This error just started showing up:

[njbowen]

Error in vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, : bad value

[iblacksand]

This error seems to originate outside of WebGestaltR since our package does not use vroom. Does this error occur regardless of the file you use?

[njbowen]

Thank you for responding. I have a feeling it is something to do with a conflicting library, or my Rstudio and R package isntallation environment, but not sure.
Here is the error with traceback: Error in vroom_(file, delim = delim %||% col_types$delim, col_names = colnames, : bad value 7. vroom(file, delim = delim %||% col_types$delim, col_names = col_names, col_types = col_types, id = id, skip = skip, col_select = col_select, name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws, escape_double = escape_double, escape_backslash = escape_backslash, ... 6. vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types, col_select = { { col_select ... 5. read_tsv(content(response), col_names = FALSE, col_types = "cc", quote = "") 4. .loadGeneSetData(hostName, organism, enrichDb, standardId, "des", cache) 3. loadGeneSet(organism = organism, enrichDatabase = enrichDatabase, enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType, enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile, cache = cache, hostName = hostName) 2. WebGestaltRGsea(organism = organism, enrichDatabase = enrichDatabase, enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType, enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile, interestGeneFile = interestGeneFile, interestGene = interestGene, ... 1. WebGestaltR(enrichMethod = "GSEA", organism = "hsapiens", enrichDatabase = "pathway_Wikipathway", interestGeneFile = rankFile, interestGeneType = "ensembl_gene_id", sigMethod = "top", topThr = 10, minNum = 5, outputDirectory = outputDirectory)

[iblacksand]

We do use readr for reading files, which does have conflicting methods with vroom, but I can still use your WebGestaltR command with both packages loaded. It also works regardless of the order I load the packages. Perhaps this is due to the package versions installed? Another possibility is your rank file is not correctly formatted.

This is my results when I run sessionInfo() in the R console. I am running readr v2.1.4 and vroom_1.6.3 with WebGestaltR v0.4.6.

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

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

other attached packages:
[1] readr_2.1.4       vroom_1.6.3       WebGestaltR_0.4.6

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10       pillar_1.9.0      compiler_4.2.2    iterators_1.0.14
 [5] tools_4.2.2       rngtools_1.5.2    bit_4.0.5         digest_0.6.32
 [9] jsonlite_1.8.7    lifecycle_1.0.3   tibble_3.2.1      lattice_0.21-8
[13] pkgconfig_2.0.3   rlang_1.1.1       doRNG_1.8.6       Matrix_1.5-4.1
[17] foreach_1.5.2     igraph_1.5.0      cli_3.6.1         curl_5.0.1
[21] parallel_4.2.2    withr_2.5.0       apcluster_1.4.10  dplyr_1.1.2
[25] httr_1.4.6        generics_0.1.3    vctrs_0.6.3       systemfonts_1.0.4
[29] hms_1.1.3         bit64_4.0.5       grid_4.2.2        tidyselect_1.2.0
[33] svglite_2.1.1     glue_1.6.2        R6_2.5.1          fansi_1.0.4
[37] tcltk_4.2.2       whisker_0.4.1     tzdb_0.4.0        magrittr_2.0.3
[41] codetools_0.2-19  utf8_1.2.3        doParallel_1.0.17 crayon_1.5.2

Could you share your results from sessionInfo()? Also if you call library("readr") to overwrite the vroom functions, does that fix the problem?

[njbowen]

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.7

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] readr_2.1.4 WebGestaltR_0.4.6 gplots_3.1.3 conflicted_1.2.0 edgeR_3.42.4 limma_3.56.2 lubridate_1.9.3 forcats_1.0.0
[9] stringr_1.5.0 dplyr_1.1.3 purrr_1.0.2 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.3 tidyverse_2.0.0 maftools_2.16.0

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 magrittr_2.0.3 farver_2.1.1 rmarkdown_2.25
[7] fs_1.6.3 zlibbioc_1.46.0 vctrs_0.6.3 memoise_2.0.1 RCurl_1.98-1.12 ggtree_3.8.2
[13] htmltools_0.5.6.1 curl_5.1.0 gridGraphics_0.5-1 KernSmooth_2.23-22 plyr_1.8.9 cachem_1.0.8
[19] whisker_0.4.1 igraph_1.5.1 iterators_1.0.14 lifecycle_1.0.3 pkgconfig_2.0.3 Matrix_1.6-1.1
[25] R6_2.5.1 fastmap_1.1.1 gson_0.1.0 GenomeInfoDbData_1.2.10 digest_0.6.33 aplot_0.2.2
[31] enrichplot_1.20.3 colorspace_2.1-0 patchwork_1.1.3 AnnotationDbi_1.62.2 S4Vectors_0.38.2 RSQLite_2.3.1
[37] fansi_1.0.5 timechange_0.2.0 httr_1.4.7 polyclip_1.10-6 compiler_4.3.1 rngtools_1.5.2
[43] doParallel_1.0.17 bit64_4.0.5 withr_2.5.1 downloader_0.4 BiocParallel_1.34.2 viridis_0.6.4
[49] DBI_1.1.3 apcluster_1.4.11 ggforce_0.4.1 MASS_7.3-60 HDO.db_0.99.1 caTools_1.18.2
[55] gtools_3.9.4 DNAcopy_1.74.1 tools_4.3.1 ape_5.7-1 scatterpie_0.2.1 glue_1.6.2
[61] nlme_3.1-163 GOSemSim_2.26.1 grid_4.3.1 shadowtext_0.1.2 reshape2_1.4.4 fgsea_1.26.0
[67] generics_0.1.3 gtable_0.3.4 tzdb_0.4.0 data.table_1.14.8 hms_1.1.3 tidygraph_1.2.3
[73] utf8_1.2.3 XVector_0.40.0 BiocGenerics_0.46.0 foreach_1.5.2 ggrepel_0.9.3 pillar_1.9.0
[79] vroom_1.6.4 yulab.utils_0.1.0 splines_4.3.1 tweenr_2.0.2 treeio_1.24.3 lattice_0.21-9
[85] survival_3.5-7 bit_4.0.5 tidyselect_1.2.0 GO.db_3.17.0 locfit_1.5-9.8 Biostrings_2.68.1
[91] knitr_1.44 gridExtra_2.3 IRanges_2.34.1 svglite_2.1.1 stats4_4.3.1 xfun_0.40
[97] graphlayouts_1.0.1 Biobase_2.60.0 stringi_1.7.12 lazyeval_0.2.2 ggfun_0.1.3 yaml_2.3.7
[103] evaluate_0.22 codetools_0.2-19 ggraph_2.1.0 qvalue_2.32.0 ggplotify_0.1.2 cli_3.6.1
[109] systemfonts_1.0.5 munsell_0.5.0 Rcpp_1.0.11 GenomeInfoDb_1.36.4 png_0.1-8 parallel_4.3.1
[115] blob_1.2.4 clusterProfiler_4.8.3 doRNG_1.8.6 DOSE_3.26.2 bitops_1.0-7 viridisLite_0.4.2
[121] tidytree_0.4.5 scales_1.2.1 crayon_1.5.2 rlang_1.1.1 cowplot_1.1.1 fastmatch_1.1-4
[127] KEGGREST_1.40.1

[njbowen]

still get error when loading library(readr) just before calling WebGestaltR

[njbowen]

seems to be a vroom issue, i deleted vroom, reinstalled vroom 1.6.3 and error disappeared.

also saw this https://github.com/tidyverse/vroom/issues/519

[iblacksand]

Glad you found the issue!