#' helper function for extracting BiocCheck outputs
#' @param bcclist list of outputs of BiocCheck::BiocCheck
#' @examples
#' data(demo_bcchk_out)
#' bl = bcclist_to_dataframes(demo_bcchk_out)
#' sapply(bl, dim)
#' @export
bcclist_to_dataframes = function(bcclist) {
nms = names(bcclist)
allerrs = lapply(bcclist, "[[", "errors")
erlens = vapply(allerrs, nrow, integer(1))
allwrn = lapply(bcclist, "[[", "warnings")
warens = vapply(allwrn, nrow, integer(1))
ernms = rep(nms,erlens)
wrnms = rep(nms,warens)
errdf = do.call(rbind, allerrs)
wrndf = do.call(rbind, allwrn)
colnames(errdf)[1:2] = c("type", "message")
colnames(wrndf)[1:2] = c("type", "message")
errors = data.frame(package=ernms, type=errdf$type, message=errdf$message,
commit_date=errdf$commit_date, check_date = errdf$check_date, version=errdf$version)
warnings = data.frame(package=wrnms, type=wrndf$type, message=wrndf$message,
commit_date=wrndf$commit_date, check_date = wrndf$check_date, version=wrndf$version)
list(errors=errors, warnings=warnings)
}
#' use outputs of get_checks and get_bcc to build a database of all events of error or warning
#' @param dbname character(1) a sqlite database name
#' @param rcmdcheck_obj_dir character(1) path to a collection of rcmdcheck outputs
#' @param bccheck_obj_dir character(1) path to a collection of bco2df outputs, produced after running
#' BiocCheck on sources
#' @param exists_ok logical(1) passed to `status_db_init`
#' @export
build_sqlite_db = function( dbname = "chks.sqlite", rcmdcheck_obj_dir, bccheck_obj_dir,
exists_ok = FALSE ) {
allrcc = lapply(dir(rcmdcheck_obj_dir, full.names=TRUE), readRDS)
bad = vapply(allrcc, function(x) inherits(x, "try-error"), logical(1))
if (sum(bad)>0) allrcc = allrcc[-which(bad)]
rcc_dfs = rcclist_to_dataframes(allrcc)
status_db_init(dbname, rcc_dfs, exists_ok=exists_ok)
allbcc = lapply(dir(bccheck_obj_dir, full.names=TRUE), readRDS)
nms = gsub("_.*", "", dir(bccheck_obj_dir))
bad = vapply(allbcc, function(x) inherits(x, "try-error"), logical(1))
if (sum(bad)>0) {
allbcc = allbcc[-which(bad)]
nms = nms[-which(bad)]
}
names(allbcc) = nms
aa = bcclist_to_dataframes(allbcc)
update_status_db(dbname, "BcChkERR", newdf=aa$errors)
update_status_db(dbname, "BcChkWARN", newdf=aa$warnings)
}
#rcmdcheck_obj_dir = "./chks316"
#bccheck_obj_dir = "./bcobj"
#
#build_sqlite_db( "newchk2.sqlite", rcmdcheck_obj_dir = rcmdcheck_obj_dir,
# bccheck_obj_dir = bccheck_obj_dir , exists_ok = TRUE)
make_df_component = function(rcclist, component="notes") {
pks = sapply(rcclist, "[[", "package")
nol = lapply(rcclist, "[[", component)
date_commit = vapply(rcclist, function(x) {
date_string(attr(x, "last_commit_date")) }, character(1))
date_check = vapply(rcclist, function(x) {
date_string(attr(x, "check_date")) }, character(1))
pkv = vapply(rcclist, function(x) {
attr(x, "pkgversion") }, character(1))
if (component == "description") {
nol = lapply(nol, function(x) strsplit(x, "\n")[[1]])
}
nn = sapply(nol,length)
zn = which(nn==0)
if (length(zn)>0)
nol[zn] = paste0("NO ", toupper(component))
nls = sapply(nol, length)
npk = rep(pks, nls)
ndcom = rep(date_commit, nls)
ndche = rep(date_check, nls)
ndpkv = rep(pkv, nls)
ans = data.frame(package=npk, tmp=unlist(nol), date_commit=ndcom, date_check=ndche, version=ndpkv, stringsAsFactors=FALSE)
names(ans)[2] = component
ans
}
date_string = function(x) as.character(as.Date(x, origin="1970-01-01"))
#' produce list of data.frames for storage of R CMD check results in SQLite
#' @param rcclist list of results of rcmdcheck::rcmdcheck
#' @examples
#' data(demo_rcmdcheck_out)
#' dfs = rcclist_to_dataframes(demo_rcmdcheck_out)
#' names(dfs)
#' @export
rcclist_to_dataframes = function(rcclist) {
pks = vapply(rcclist, function(x) x$package, character(1))
vers = vapply(rcclist, function(x) x$version, character(1)) # might need to coerce Nov 4 2022
notes_df = make_df_component(rcclist, component="notes")
err_df = make_df_component(rcclist, component="errors")
warn_df = make_df_component(rcclist, component="warnings")
inst_df = make_df_component(rcclist, component="install_out")
desc_df = make_df_component(rcclist, component="description")
date_commit = vapply(rcclist, function(x) {
date_string(attr(x, "last_commit_date")) }, character(1))
date_check = vapply(rcclist, function(x) {
date_string(attr(x, "check_date")) }, character(1))
pkv = vapply(rcclist, function(x) {
attr(x, "pkgversion") }, character(1))
list(basic = data.frame(package=pks, version=vers, date_commit=date_commit,
date_check=date_check, version=pkv, stringsAsFactors=FALSE),
notes = notes_df, warnings=warn_df, errors=err_df, inst=inst_df, desc=desc_df)
}
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