Hello, I have already succesfully used the geneGOEnricher function of the NoRCE package in the past but now it seems there is an issue even when I use sample code as reported in the package helps, i.e.:
ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg38', near=TRUE, genetype = 'Ensembl_gene')
Error in h(simpleError(msg, call)) :
errore durante la valutazione dell'argomento 'object' nella selezione di un metodo per la funzione 'getTable': Unknown track: wgEncodeGencodeV31
In addition: Warning message:
In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.utf8 LC_CTYPE=Italian_Italy.utf8 LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.utf8
time zone: Europe/Rome
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] NoRCE_1.16.0
loaded via a namespace (and not attached):
[1] later_1.3.2 BiocIO_1.14.0 bitops_1.0-7 filelock_1.0.3
[5] tibble_3.2.1 XML_3.99-0.17 lifecycle_1.0.4 httr2_1.0.3
[9] edgeR_4.2.0 lattice_0.22-6 alabaster.base_1.4.1 magrittr_2.0.3
[13] openxlsx_4.2.5.2 limma_3.60.2 yaml_2.3.8 remotes_2.5.0
[17] metapod_1.12.0 httpuv_1.6.15 zip_2.3.1 sessioninfo_1.2.2
[21] pkgbuild_1.4.4 DBI_1.2.3 RColorBrewer_1.1-3 abind_1.4-5
[25] pkgload_1.4.0 zlibbioc_1.49.3 GenomicRanges_1.55.4 purrr_1.0.2
[29] BiocGenerics_0.50.0 RCurl_1.98-1.16 rappdirs_0.3.3 GenomeInfoDbData_1.2.12
[33] IRanges_2.37.1 S4Vectors_0.41.7 ggrepel_0.9.5 irlba_2.3.5.1
[37] pheatmap_1.0.12 dqrng_0.4.1 DelayedMatrixStats_1.26.0 codetools_0.2-20
[41] DelayedArray_0.30.1 xml2_1.3.6 scuttle_1.14.0 tidyselect_1.2.1
[45] UCSC.utils_1.0.0 ScaledMatrix_1.12.0 viridis_0.6.5 matrixStats_1.3.0
[49] stats4_4.4.0 BiocFileCache_2.12.0 GenomicAlignments_1.40.0 jsonlite_1.8.8
[53] BiocNeighbors_1.22.0 ellipsis_0.3.2 scater_1.32.1 tools_4.4.0
[57] progress_1.2.3 Rcpp_1.0.12 glue_1.7.0 gridExtra_2.3
[61] SparseArray_1.4.8 DESeq2_1.44.0 MatrixGenerics_1.16.0 usethis_3.0.0
[65] GenomeInfoDb_1.40.1 dplyr_1.1.4 HDF5Array_1.32.0 gypsum_1.0.1
[69] BiocManager_1.30.25 fastmap_1.2.0 rhdf5filters_1.16.0 bluster_1.14.0
[73] fansi_1.0.6 digest_0.6.35 rsvd_1.0.5 R6_2.5.1
[77] mime_0.12 colorspace_2.1-0 GO.db_3.19.1 biomaRt_2.60.1
[81] RSQLite_2.3.7 celldex_1.14.0 utf8_1.2.4 generics_0.1.3
[85] rtracklayer_1.64.0 prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4
[89] S4Arrays_1.4.1 pkgconfig_2.0.3 gtable_0.3.5 blob_1.2.4
[93] SingleCellExperiment_1.26.0 XVector_0.43.1 htmltools_0.5.8.1 profvis_0.3.8
[97] scales_1.3.0 alabaster.matrix_1.4.0 Biobase_2.64.0 png_0.1-8
[101] scran_1.32.0 rstudioapi_0.16.0 reshape2_1.4.4 tzdb_0.4.0
[105] rjson_0.2.22 curl_5.2.1 cachem_1.1.0 rhdf5_2.48.0
[109] stringr_1.5.1 BiocVersion_3.19.1 parallel_4.4.0 miniUI_0.1.1.1
[113] vipor_0.4.7 AnnotationDbi_1.66.0 restfulr_0.0.15 pillar_1.9.0
[117] grid_4.4.0 alabaster.schemas_1.4.0 vctrs_0.6.5 urlchecker_1.0.1
[121] promises_1.3.0 BiocSingular_1.20.0 dbplyr_2.5.0 beachmat_2.20.0
[125] xtable_1.8-4 cluster_2.1.6 beeswarm_0.4.0 readr_2.1.5
[129] GenomicFeatures_1.56.0 cli_3.6.2 locfit_1.5-9.9 compiler_4.4.0
[133] Rsamtools_2.20.0 rlang_1.1.4 crayon_1.5.3 plyr_1.8.9
[137] fs_1.6.4 ggbeeswarm_0.7.2 stringi_1.8.4 viridisLite_0.4.2
[141] alabaster.se_1.4.1 BiocParallel_1.38.0 munsell_0.5.1 Biostrings_2.72.1
[145] devtools_2.4.5 Matrix_1.7-0 ExperimentHub_2.12.0 hms_1.1.3
[149] sparseMatrixStats_1.16.0 bit64_4.0.5 ggplot2_3.5.1 Rhdf5lib_1.26.0
[153] KEGGREST_1.44.1 statmod_1.5.0 shiny_1.9.1 SummarizedExperiment_1.34.0
[157] alabaster.ranges_1.4.2 AnnotationHub_3.12.0 igraph_2.0.3 memoise_2.0.1
[161] bit_4.0.5
Could you provide some help to fix this error?
Thanks in advance!