Closed isha-ashi closed 1 year ago
While using WebGestaltR() function; I encounter following error:
Loading the functional categories... Error in `select()`: ! <text>:1:5: unexpected symbol 1: Use of ^ Run `rlang::last_error()` to see where the error occurred. There were 50 or more warnings (use warnings() to see the first 50) > rlang::last_error() <simpleError in select(geneSet, -.data$database): <text>:1:5: unexpected symbol 1: Use of ^> > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] harmony_0.1.0 Rcpp_1.0.9 WebGestaltR_0.4.4 loaded via a namespace (and not attached): [1] Seurat_4.3.0 Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.4 [7] spatstat.data_3.0-0 rstudioapi_0.13 leiden_0.4.3 listenv_0.8.0 ggrepel_0.9.2 bit64_4.0.5 [13] fansi_1.0.3 codetools_0.2-18 splines_4.2.0 doParallel_1.0.17 knitr_1.39 polyclip_1.10-4 [19] jsonlite_1.8.3 apcluster_1.4.9 ica_1.0-3 cluster_2.1.3 png_0.1-7 uwot_0.1.14 [25] spatstat.sparse_3.0-0 shiny_1.7.3 sctransform_0.3.5 readr_2.1.2 compiler_4.2.0 httr_1.4.4 [31] assertthat_0.2.1 SeuratObject_4.1.3 Matrix_1.5-3 fastmap_1.1.0 lazyeval_0.2.2 cli_3.4.1 [37] later_1.3.0 htmltools_0.5.3 tools_4.2.0 igraph_1.3.5 gtable_0.3.1 glue_1.6.2 [43] RANN_2.6.1 reshape2_1.4.4 dplyr_1.0.10 doRNG_1.8.2 scattermore_0.8 vctrs_0.4.1 [49] nlme_3.1-157 spatstat.explore_3.0-5 svglite_2.1.0.9000 progressr_0.11.0 iterators_1.0.14 lmtest_0.9-40 [55] spatstat.random_3.0-1 xfun_0.31 stringr_1.4.1 globals_0.16.2 mime_0.12 miniUI_0.1.1.1 [61] lifecycle_1.0.1 irlba_2.3.5.1 rngtools_1.5.2 goftest_1.2-3 future_1.29.0 MASS_7.3-57 [67] zoo_1.8-11 scales_1.2.1 vroom_1.5.7 spatstat.utils_3.0-1 hms_1.1.1 promises_1.2.0.1 [73] parallel_4.2.0 RColorBrewer_1.1-3 curl_4.3.3 gridExtra_2.3 reticulate_1.26 pbapply_1.6-0 [79] ggplot2_3.3.6 stringi_1.7.8 foreach_1.5.2 rlang_1.0.4 pkgconfig_2.0.3 systemfonts_1.0.4 [85] matrixStats_0.63.0 lattice_0.20-45 tensor_1.5 ROCR_1.0-11 purrr_0.3.5 patchwork_1.1.2 [91] htmlwidgets_1.5.4 cowplot_1.1.1 bit_4.0.4 tidyselect_1.2.0 parallelly_1.32.1 RcppAnnoy_0.0.20 [97] plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3 DBI_1.1.3 pillar_1.8.1 [103] whisker_0.4 withr_2.5.0 fitdistrplus_1.1-8 abind_1.4-5 survival_3.3-1 sp_1.5-1 [109] tibble_3.1.8 future.apply_1.10.0 crayon_1.5.2 KernSmooth_2.23-20 utf8_1.2.2 spatstat.geom_3.0-3 [115] plotly_4.10.1 tzdb_0.3.0 grid_4.2.0 data.table_1.14.6 digest_0.6.30 xtable_1.8-4 [121] tidyr_1.2.1 httpuv_1.6.6 munsell_0.5.0 viridisLite_0.4.1
My assumption is error is occuring at line 160 geneSet <- select(geneSet, -.data$database) in loadGeneSet() function. Can this be fixed?
Thanks. This should only affect when you input database as a single database wrapped in list e.g. c("A").
While using WebGestaltR() function; I encounter following error:
My assumption is error is occuring at line 160 geneSet <- select(geneSet, -.data$database) in loadGeneSet() function. Can this be fixed?