CPTAC STAR - Counts download ERROR

query <- GDCquery(
  project = "CPTAC-3",
  data.category = "Transcriptome Profiling",
  data.type = "Gene Expression Quantification",
    workflow.type = "STAR - Counts"
)
GDCdownload(query)
data <- GDCprepare(query)

o GDCquery: Searching in GDC database

--------------------------------------

Genome of reference: hg38

--------------------------------------------

oo Accessing GDC. This might take a while...

--------------------------------------------

ooo Project: CPTAC-3

--------------------

oo Filtering results

--------------------

ooo By data.type

ooo By workflow.type

----------------

oo Checking data

----------------

ooo Check if there are duplicated cases

ooo Check if there results for the query

-------------------

o Preparing output

-------------------

Downloading data for project CPTAC-3

GDCdownload will download 1275 files. A total of 5.398445768 GB

The total size of files is big. We will download files in chunks

Downloading chunk 1 of 6 (236 files, size = 999.218003 MB) as Wed_Apr_20_10_21_48_2022_0.tar.gz

Downloading: 270 MB       
Downloading chunk 2 of 6 (236 files, size = 999.227677 MB) as Wed_Apr_20_10_21_48_2022_1.tar.gz

Downloading: 270 MB     
Downloading chunk 3 of 6 (236 files, size = 999.278538 MB) as Wed_Apr_20_10_21_48_2022_2.tar.gz

Downloading: 270 MB     
Downloading chunk 4 of 6 (236 files, size = 999.261156 MB) as Wed_Apr_20_10_21_48_2022_3.tar.gz

Downloading: 270 MB     
Downloading chunk 5 of 6 (236 files, size = 999.215084 MB) as Wed_Apr_20_10_21_48_2022_4.tar.gz

Downloading: 270 MB     
Downloading chunk 6 of 6 (95 files, size = 402.24531 MB) as Wed_Apr_20_10_21_48_2022_5.tar.gz

|====================================================|100%                      Completed after 3 m 
Error: Can't subset columns that don't exist.
x Locations 2, 3, and 4 don't exist.
i There are only 1 column.
Traceback:

1. GDCprepare(query)
2. readTranscriptomeProfiling(files = files, data.type = ifelse(!is.na(query$data.type), 
 .     as.character(query$data.type), unique(query$results[[1]]$data_type)), 
 .     workflow.type = unique(query$results[[1]]$analysis_workflow_type), 
 .     cases = cases, summarizedExperiment)
3. suppressMessages({
 .     df <- x %>% map_dfc(.f = function(y) y[, 2:4])
 .     df <- bind_cols(x[[1]][, 1], df)
 . })
4. withCallingHandlers(expr, message = function(c) if (inherits(c, 
 .     classes)) tryInvokeRestart("muffleMessage"))
5. x %>% map_dfc(.f = function(y) y[, 2:4])
6. map_dfc(., .f = function(y) y[, 2:4])
7. map(.x, .f, ...)
8. .f(.x[[i]], ...)
9. y[, 2:4]
10. `[.spec_tbl_df`(y, , 2:4)
11. NextMethod(`[`)
12. `[.tbl_df`(y, , 2:4)
13. vectbl_as_col_location(j, length(x), names(x), j_arg = j_arg, 
  .     assign = FALSE)
14. subclass_col_index_errors(vec_as_location(j, n, names), j_arg = j_arg, 
  .     assign = assign)
15. withCallingHandlers(expr, vctrs_error_subscript = function(cnd) {
  .     cnd$subscript_arg <- j_arg
  .     cnd$subscript_elt <- "column"
  .     if (isTRUE(assign) && !isTRUE(cnd$subscript_action %in% c("negate"))) {
  .         cnd$subscript_action <- "assign"
  .     }
  .     cnd_signal(cnd)
  . })
16. vec_as_location(j, n, names)
17. (function () 
  . stop_subscript_oob(i = i, subscript_type = subscript_type, size = size, 
  .     subscript_action = subscript_action, subscript_arg = subscript_arg))()
18. stop_subscript_oob(i = i, subscript_type = subscript_type, size = size, 
  .     subscript_action = subscript_action, subscript_arg = subscript_arg)
19. stop_subscript(class = "vctrs_error_subscript_oob", i = i, subscript_type = subscript_type, 
  .     ...)
20. abort(class = c(class, "vctrs_error_subscript"), i = i, ...)
21. signal_abort(cnd)
22. signalCondition(cnd)
23. (function (cnd) 
  . {
  .     cnd$subscript_arg <- j_arg
  .     cnd$subscript_elt <- "column"
  .     if (isTRUE(assign) && !isTRUE(cnd$subscript_action %in% c("negate"))) {
  .         cnd$subscript_action <- "assign"
  .     }
  .     cnd_signal(cnd)
  . })(structure(list(message = "", trace = structure(list(calls = list(
  .     IRkernel::main(), kernel$run(), IRkernel:::handle_shell(), 
  .     executor$execute(msg), base::tryCatch(evaluate(request$content$code, 
  .         envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L), 
  .         interrupt = function(cond) {
  .             log_debug("Interrupt during execution")
  .             interrupted <<- TRUE
  .         }, error = .self$handle_error), base:::tryCatchList(expr, 
  .         classes, parentenv, handlers), base:::tryCatchOne(tryCatchList(expr, 
  .         names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, 
  .         handlers[[nh]]), base:::doTryCatch(return(expr), name, 
  .         parentenv, handler), base:::tryCatchList(expr, names[-nh], 
  .         parentenv, handlers[-nh]), base:::tryCatchOne(expr, names, 
  .         parentenv, handlers[[1L]]), base:::doTryCatch(return(expr), 
  .         name, parentenv, handler), evaluate::evaluate(request$content$code, 
  .         envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L), 
  .     evaluate:::evaluate_call(expr, parsed$src[[i]], envir = envir, 
  .         enclos = enclos, debug = debug, last = i == length(out), 
  .         use_try = stop_on_error != 2L, keep_warning = keep_warning, 
  .         keep_message = keep_message, output_handler = output_handler, 
  .         include_timing = include_timing), evaluate:::timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
  .         envir, enclos)), warning = wHandler, error = eHandler, 
  .         message = mHandler))), evaluate:::handle(ev <- withCallingHandlers(withVisible(eval(expr, 
  .         envir, enclos)), warning = wHandler, error = eHandler, 
  .         message = mHandler)), base::try(f, silent = TRUE), base::tryCatch(expr, 
  .         error = function(e) {
  .             call <- conditionCall(e)
  .             if (!is.null(call)) {
  .                 if (identical(call[[1L]], quote(doTryCatch))) 
  .                   call <- sys.call(-4L)
  .                 dcall <- deparse(call)[1L]
  .                 prefix <- paste("Error in", dcall, ": ")
  .                 LONG <- 75L
  .                 sm <- strsplit(conditionMessage(e), "\n")[[1L]]
  .                 w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], 
  .                   type = "w")
  .                 if (is.na(w)) 
  .                   w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
  .                     type = "b")
  .                 if (w > LONG) 
  .                   prefix <- paste0(prefix, "\n  ")
  .             }
  .             else prefix <- "Error : "
  .             msg <- paste0(prefix, conditionMessage(e), "\n")
  .             .Internal(seterrmessage(msg[1L]))
  .             if (!silent && isTRUE(getOption("show.error.messages"))) {
  .                 cat(msg, file = outFile)
  .                 .Internal(printDeferredWarnings())
  .             }
  .             invisible(structure(msg, class = "try-error", condition = e))
  .         }), base:::tryCatchList(expr, classes, parentenv, handlers), 
  .     base:::tryCatchOne(expr, names, parentenv, handlers[[1L]]), 
  .     base:::doTryCatch(return(expr), name, parentenv, handler), 
  .     base::withCallingHandlers(withVisible(eval(expr, envir, enclos)), 
  .         warning = wHandler, error = eHandler, message = mHandler), 
  .     base::withVisible(eval(expr, envir, enclos)), base::eval(expr, 
  .         envir, enclos), base::eval(expr, envir, enclos), TCGAbiolinks::GDCprepare(query), 
  .     TCGAbiolinks:::readTranscriptomeProfiling(files = files, 
  .         data.type = ifelse(!is.na(query$data.type), as.character(query$data.type), 
  .             unique(query$results[[1]]$data_type)), workflow.type = unique(query$results[[1]]$analysis_workflow_type), 
  .         cases = cases, summarizedExperiment), base::suppressMessages({
  .         df <- x %>% map_dfc(.f = function(y) y[, 2:4])
  .         df <- bind_cols(x[[1]][, 1], df)
  .     }), base::withCallingHandlers(expr, message = function(c) if (inherits(c, 
  .         classes)) tryInvokeRestart("muffleMessage")), x %>% map_dfc(.f = function(y) y[, 
  .         2:4]), purrr::map_dfc(., .f = function(y) y[, 2:4]), 
  .     purrr::map(.x, .f, ...), TCGAbiolinks:::.f(.x[[i]], ...), 
  .     y[, 2:4], readr:::`[.spec_tbl_df`(y, , 2:4), base::NextMethod(`[`), 
  .     tibble:::`[.tbl_df`(y, , 2:4), tibble:::vectbl_as_col_location(j, 
  .         length(x), names(x), j_arg = j_arg, assign = FALSE), 
  .     tibble:::subclass_col_index_errors(vec_as_location(j, n, 
  .         names), j_arg = j_arg, assign = assign), base::withCallingHandlers(expr, 
  .         vctrs_error_subscript = function(cnd) {
  .             cnd$subscript_arg <- j_arg
  .             cnd$subscript_elt <- "column"
  .             if (isTRUE(assign) && !isTRUE(cnd$subscript_action %in% 
  .                 c("negate"))) {
  .                 cnd$subscript_action <- "assign"
  .             }
  .             cnd_signal(cnd)
  .         }), vctrs::vec_as_location(j, n, names), (function () 
  .     stop_subscript_oob(i = i, subscript_type = subscript_type, 
  .         size = size, subscript_action = subscript_action, subscript_arg = subscript_arg))(), 
  .     vctrs:::stop_subscript_oob(i = i, subscript_type = subscript_type, 
  .         size = size, subscript_action = subscript_action, subscript_arg = subscript_arg), 
  .     vctrs:::stop_subscript(class = "vctrs_error_subscript_oob", 
  .         i = i, subscript_type = subscript_type, ...)), parents = c(0L, 
  . 1L, 2L, 3L, 4L, 5L, 6L, 7L, 6L, 9L, 10L, 4L, 12L, 13L, 13L, 15L, 
  . 16L, 17L, 18L, 19L, 13L, 13L, 13L, 23L, 0L, 25L, 26L, 27L, 26L, 
  . 0L, 30L, 31L, 32L, 32L, 32L, 32L, 36L, 37L, 38L, 37L, 40L, 41L, 
  . 42L), indices = 1:43), class = "rlang_trace", version = 1L), 
  .     parent = NULL, i = 2:4, subscript_type = "numeric", size = 1L, 
  .     subscript_action = NULL, subscript_arg = ""), class = c("vctrs_error_subscript_oob", 
  . "vctrs_error_subscript", "rlang_error", "error", "condition")))
24. cnd_signal(cnd)
25. rlang:::signal_abort(x)
BioinformaticsFMRP / TCGAbiolinks

CPTAC STAR - Counts download ERROR #505
