Failed to collect lazy table

[slowkow]

>   dice <- celldex::DatabaseImmuneCellExpressionData()
Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.

> rlang::last_trace()
Backtrace:
     ▆
  1. ├─celldex::DatabaseImmuneCellExpressionData()
  2. │ └─celldex:::.create_se(...)
  3. │   └─celldex:::.ExperimentHub()
  4. │     └─ExperimentHub::ExperimentHub()
  5. │       └─AnnotationHub::.Hub(...)
  6. │         └─AnnotationHub:::.create_cache(...)
  7. │           └─BiocFileCache::BiocFileCache(cache = cache, ask = ask)
  8. │             └─BiocFileCache:::.sql_create_db(bfc)
  9. │               └─BiocFileCache:::.sql_validate_version(bfc)
 10. │                 └─BiocFileCache:::.sql_schema_version(bfc)
 11. │                   ├─base::tryCatch(...)
 12. │                   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13. │                   └─tbl(src, "metadata") %>% collect(Inf)
 14. ├─dplyr::collect(., Inf)
 15. └─dbplyr:::collect.tbl_sql(., Inf)
 16.   ├─base::withCallingHandlers(...)
 17.   └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

> traceback()
29: stop(fallback)
28: signal_abort(cnd, .file)
27: rlang::abort(message, ..., call = call, use_cli_format = TRUE,
        .frame = .frame)
26: cli_abort("Failed to collect lazy table.", parent = cnd)
25: (function (cnd)
    {
        cli_abort("Failed to collect lazy table.", parent = cnd)
    })(structure(list(message = structure("Arguments in `...` must be used.", names = ""),
        trace = structure(list(call = list(celldex::DatabaseImmuneCellExpressionData(),
            .create_se("dice", version, assays = "logcounts", rm.NA = "none",
                has.rowdata = FALSE, has.coldata = TRUE), .ExperimentHub(),
            ExperimentHub(), .Hub("ExperimentHub", hub, cache, proxy,
                localHub, ask, ...), .create_cache(.class, url, cache,
                proxy, localHub, ask), BiocFileCache(cache = cache,
                ask = ask), .sql_create_db(bfc), .sql_validate_version(bfc),
            .sql_schema_version(bfc), tryCatch({
                info <- .sql_connect_RO(.sql_dbfile(bfc))
                con <- info$con
                src <- src_dbi(con)
                tbl <- tbl(src, "metadata") %>% collect(Inf)
            }, finally = {
                .sql_disconnect(info)
            }), tryCatchList(expr, classes, parentenv, handlers),
            tbl(src, "metadata") %>% collect(Inf), collect(., Inf),
            collect.tbl_sql(., Inf), withCallingHandlers(out <- db_collect(x$src$con,
                sql, n = n, warn_incomplete = warn_incomplete, ...),
                error = function(cnd) {
                    cli_abort("Failed to collect lazy table.", parent = cnd)
                }), db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete,
                ...), `<fn>`(), check_dots(env, error, action, call),
            action_dots(error = error, action = action, message = "Arguments in `...` must be used.",
                note = c(i = "Did you misspell an argument name?"),
                dots_i = unused, class = "rlib_error_dots_unused",
                call = call, env = env), try_dots(action(c(message,
                x = bullet_header, set_names(bullets, "*"), note),
                class = c(class, "rlib_error_dots"), ...)), action(c(message,
                x = bullet_header, set_names(bullets, "*"), note),
                class = c(class, "rlib_error_dots"), ...)), parent = c(0L,
        1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 10L, 0L, 0L,
        15L, 15L, 17L, 18L, 19L, 20L, 20L), visible = c(TRUE, TRUE,
        TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
        TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE,
        FALSE), namespace = c("celldex", "celldex", "celldex", "ExperimentHub",
        "AnnotationHub", "AnnotationHub", "BiocFileCache", "BiocFileCache",
        "BiocFileCache", "BiocFileCache", "base", "base", NA, "dplyr",
        "dbplyr", "base", "dbplyr", "rlang", "rlang", "rlang", "base",
        "rlang"), scope = c("::", ":::", ":::", "::", "::", ":::",
        "::", ":::", ":::", ":::", "::", "local", NA, "::", ":::",
        "::", "::", "local", ":::", ":::", "local", "local"), error_frame = c(FALSE,
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE,
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE,
        FALSE, FALSE, FALSE)), row.names = c(NA, -22L), version = 2L, class = c("rlang_trace",
        "rlib_trace", "tbl", "data.frame")), parent = NULL, body = c(x = "Problematic argument:",
        `*` = "..1 = Inf", i = "Did you misspell an argument name?"
        ), rlang = list(inherit = TRUE), call = db_collect(x$src$con,
            sql, n = n, warn_incomplete = warn_incomplete, ...),
        use_cli_format = TRUE), class = c("rlib_error_dots_unused",
    "rlib_error_dots", "rlang_error", "error", "condition")))
24: signalCondition(cnd)
23: signal_abort(cnd, .file)
22: action(c(message, x = bullet_header, set_names(bullets, "*"),
        note), class = c(class, "rlib_error_dots"), ...)
21: try_dots(action(c(message, x = bullet_header, set_names(bullets,
        "*"), note), class = c(class, "rlib_error_dots"), ...))
20: action_dots(error = error, action = action, message = "Arguments in `...` must be used.",
        note = c(i = "Did you misspell an argument name?"), dots_i = unused,
        class = "rlib_error_dots_unused", call = call, env = env)
19: check_dots(env, error, action, call)
18: (function ()
    check_dots(env, error, action, call))()
17: db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete,
        ...)
16: withCallingHandlers(out <- db_collect(x$src$con, sql, n = n,
        warn_incomplete = warn_incomplete, ...), error = function(cnd) {
        cli_abort("Failed to collect lazy table.", parent = cnd)
    })
15: collect.tbl_sql(., Inf)
14: collect(., Inf)
13: tbl(src, "metadata") %>% collect(Inf)
12: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch({
        info <- .sql_connect_RO(.sql_dbfile(bfc))
        con <- info$con
        src <- src_dbi(con)
        tbl <- tbl(src, "metadata") %>% collect(Inf)
    }, finally = {
        .sql_disconnect(info)
    })
10: .sql_schema_version(bfc)
9: .sql_validate_version(bfc)
8: .sql_create_db(bfc)
7: BiocFileCache(cache = cache, ask = ask)
6: .create_cache(.class, url, cache, proxy, localHub, ask)
5: .Hub("ExperimentHub", hub, cache, proxy, localHub, ask, ...)
4: ExperimentHub()
3: .ExperimentHub()
2: .create_se("dice", version, assays = "logcounts", rm.NA = "none",
       has.rowdata = FALSE, has.coldata = TRUE)
1: celldex::DatabaseImmuneCellExpressionData()

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11                   lattice_0.20-45               png_0.1-8
 [4] Biostrings_2.66.0             digest_0.6.35                 utf8_1.2.4
 [7] mime_0.12                     BiocFileCache_2.6.1           R6_2.5.1
[10] GenomeInfoDb_1.34.9           stats4_4.2.3                  RSQLite_2.3.7
[13] httr_1.4.6                    ggplot2_3.5.1                 pillar_1.9.0
[16] sparseMatrixStats_1.10.0      zlibbioc_1.44.0               rlang_1.1.3
[19] curl_5.2.1                    blob_1.2.4                    S4Vectors_0.36.2
[22] Matrix_1.5-3                  AnnotationHub_3.6.0           RCurl_1.98-1.12
[25] bit_4.0.5                     munsell_0.5.0                 shiny_1.7.4
[28] DelayedArray_0.24.0           compiler_4.2.3                httpuv_1.6.11
[31] pkgconfig_2.0.3               BiocGenerics_0.44.0           htmltools_0.5.8.1
[34] SummarizedExperiment_1.28.0   tidyselect_1.2.1              KEGGREST_1.38.0
[37] tibble_3.2.1                  GenomeInfoDbData_1.2.9        interactiveDisplayBase_1.36.0
[40] matrixStats_1.4.0             IRanges_2.32.0                fansi_1.0.6
[43] crayon_1.5.2                  dplyr_1.1.4                   dbplyr_2.5.0
[46] later_1.3.1                   bitops_1.0-7                  rappdirs_0.3.3
[49] celldex_1.8.0                 grid_4.2.3                    xtable_1.8-4
[52] gtable_0.3.4                  lifecycle_1.0.4               DBI_1.2.3
[55] magrittr_2.0.3                scales_1.3.0.9000             cli_3.6.2
[58] cachem_1.1.0                  XVector_0.38.0                promises_1.2.0.1
[61] DelayedMatrixStats_1.20.0     ellipsis_0.3.2                filelock_1.0.3
[64] generics_0.1.3                vctrs_0.6.5                   tools_4.2.3
[67] bit64_4.0.5                   Biobase_2.58.0                glue_1.7.0
[70] purrr_1.0.2                   BiocVersion_3.16.0            MatrixGenerics_1.10.0
[73] fastmap_1.2.0                 yaml_2.3.8                    AnnotationDbi_1.60.2
[76] colorspace_2.1-0              ExperimentHub_2.6.0           BiocManager_1.30.22
[79] GenomicRanges_1.50.2          memoise_2.0.1

[LTLA]

celldex is on 1.14.0, you're several versions behind.

[evelyn5695]

I met the same problem. library(ExperimentHub), then it worked

[eandresleon]

#26 (comment)