runEscape() function not found

[ayin0510]

Hi Nick, I am running into an issue with the runEscape() function for the following code:

ES_D7 <- runEscape(dlist_big_merge_D7, method="ssGSEA", gene.sets=GS.hallmark, groups=5000, min.size=5, new.assay.name="escape.ssGSEA", BPPARAM=SnowParam(workers=8))

Error in runEscape(dlist_big_merge_D7, method = "ssGSEA", gene.sets = GS.hallmark, : could not find function "runEscape"

Prior to running this code, I already removed and re-installed the latest version of escape (2.1.1) using devtools::install_github("ncborcherding/escape"). I am using R 4.3.1 for this.

Any insight into this error would be greatly appreciated, thank you so much!

[ncborcherding]

Hey @ayin0510,

Everything looks good when it comes to the function call.

Have you tried restarting your R session after installing escape? This is a super common issue.

If not - let me know and I am happy to troubleshoot with you.

Nick

[cedmo001]

Hello @ncborcherding and @ayin0510 ,

I am also having this issue, and tried the above recommendation and had no luck. Any chance you can help me solve this?

BW, C

[ncborcherding]

@cedmo001

Are you using an escape versions >= 2.0?

What is the output of:

sessionInfo()

Nick

[cedmo001]

Hiya,

Looks like version 1.8... but I installed using BiocManager. I'm using R on a HPC, and can't access R version 4.4, so looks like that might be the issue?

BW, C

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

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

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

other attached packages: [1] escape_1.8.0 cowplot_1.1.3 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.1
[6] dplyr_1.1.4 purrr_1.0.2 readr_2.1.4 tidyr_1.3.1 tibble_3.2.1
[11] ggplot2_3.5.1 tidyverse_2.0.0 SeuratObject_4.1.4 Seurat_4.4.0

loaded via a namespace (and not attached): [1] backports_1.4.1 plyr_1.8.9 igraph_2.0.3
[4] lazyeval_0.2.2 sp_2.1-3 GSEABase_1.60.0
[7] splines_4.2.2 BiocParallel_1.32.6 listenv_0.9.1
[10] scattermore_1.2 GenomeInfoDb_1.34.9 digest_0.6.36
[13] htmltools_0.5.8.1 fansi_1.0.6 magrittr_2.0.3
[16] memoise_2.0.1 ScaledMatrix_1.6.0 tensor_1.5
[19] cluster_2.1.4 ROCR_1.0-11 tzdb_0.4.0
[22] globals_0.16.2 Biostrings_2.66.0 annotate_1.76.0
[25] matrixStats_1.1.0 timechange_0.3.0 spatstat.sparse_3.0-3
[28] colorspace_2.1-0 blob_1.2.4 ggrepel_0.9.5
[31] xfun_0.45 crayon_1.5.3 RCurl_1.98-1.14
[34] jsonlite_1.8.8 graph_1.76.0 progressr_0.14.0
[37] spatstat.data_3.0-4 survival_3.4-0 zoo_1.8-12
[40] glue_1.7.0 polyclip_1.10-6 gtable_0.3.5
[43] zlibbioc_1.44.0 XVector_0.38.0 leiden_0.4.3.1
[46] DelayedArray_0.24.0 BiocSingular_1.14.0 Rhdf5lib_1.20.0
[49] SingleCellExperiment_1.20.1 future.apply_1.11.1 HDF5Array_1.26.0
[52] BiocGenerics_0.44.0 msigdbr_7.5.1 abind_1.4-5
[55] scales_1.3.0 DBI_1.2.3 spatstat.random_3.1-5
[58] miniUI_0.1.1.1 Rcpp_1.0.12 viridisLite_0.4.2
[61] xtable_1.8-4 reticulate_1.38.0 rsvd_1.0.5
[64] bit_4.0.5 GSVA_1.46.0 stats4_4.2.2
[67] htmlwidgets_1.6.4 httr_1.4.7 RColorBrewer_1.1-3
[70] ica_1.0-3 pkgconfig_2.0.3 XML_3.99-0.17
[73] uwot_0.2.2 deldir_2.0-2 utf8_1.2.4
[76] tidyselect_1.2.1 rlang_1.1.4 reshape2_1.4.4
[79] later_1.3.2 AnnotationDbi_1.60.2 munsell_0.5.1
[82] tools_4.2.2 cachem_1.1.0 cli_3.6.3
[85] UCell_2.2.0 generics_0.1.3 RSQLite_2.3.7
[88] broom_1.0.3 ggridges_0.5.4 fastmap_1.2.0
[91] goftest_1.2-3 babelgene_22.9 knitr_1.47
[94] bit64_4.0.5 fitdistrplus_1.1-11 RANN_2.6.1
[97] KEGGREST_1.38.0 sparseMatrixStats_1.10.0 pbapply_1.7-2
[100] future_1.33.1 nlme_3.1-160 mime_0.12
[103] compiler_4.2.2 rstudioapi_0.15.0 plotly_4.10.4
[106] png_0.1-8 spatstat.utils_3.0-4 stringi_1.8.4
[109] lattice_0.20-45 Matrix_1.6-5 vctrs_0.6.5
[112] rhdf5filters_1.10.1 pillar_1.9.0 lifecycle_1.0.4
[115] BiocManager_1.30.23 spatstat.geom_3.2-4 lmtest_0.9-40
[118] BiocNeighbors_1.16.0 RcppAnnoy_0.0.22 data.table_1.15.4
[121] bitops_1.0-7 irlba_2.3.5.1 GenomicRanges_1.50.2
[124] httpuv_1.6.15 patchwork_1.1.2 R6_2.5.1
[127] promises_1.3.0 KernSmooth_2.23-20 gridExtra_2.3
[130] IRanges_2.32.0 parallelly_1.37.1 codetools_0.2-18
[133] MASS_7.3-58.1 rhdf5_2.42.1 SummarizedExperiment_1.28.0 [136] withr_3.0.0 sctransform_0.4.0 S4Vectors_0.36.2
[139] GenomeInfoDbData_1.2.9 parallel_4.2.2 hms_1.1.3
[142] beachmat_2.14.2 grid_4.2.2 DelayedMatrixStats_1.20.0
[145] MatrixGenerics_1.10.0 Rtsne_0.17 spatstat.explore_3.2-1
[148] Biobase_2.58.0 shiny_1.8.1.1

[ncborcherding]

Looks like that is the issue. But it should still work for you, the relevant vignette would be located here

Nick

[cedmo001]

Perfect! Thanks so much for the help! (and so quickly)

C