(lines, m), useBytes = TRUE))) {
                "NOTE"
            } else {
                "PROBLEM"
            }
        } else {
            "OK"
        }
        list(status = status, lines = lines[ind])
    })
    names(results) <- sub("\\.Rcheck$", "", basename(dirname(logs)))

    results
}

analyze_check_log <-
function(log, drop_ok = TRUE)
{
    make_results <- function(package, version, flags, chunks)
        list(Package = package, Version = version,
             Flags = flags, Chunks = chunks)

    ## Alternatives for left and right quotes.
    lqa <- "'|\xe2\x80\x98"
    rqa <- "'|\xe2\x80\x99"
    ## Group when used ...

    drop_ok_status_tags <- c("OK", "NONE", "SKIPPED")

    ## Start by reading in.
    lines <- read_check_log(log)

    ## Re-encode to UTF-8 using the session charset info.
    ## All regexp computations will be done using perl = TRUE and
    ## useBytes = TRUE.
    re <- "^\\* using session charset: "
    pos <- grep(re, lines, perl = TRUE, useBytes = TRUE)
    if(length(pos)) {
        enc <- sub(re, "", lines[pos[1L]])
        lines <- iconv(lines, enc, "UTF-8", sub = "byte")
        ## If the check log uses ASCII, there should be no non-ASCII
        ## characters in the message lines: could check for this.
    } else return()

    ## Get header.
    re <- sprintf("^\\* this is package (%s)(.*)(%s) version (%s)(.*)(%s)$",
                  lqa, rqa, lqa, rqa)
    pos <- grep(re, lines, perl = TRUE, useBytes = TRUE)
    if(length(pos)) {
        pos <- pos[1L]
        txt <- lines[pos]
        package <- sub(re, "\\2", txt, perl = TRUE, useBytes = TRUE)
        version <- sub(re, "\\5", txt, perl = TRUE, useBytes = TRUE)
        header <- lines[seq_len(pos - 1L)]
        lines <- lines[-seq_len(pos)]
        ## Get check options from header.
        re <- sprintf("^\\* using options? (%s)(.*)(%s)$", lqa, rqa)
        flags <- if(length(pos <- grep(re, header,
                                       perl = TRUE, useBytes = TRUE))) {
            sub(re, "\\2", header[pos[1L]],
                perl = TRUE, useBytes = TRUE)
        } else ""
    } else return()

    ## Get footer.
    ## Some check systems explicitly record the elapsed time in the
    ## last line:
    len <- length(lines)
    if(grepl("^\\* elapsed time ", lines[len],
             perl = TRUE, useBytes = TRUE)) {
        lines <- lines[-len]
        len <- len - 1L
    }
    num <- length(grep("^(NOTE|WARNING): There",
                       lines[c(len - 1L, len)]))
    if(num > 0L) {
        pos <- seq.int(len - num + 1L, len)
        lines <- lines[-pos]
    }

    analyze_lines <- function(lines) {
        ## We might still have
        ##   * package encoding:
        ## entries for packages declaring a package encoding.
        ## Hopefully all other log entries we still have are
        ##   * checking
        ##   * creating
        ## ones ... apparently, with the exception of
        ##   ** running examples for arch
        ##   ** running tests for arch
        ## So let's drop everything up to the first such entry.
        re <- "^\\*\\*? ((checking|creating|running examples for arch|running tests for arch) .*) \\.\\.\\.( (\\[[^ ]*\\]))? (.*)$"
        ind <- grepl(re, lines, perl = TRUE, useBytes = TRUE)
        csi <- cumsum(ind)
        ind <- (csi > 0)
        chunks <- 
            lapply(split(lines[ind], csi[ind]),
                   function(s) {
                       ## Note that setting
                       ##   _R_CHECK_TEST_TIMING_=yes
                       ##   _R_CHECK_VIGNETTE_TIMING_=yes
                       ## will result in a different chunk format ...
                       line <- s[1L]
                       list(check =
                            sub(re, "\\1", line, perl = TRUE, useBytes = TRUE),
                            status =
                            sub(re, "\\5", line, perl = TRUE, useBytes = TRUE),
                            output = paste(s[-1L], collapse = "\n"))
                   })

        status <- vapply(chunks, `[[`, "", "status")
        if(identical(drop_ok, TRUE) ||
           (is.na(drop_ok) && all(status != "ERROR")))
            chunks <- chunks[is.na(match(status, drop_ok_status_tags))]
        
        chunks
    }

    chunks <- analyze_lines(lines)
    if(!length(chunks) && is.na(drop_ok)) {
        chunks <- list(list(check = "*", status = "OK", output = ""))
    }

    make_results(package, version, flags, chunks)
}

check_packages_in_dir_details <-
function(dir, logs = NULL, drop_ok = TRUE)
{
    ## Build a data frame with columns
    ##   Package Version Check Status Output Flags
    ## and some optimizations (in particular, Check Status Flags can be
    ## factors).

    db_from_logs <- function(logs, drop_ok) {
        out <- lapply(logs, analyze_check_log, drop_ok)
        out <- out[sapply(out, length) > 0L]
        if(!length(out))
            return(matrix(character(), ncol = 6L))
        chunks <- lapply(out, `[[`, "Chunks")
        package <- sapply(out, `[[`, "Package")
        lens <- sapply(chunks, length)
        cbind(rep.int(package, lens),
              rep.int(sapply(out, `[[`, "Version"), lens),
              matrix(as.character(unlist(chunks)), ncol = 3L,
                     byrow = TRUE),
              rep.int(sapply(out, `[[`, "Flags"),
                      lens))
    }

    if(is.null(logs))
        logs <- Sys.glob(file.path(dir, "*.Rcheck", "00check.log"))

    db <- db_from_logs(logs, drop_ok)
    colnames(db) <- c("Package", "Version", "Check", "Status",
                      "Output", "Flags")

    ## Now some cleanups.
    
    ## Alternatives for left and right quotes.
    lqa <- "'|\xe2\x80\x98"
    rqa <- "'|\xe2\x80\x99"
    ## Group when used ...

    mysub <- function(p, r, x) sub(p, r, x, perl = TRUE, useBytes = TRUE)
    
    checks <- db[, "Check"]
    checks <- mysub(sprintf("checking whether package (%s).*(%s) can be installed",
                            lqa, rqa),
                    "checking whether package can be installed", checks)
    checks <- mysub("creating .*-Ex.R",
                    "checking examples creation", checks)
    checks <- mysub("creating .*-manual\\.tex",
                    "checking manual creation", checks)
    checks <- mysub("checking .*-manual\\.tex", "checking manual", checks)
    checks <- mysub(sprintf("checking package vignettes in (%s)inst/doc(%s)",
                            lqa, rqa),
                    "checking package vignettes", checks)
    checks <- mysub("^checking *", "", checks)
    db[, "Check"] <- checks
    ## In fact, for tabulation purposes it would even be more convenient
    ## to shorten the check names ...
    
    db[, "Output"] <- mysub("[[:space:]]+$", "", db[, "Output"])
    
    db <- as.data.frame(db, stringsAsFactors = FALSE)
    db$Check <- as.factor(db$Check)
    db$Status <- as.factor(db$Status)

    db
}