Not retrieving msigdb genesets
1
0
Entering edit mode
@2ddb64f4
Last seen 17 months ago
United States

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
EnrichmentBrowser • 927 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

Is the error consistent? It can happen that there are glitches downloading data, and maybe you just need to try again. FWIW, it works fine for me.

> hall.gs <- getGenesets("hsa","msigdb", "SYMBOL", cat = "H")
> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] org.Hs.eg.db_3.15.0         AnnotationDbi_1.58.0       
 [3] msigdbr_7.5.1               EnrichmentBrowser_2.26.0   
 [5] graph_1.74.0                SummarizedExperiment_1.26.1
 [7] Biobase_2.56.0              GenomicRanges_1.48.0       
 [9] GenomeInfoDb_1.32.3         IRanges_2.30.1             
[11] S4Vectors_0.34.0            BiocGenerics_0.42.0        
[13] MatrixGenerics_1.8.1        matrixStats_0.62.0         
[15] BiocManager_1.30.18        

loaded via a namespace (and not attached):
 [1] KEGGgraph_1.56.0       Rcpp_1.0.9             lattice_0.20-45       
 [4] png_0.1-7              Biostrings_2.64.1      assertthat_0.2.1      
 [7] utf8_1.2.2             BiocFileCache_2.4.0    R6_2.5.1              
[10] RSQLite_2.2.16         httr_1.4.4             pillar_1.8.1          
[13] zlibbioc_1.42.0        rlang_1.0.4            curl_4.3.2            
[16] annotate_1.74.0        Rgraphviz_2.40.0       blob_1.2.3            
[19] Matrix_1.4-1           RCurl_1.98-1.8         bit_4.0.4             
[22] DelayedArray_0.22.0    compiler_4.2.0         pkgconfig_2.0.3       
[25] tidyselect_1.1.2       KEGGREST_1.36.3        tibble_3.1.8          
[28] GenomeInfoDbData_1.2.8 XML_3.99-0.10          fansi_1.0.3           
[31] crayon_1.5.1           dplyr_1.0.9            dbplyr_2.2.1          
[34] bitops_1.0-7           rappdirs_0.3.3         grid_4.2.0            
[37] xtable_1.8-4           GSEABase_1.58.0        lifecycle_1.0.1       
[40] DBI_1.1.3              magrittr_2.0.3         cli_3.3.0             
[43] cachem_1.0.6           XVector_0.36.0         ellipsis_0.3.2        
[46] filelock_1.0.2         generics_0.1.3         vctrs_0.4.1           
[49] tools_4.2.0            bit64_4.0.5            glue_1.6.2            
[52] purrr_0.3.4            fastmap_1.1.0          babelgene_22.9        
[55] memoise_2.0.1
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Entering edit mode

Thank you, James. It works fine now.

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