Nothing
library(cBioPortalData)
denv <- new.env(parent = emptyenv())
setwd("~/gh/cBioPortalData")
load("./data/studiesTable.rda", envir = denv)
studiesTable <- denv[["studiesTable"]]
## PACK BUILD
message("PACK BUILD")
studies <- studiesTable$cancer_study_id
studies <- stats::setNames(studies, studies)
comp_pack <- vector("logical", length(studies))
names(comp_pack) <- studies
err_pack <- vector("character", length(studies))
names(err_pack) <- studies
if (identical(system("hostname"), "supermicro") &&
identical(Sys.getenv("USER"), "mramos")) {
library(BiocParallel)
registered()
params <- MulticoreParam(
workers = 30, stop.on.error = FALSE, progressbar = TRUE
)
res_pack <- bplapply(X = studies, FUN = function(x) {
err <- character(1L)
if (identical(x, "ccrcc_utokyo_2013")) {
comp <- FALSE
} else {
dats <- tryCatch({
cBioPortalData::cBioDataPack(cancer_study_id = x, ask = FALSE)
}, error = function(e) conditionMessage(e))
success <- is(dats, "MultiAssayExperiment")
if (!success)
err <- dats
comp <- success
}
list(comp_pack = comp, err_pack = err)
}, BPPARAM = params)
comp_pack <- vapply(res_pack, `[[`, logical(1L), 1L)
err_pack <- vapply(res_pack, `[[`, character(1L), 2L)
} else {
for (pack_stud in studies) {
message("Working on: ", pack_stud)
## avoid segfault
if (identical(pack_stud, "ccrcc_utokyo_2013")) {
comp_pack[[pack_stud]] <- FALSE
} else {
dats <- tryCatch({
cBioDataPack(cancer_study_id = pack_stud, ask = FALSE)
}, error = function(e) conditionMessage(e))
success <- is(dats, "MultiAssayExperiment")
if (success)
comp_pack[[pack_stud]] <- success
else
err_pack[[pack_stud]] <- dats
}
## try to free up memory
gc()
}
}
err_pack <- Filter(nchar, err_pack)
err_info_pack <- lapply(setNames(nm = unique(err_pack)),
function(x) names(err_pack)[err_pack == x])
# table(err_pack)
save(err_info_pack, file = "inst/extdata/err_info_pack.rda")
denv <- new.env(parent = emptyenv())
data("studiesTable", package = "cBioPortalData", envir = denv)
previous <- denv[["studiesTable"]]
prev <- previous[["pack_build"]]
if (!identical(prev, comp_pack)) {
studiesTable[["pack_build"]] <- comp_pack
usethis::use_data(studiesTable, overwrite = TRUE)
}
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