Entering edit mode
Hi, I'm unable to retrieve Msigdb genesets in v2.27.0. Go genesets seem to work fine.
> H <- EnrichmentBrowser::getGenesets(org = "hsa", db = "msigdb", cat = "H",
+ gene.id.type = "SYMBOL" )
Error in `select()`:
! <text>:1:5: unexpected symbol
1: Use of
^
Run `rlang::last_error()` to see where the error occurred.
> traceback()
41: stop(fallback)
40: signal_abort(cnd)
39: cnd_signal(cnd)
38: h(simpleError(msg, call))
37: .handleSimpleError(function (cnd)
{
cnd$call <- call
cnd$parent <- NULL
cnd_signal(cnd)
}, "<text>:1:5: unexpected symbol\n1: Use of\n ^", base::quote(parse(text = elt)))
36: parse(text = elt)
35: as.list(parse(text = elt))
34: FUN(X[[i]], ...)
33: lapply(.x, .f, ...)
32: map(x, function(elt) as.list(parse(text = elt)))
31: chr_parse_exprs(x)
30: parse_exprs(x)
29: parse_expr(what)
28: spec_what(spec, "spec", signaller)
27: spec(what, env = env)
26: signal_stage("deprecated", what)
25: lifecycle::deprecate_soft("1.2.0", what, details = cli::format_inline("Please use {.code {str}} instead of `.data${var}`"),
user_env = env)
24: call_kind(expr, context_mask, error_call)
23: expr_kind(expr, context_mask, error_call)
22: walk_data_tree(new, data_mask, context_mask)
21: reduce_sels(node, data_mask, context_mask, init = init)
20: eval_c(expr, data_mask, context_mask)
19: walk_data_tree(expr, data_mask, context_mask)
18: vars_select_eval(vars, expr, strict = strict, data = x, name_spec = name_spec,
uniquely_named = uniquely_named, allow_rename = allow_rename,
allow_empty = allow_empty, allow_predicates = allow_predicates,
type = type, error_call = error_call)
17: withCallingHandlers(expr, vctrs_error_subscript = function(cnd) {
{
.__handler_frame__. <- TRUE
.__setup_frame__. <- frame
}
out <- handlers[[1L]](cnd)
if (!inherits(out, "rlang_zap"))
throw(out)
})
16: try_fetch(expr, vctrs_error_subscript = function(cnd) {
cnd$subscript_action <- subscript_action(type)
cnd$subscript_elt <- "column"
cnd_signal(cnd)
})
15: with_subscript_errors(out <- vars_select_eval(vars, expr, strict = strict,
data = x, name_spec = name_spec, uniquely_named = uniquely_named,
allow_rename = allow_rename, allow_empty = allow_empty, allow_predicates = allow_predicates,
type = type, error_call = error_call), type = type)
14: eval_select_impl(data, names(data), as_quosure(expr, env), include = include,
exclude = exclude, strict = strict, name_spec = name_spec,
allow_rename = allow_rename, allow_empty = allow_empty, allow_predicates = allow_predicates,
error_call = error_call, )
13: tidyselect::eval_select(expr(c(...)), .data)
12: withCallingHandlers(expr, error = function(cnd) {
cnd$call <- call
cnd$parent <- NULL
cnd_signal(cnd)
})
11: tidyselect_fix_call(tidyselect::eval_select(expr(c(...)), .data),
call = error_call)
10: select.data.frame(., species_name = .data$scientific_name, species_common_name = .data$common_name)
9: select(., species_name = .data$scientific_name, species_common_name = .data$common_name)
8: rbind(., c("Homo sapiens", "human"))
7: distinct(.)
6: arrange(., .data$species_name)
5: species() %>% as_tibble() %>% select(species_name = .data$scientific_name,
species_common_name = .data$common_name) %>% rbind(c("Homo sapiens",
"human")) %>% distinct() %>% arrange(.data$species_name)
4: msigdbr::msigdbr_species()
3: morg %in% msigdbr::msigdbr_species()$species_name
2: .getMSigDb(org, gene.id.type, cache, return.type, ...)
1: EnrichmentBrowser::getGenesets(org = "hsa", db = "msigdb", cat = "H",
gene.id.type = "SYMBOL")
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] msigdbr_7.5.1
loaded via a namespace (and not attached):
[1] KEGGgraph_1.57.0 Rcpp_1.0.9 lattice_0.20-45
[4] png_0.1-7 Biostrings_2.65.6 assertthat_0.2.1
[7] utf8_1.2.2 BiocFileCache_2.5.2 R6_2.5.1
[10] GenomeInfoDb_1.33.7 stats4_4.2.0 RSQLite_2.2.18
[13] httr_1.4.3 pillar_1.7.0 zlibbioc_1.43.0
[16] rlang_1.0.6 curl_4.3.2 rstudioapi_0.13
[19] annotate_1.75.0 Rgraphviz_2.41.1 blob_1.2.3
[22] S4Vectors_0.35.4 Matrix_1.4-1 RCurl_1.98-1.9
[25] bit_4.0.4 DelayedArray_0.23.2 compiler_4.2.0
[28] pkgconfig_2.0.3 BiocGenerics_0.43.4 tidyselect_1.2.0
[31] SummarizedExperiment_1.27.3 KEGGREST_1.37.3 tibble_3.1.7
[34] GenomeInfoDbData_1.2.9 IRanges_2.31.2 matrixStats_0.62.0
[37] XML_3.99-0.11 fansi_1.0.3 withr_2.5.0
[40] crayon_1.5.1 dplyr_1.0.10 dbplyr_2.2.1
[43] rappdirs_0.3.3 bitops_1.0-7 grid_4.2.0
[46] xtable_1.8-4 GSEABase_1.59.0 lifecycle_1.0.1
[49] DBI_1.1.3 magrittr_2.0.3 graph_1.75.0
[52] cli_3.3.0 cachem_1.0.6 XVector_0.37.1
[55] EnrichmentBrowser_2.27.0 ellipsis_0.3.2 filelock_1.0.2
[58] vctrs_0.4.1 generics_0.1.3 tools_4.2.0
[61] bit64_4.0.5 Biobase_2.57.1 glue_1.6.2
[64] purrr_0.3.4 MatrixGenerics_1.9.1 fastmap_1.1.0
[67] babelgene_22.9 AnnotationDbi_1.59.1 GenomicRanges_1.49.1
[70] memoise_2.0.1
Thank you, James. It works fine now.