Error could not find function "show_waiter"

[MustafaElshani]

This error Warning: Error in show_waiter: could not find function "show_waiter" 73: observeEventHandler 2: runApp 1: startBingleSeq appears in differential Expression (bulk analysis) when Run DE Analysis even with sample data, Shiny closes instantly

[dbdimitrov]

Hi,

I believe I might know why this happens.

Could you please post your sessionInfo() just to confirm my suspicions that there might be a change in the package calling this function. I could also check myself.

Thanks in advance!

[MustafaElshani]

`> sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 21296)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages: [1] BingleSeq_0.3.6 viper_1.24.0
[3] plotly_4.9.3.9000 dorothea_1.2.0
[5] progeny_1.12.0 forcats_0.5.0
[7] stringr_1.4.0 purrr_0.3.4
[9] readr_1.4.0 tidyr_1.1.2
[11] tibble_3.0.5 tidyverse_1.3.0
[13] pheatmap_1.0.12 goseq_1.42.0
[15] geneLenDataBase_1.26.0 BiasedUrn_1.07
[17] SC3_1.18.0 scran_1.18.3
[19] Seurat_3.2.3 monocle_2.18.0
[21] DDRTree_0.1.5 irlba_2.3.3
[23] VGAM_1.1-5 Matrix_1.3-2
[25] MAST_1.16.0 SingleCellExperiment_1.12.0 [27] edgeR_3.32.1 limma_3.46.0
[29] DESeq2_1.30.0 SummarizedExperiment_1.20.0 [31] MatrixGenerics_1.2.0 matrixStats_0.57.0
[33] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
[35] sva_3.38.0 BiocParallel_1.24.1
[37] genefilter_1.72.1 mgcv_1.8-33
[39] nlme_3.1-151 Harman_1.18.0
[41] ggrepel_0.9.1 gridExtra_2.3
[43] reshape2_1.4.4 fastcluster_1.1.25
[45] factoextra_1.0.7 VennDiagram_1.6.20
[47] futile.logger_1.4.3 ggplot2_3.3.3
[49] DT_0.17.1 dplyr_1.0.3
[51] waiter_0.2.0 shinyWidgets_0.5.6
[53] shinyFiles_0.9.0 shinyjs_2.0.0
[55] shiny_1.5.0 ideal_1.14.0
[57] topGO_2.42.0 SparseM_1.78
[59] GO.db_3.12.1 AnnotationDbi_1.52.0
[61] IRanges_2.24.1 S4Vectors_0.28.1
[63] Biobase_2.50.0 graph_1.68.0
[65] BiocGenerics_0.36.0

loaded via a namespace (and not attached): [1] rsvd_1.0.3 ica_1.0-2
[3] class_7.3-18 Rsamtools_2.6.0
[5] foreach_1.5.1 lmtest_0.9-38
[7] crayon_1.3.4 MASS_7.3-53
[9] backports_1.2.1 WriteXLS_6.1.0
[11] reprex_0.3.0 qlcMatrix_0.9.7
[13] rlang_0.4.10 readxl_1.3.1
[15] XVector_0.30.0 ROCR_1.0-11
[17] pcaExplorer_2.16.0 GOstats_2.56.0
[19] bcellViper_1.26.0 bit64_4.0.5
[21] glue_1.4.2 rngtools_1.5
[23] sctransform_0.3.2 UpSetR_1.4.0
[25] shinyAce_0.4.1 shinydashboard_0.7.1
[27] haven_2.3.1 tidyselect_1.1.0
[29] fitdistrplus_1.1-3 XML_3.99-0.5
[31] zoo_1.8-8 GenomicAlignments_1.26.0 [33] xtable_1.8-4 magrittr_2.0.1
[35] evaluate_0.14 cli_2.2.0
[37] scuttle_1.0.4 zlibbioc_1.36.0
[39] rstudioapi_0.13 doRNG_1.8.2
[41] miniUI_0.1.1.1 rpart_4.1-15
[43] lambda.r_1.2.4 tinytex_0.29
[45] BiocSingular_1.6.0 xfun_0.20
[47] askpass_1.1 cluster_2.1.0
[49] caTools_1.18.1 TSP_1.1-10
[51] threejs_0.3.3 listenv_0.8.0
[53] dendextend_1.14.0 Biostrings_2.58.0
[55] png_0.1-7 future_1.21.0
[57] withr_2.4.0 shinyBS_0.61
[59] bitops_1.0-6 slam_0.1-48
[61] cellranger_1.1.0 RBGL_1.66.0
[63] plyr_1.8.6 GSEABase_1.52.1
[65] pcaPP_1.9-73 sparsesvd_0.2
[67] e1071_1.7-4 dqrng_0.2.1
[69] pillar_1.4.7 gplots_3.1.1
[71] GenomicFeatures_1.42.1 fs_1.5.0
[73] kernlab_0.9-29 DelayedMatrixStats_1.12.2 [75] vctrs_0.3.6 ellipsis_0.3.1
[77] generics_0.1.0 NMF_0.23.0
[79] tools_4.0.3 munsell_0.5.0
[81] DelayedArray_0.16.1 fastmap_1.0.1
[83] HSMMSingleCell_1.10.0 compiler_4.0.3
[85] abind_1.4-5 httpuv_1.5.5
[87] rtracklayer_1.50.0 segmented_1.3-1
[89] pkgmaker_0.32.2 GenomeInfoDbData_1.2.4
[91] lattice_0.20-41 deldir_0.2-9
[93] AnnotationForge_1.32.0 later_1.1.0.1
[95] BiocFileCache_1.14.0 jsonlite_1.7.2
[97] scales_1.1.1 docopt_0.7.1
[99] pbapply_1.4-3 sparseMatrixStats_1.2.0
[101] lazyeval_0.2.2 promises_1.1.1
[103] spatstat_1.64-1 doParallel_1.0.16
[105] goftest_1.2-2 spatstat.utils_2.0-0
[107] reticulate_1.18 rmarkdown_2.6
[109] cowplot_1.1.1 statmod_1.4.35
[111] webshot_0.5.2 Rtsne_0.15
[113] uwot_0.1.10 igraph_1.2.6
[115] survival_3.2-7 yaml_2.2.1
[117] rintrojs_0.2.2 htmltools_0.5.1.1
[119] memoise_1.1.0 locfit_1.5-9.4
[121] seriation_1.2-9 viridisLite_0.3.0
[123] rrcov_1.5-5 digest_0.6.27
[125] assertthat_0.2.1 mime_0.9
[127] rappdirs_0.3.1 densityClust_0.3
[129] futile.options_1.0.1 registry_0.5-1
[131] RSQLite_2.2.3 future.apply_1.7.0
[133] data.table_1.13.6 blob_1.2.1
[135] lpsymphony_1.18.0 fastICA_1.2-2
[137] Cairo_1.5-12.2 mixtools_1.2.0
[139] RCurl_1.98-1.2 broom_0.7.3
[141] hms_1.0.0 modelr_0.1.8
[143] colorspace_2.0-0 base64enc_0.1-3
[145] Rcpp_1.0.6 RANN_2.6.1
[147] mvtnorm_1.1-1 fansi_0.4.2
[149] IHW_1.18.0 parallelly_1.23.0
[151] R6_2.5.0 ggridges_0.5.3
[153] lifecycle_0.2.0 formatR_1.7
[155] bluster_1.0.0 curl_4.3
[157] leiden_0.3.6 robustbase_0.93-7
[159] RcppAnnoy_0.0.18 RColorBrewer_1.1-2
[161] iterators_1.0.13 htmlwidgets_1.5.3
[163] beachmat_2.6.4 polyclip_1.10-0
[165] biomaRt_2.46.1 crosstalk_1.1.1.9000
[167] rvest_0.3.6 globals_0.14.0
[169] openssl_1.4.3 patchwork_1.1.1
[171] lubridate_1.7.9.2 codetools_0.2-18
[173] FNN_1.1.3 gtools_3.8.2
[175] prettyunits_1.1.1 dbplyr_2.0.0
[177] gridBase_0.4-7 gtable_0.3.0
[179] DBI_1.1.1 tensor_1.5
[181] httr_1.4.2 KernSmooth_2.23-18
[183] stringi_1.5.3 progress_1.2.2
[185] heatmaply_1.1.1 annotate_1.68.0
[187] viridis_0.5.1 rentrez_1.2.3
[189] fdrtool_1.2.16 Rgraphviz_2.34.0
[191] xml2_1.3.2 combinat_0.0-8
[193] BiocNeighbors_1.8.2 geneplotter_1.68.0
[195] Category_2.56.0 scattermore_0.7
[197] DEoptimR_1.0-8 bit_4.0.4
[199] spatstat.data_1.7-0 pkgconfig_2.0.3
[201] knitr_1.30 `

[dbdimitrov]

Hi,

I double checked and it appears to be that the waiter package has changed to use "waiter_show" rather than "show_waiter" as the function name to call the loading screens.

I will try to find some time to update BingleSeq to appropriately request the latest version of waiter and call the appropriate function name this week.

In the meantime, if urgent, you could downgrade waiter to version 0.1.3 and it should work.

Cheers.

[dbdimitrov]

Hi,

This issue should be resolved now.