Error in eval(e, x, parent.frame()) : object 'IsPassed' not found

Hi,

Thanks for developing this package!

as I run 'Build_AUCell_Rankings' function in AUCell analysis with SingCellaR package, I get the following error: Error in eval(e, x, parent.frame()) : object 'IsPassed' not found

I have tried it on both mac and ubuntu, the problem still exists. could you tell me why this error occur and how can I fix it, please?

Thanks for any help!

complete script of this analysis and the session info are attached in the following.

script

library(SingCellaR)
library(AUCell)
library(SingleCellExperiment)

GBM <- readRDS(file = 'immune cells-before AUcell.rds')
sce <-SingleCellExperiment(assays = list(counts = GBM@assays$RNA@data))
SingCellaR_obj <-new("SingCellaR", sce)
Build_AUCell_Rankings(SingCellaR_obj, AUCell_buildRankings.file = "rankings.AUCells.rdata")

session info R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.2.1

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-arm64/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: Asia/Tehran tzcode source: internal

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

other attached packages: [1] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 [3] Biobase_2.60.0 GenomicRanges_1.52.0
[5] GenomeInfoDb_1.36.1 IRanges_2.34.1
[7] S4Vectors_0.38.1 BiocGenerics_0.46.0
[9] MatrixGenerics_1.12.2 matrixStats_1.0.0
[11] AUCell_1.26.0 SingCellaR_1.2.1
[13] devtools_2.4.5 usethis_2.2.3

loaded via a namespace (and not attached): [1] RcppAnnoy_0.0.21 splines_4.3.0
[3] later_1.3.1 LinkedMatrix_1.4.0
[5] bitops_1.0-7 R.oo_1.25.0
[7] tibble_3.2.1 polyclip_1.10-4
[9] graph_1.78.0 XML_3.99-0.14
[11] lifecycle_1.0.3 rstatix_0.7.2
[13] rprojroot_2.0.3 doParallel_1.0.17
[15] globals_0.16.2 processx_3.8.2
[17] lattice_0.21-8 MASS_7.3-60
[19] backports_1.4.1 magrittr_2.0.3
[21] limma_3.56.2 plotly_4.10.2
[23] remotes_2.5.0 httpuv_1.6.11
[25] Seurat_4.3.0.1 sctransform_0.3.5
[27] sp_2.0-0 sessioninfo_1.2.2
[29] pkgbuild_1.4.4 spatstat.sparse_3.0-2
[31] reticulate_1.30 DBI_1.1.3
[33] cowplot_1.1.1 pbapply_1.7-2
[35] RColorBrewer_1.1-3 abind_1.4-5
[37] pkgload_1.3.4 zlibbioc_1.46.0
[39] Rtsne_0.16 R.utils_2.12.2
[41] purrr_1.0.1 RCurl_1.98-1.12
[43] rappdirs_0.3.3 circlize_0.4.16
[45] GenomeInfoDbData_1.2.10 ggrepel_0.9.3
[47] irlba_2.3.5.1 listenv_0.9.0
[49] spatstat.utils_3.0-3 goftest_1.2-3
[51] annotate_1.78.0 spatstat.random_3.1-5
[53] fitdistrplus_1.1-11 parallelly_1.36.0
[55] DelayedMatrixStats_1.22.6 DelayedArray_0.26.7
[57] leiden_0.4.3 codetools_0.2-19
[59] tidyselect_1.2.0 shape_1.4.6
[61] spatstat.explore_3.2-1 jsonlite_1.8.7
[63] GetoptLong_1.0.5 ellipsis_0.3.2
[65] progressr_0.13.0 ggridges_0.5.4
[67] survival_3.5-5 iterators_1.0.14
[69] foreach_1.5.2 tools_4.3.0
[71] ica_1.0-3 Rcpp_1.0.11
[73] glue_1.6.2 gridExtra_2.3
[75] here_1.0.1 dplyr_1.1.2
[77] BiocManager_1.30.21.1 fastmap_1.1.1
[79] fansi_1.0.4 callr_3.7.3
[81] digest_0.6.33 R6_2.5.1
[83] mime_0.12 colorspace_2.1-0
[85] scattermore_1.2 tensor_1.5
[87] RSQLite_2.3.1 spatstat.data_3.0-1
[89] R.methodsS3_1.8.2 utf8_1.2.3
[91] tidyr_1.3.0 generics_0.1.3
[93] cccd_1.6 data.table_1.14.8
[95] FNN_1.1.3.2 httr_1.4.6
[97] htmlwidgets_1.6.2 S4Arrays_1.0.4
[99] uwot_0.1.16 pkgconfig_2.0.3
[101] gtable_0.3.3 blob_1.2.4
[103] ComplexHeatmap_2.16.0 lmtest_0.9-40
[105] XVector_0.40.0 htmltools_0.5.8.1
[107] carData_3.0-5 fgsea_1.26.0
[109] profvis_0.3.8 GSEABase_1.62.0
[111] clue_0.3-65 SeuratObject_4.1.3
[113] scales_1.2.1 png_0.1-8
[115] crochet_2.3.0 rstudioapi_0.15.0
[117] reshape2_1.4.4 rjson_0.2.21
[119] nlme_3.1-162 curl_5.2.1
[121] proxy_0.4-27 cachem_1.0.8
[123] zoo_1.8-12 GlobalOptions_0.1.2
[125] stringr_1.5.0 KernSmooth_2.23-22
[127] parallel_4.3.0 miniUI_0.1.1.1
[129] AnnotationDbi_1.62.2 desc_1.4.3
[131] pillar_1.9.0 grid_4.3.0
[133] vctrs_0.6.3 RANN_2.6.1
[135] ggpubr_0.6.0 urlchecker_1.0.1
[137] promises_1.2.0.1 car_3.1-2
[139] xtable_1.8-4 cluster_2.1.4
[141] cli_3.6.1 compiler_4.3.0
[143] rlang_1.1.1 crayon_1.5.2
[145] ggsignif_0.6.4 future.apply_1.11.0
[147] ps_1.7.5 plyr_1.8.8
[149] fs_1.6.3 stringi_1.7.12
[151] BiocParallel_1.34.2 viridisLite_0.4.2
[153] deldir_1.0-9 Biostrings_2.68.1
[155] munsell_0.5.0 lazyeval_0.2.2
[157] spatstat.geom_3.2-4 Matrix_1.6-0
[159] patchwork_1.1.2 sparseMatrixStats_1.12.2 [161] bit64_4.0.5 future_1.33.0
[163] ggplot2_3.4.2 KEGGREST_1.40.0
[165] statmod_1.5.0 shiny_1.7.4.1
[167] ROCR_1.0-11 broom_1.0.5
[169] igraph_1.5.0 memoise_2.0.1
[171] RcppParallel_5.1.7 fastmatch_1.1-3
[173] bit_4.0.5

supatt-lab / SingCellaR

Error in eval(e, x, parent.frame()) : object 'IsPassed' not found #23