Error in dplyr::select(): ! <text>:1:5: unexpected symbol

[gwendolinelecuyer]

Hello,
I'm getting the following error when I run wilcoxauc()

DEG=wilcoxauc(sub.compare, 'treatment', seurat_assay='RNA', assay='data')

###############
Error in dplyr::select():
! :1:5: unexpected symbol
1: Use of
^
rlang::last_error()
<simpleError in dplyr::select(., .data$feature, .data$group, .data$avgExpr, .data$logFC, .data$statistic, .data$auc, .data$pval, .data$padj, .data$pct_in, .data$pct_out): :1:5: unexpected symbol
1: Use of
^>
################

I had the same kind of issue with harmony, which was solve with this post immunogenomics/harmony#173
I tried to do the same thing:

presto.tidy_results.new <- function (wide_res, features, groups)
{
res <- Reduce(cbind, lapply(wide_res, as.numeric)) %>% data.frame()
colnames(res) <- names(wide_res)
res$feature <- rep(features, times = length(groups))
res$group <- rep(groups, each = length(features))
res %>% dplyr::select(data$feature, data$group, data$avgExpr,
data$logFC, data$statistic, data$auc, data$pval,
data$padj, data$pct_in, data$pct_out)
}

environment(presto.tidy_results.new) <- asNamespace('presto')
assignInNamespace("tidy_results", presto.tidy_results.new, ns = "presto")

But I still have an error:
########
Error in dplyr::select():
! Problem while evaluating data$feature.
Run rlang::last_error() to see where the error occurred.

rlang::last_error()
<error/rlang_error>
Error in dplyr::select():
! Problem while evaluating data$feature.

---

Backtrace:

1. presto::wilcoxauc(...)
2. dplyr:::select.data.frame(...)
3. tidyselect::eval_select(expr(c(...)), .data)
4. tidyselect:::eval_select_impl(...)
5. tidyselect:::vars_select_eval(...)
6. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
7. tidyselect:::eval_c(expr, data_mask, context_mask)
8. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
9. tidyselect:::walk_data_tree(new, data_mask, context_mask)
10. tidyselect:::eval_context(expr, context_mask, call = error_call)
11. rlang::eval_tidy(as_quosure(expr, env), context_mask)
    Run rlang::last_trace() to see the full context.
    ###########

Sincerely,
Gwendoline

Here my sessionInfo
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] forcats_0.5.1 purrr_0.3.5
[3] readr_2.1.2 tidyr_1.2.0
[5] tibble_3.1.8 tidyverse_1.3.2
[7] UpSetR_1.4.0 presto_1.0.0
[9] data.table_1.14.6 Rcpp_1.0.9
[11] pheatmap_1.0.12 RColorBrewer_1.1-3
[13] ggplot2_3.3.6 reshape2_1.4.4
[15] scales_1.2.1 stringr_1.4.1
[17] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[19] Biobase_2.50.0 GenomicRanges_1.42.0
[21] GenomeInfoDb_1.26.7 IRanges_2.24.1
[23] S4Vectors_0.28.1 BiocGenerics_0.36.1
[25] MatrixGenerics_1.2.1 matrixStats_0.63.0
[27] SeuratObject_4.1.3 Seurat_4.3.0
[29] dplyr_1.0.10

loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 plyr_1.8.8
[4] igraph_1.3.4 lazyeval_0.2.2 sp_1.5-1
[7] splines_4.0.5 listenv_0.8.0 scattermore_0.8
[10] digest_0.6.30 htmltools_0.5.3 fansi_1.0.3
[13] magrittr_2.0.3 tensor_1.5 googlesheets4_1.0.1
[16] cluster_2.1.4 ROCR_1.0-11 tzdb_0.3.0
[19] globals_0.16.2 modelr_0.1.9 spatstat.sparse_3.0-0
[22] colorspace_2.0-3 rvest_1.0.2 ggrepel_0.9.2
[25] haven_2.5.0 crayon_1.5.2 RCurl_1.98-1.8
[28] jsonlite_1.8.3 progressr_0.11.0 spatstat.data_3.0-0
[31] survival_3.4-0 zoo_1.8-11 glue_1.6.2
[34] polyclip_1.10-4 gtable_0.3.1 gargle_1.2.1
[37] zlibbioc_1.36.0 XVector_0.30.0 leiden_0.4.3
[40] DelayedArray_0.16.3 future.apply_1.10.0 abind_1.4-5
[43] DBI_1.1.3 spatstat.random_3.0-1 miniUI_0.1.1.1
[46] viridisLite_0.4.1 xtable_1.8-4 reticulate_1.25
[49] htmlwidgets_1.5.4 httr_1.4.4 ellipsis_0.3.2
[52] ica_1.0-3 pkgconfig_2.0.3 uwot_0.1.14
[55] dbplyr_2.2.1 deldir_1.0-6 utf8_1.2.2
[58] tidyselect_1.2.0 rlang_1.0.6 later_1.3.0
[61] munsell_0.5.0 cellranger_1.1.0 tools_4.0.5
[64] cli_3.4.1 generics_0.1.3 broom_1.0.1
[67] ggridges_0.5.4 fastmap_1.1.0 goftest_1.2-3
[70] fs_1.5.2 fitdistrplus_1.1-8 RANN_2.6.1
[73] pbapply_1.6-0 future_1.29.0 nlme_3.1-159
[76] mime_0.12 xml2_1.3.3 compiler_4.0.5
[79] plotly_4.10.1 png_0.1-8 spatstat.utils_3.0-1
[82] reprex_2.0.1 stringi_1.7.8 lattice_0.20-45
[85] Matrix_1.5-3 vctrs_0.4.1 pillar_1.8.1
[88] lifecycle_1.0.1 spatstat.geom_3.0-3 lmtest_0.9-40
[91] RcppAnnoy_0.0.20 cowplot_1.1.1 bitops_1.0-7
[94] irlba_2.3.5.1 httpuv_1.6.2 patchwork_1.1.2
[97] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20
[100] gridExtra_2.3 parallelly_1.32.1 codetools_0.2-18
[103] MASS_7.3-58.1 assertthat_0.2.1 withr_2.5.0
[106] sctransform_0.3.5 GenomeInfoDbData_1.2.4 hms_1.1.2
[109] grid_4.0.5 googledrive_2.0.0 Rtsne_0.16
[112] spatstat.explore_3.0-5 shiny_1.7.3 lubridate_1.8.0