Description
I am using aPEAR in Rstudio, with the version aPEAR_1.0. It worked perfectly in a cloud computing env. However, in Rstudio, when I tried to use findPathClusters, I got the error telling me the function could not be found. I wonder if you could advise in this regard.
versions is as follows:
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1 IRanges_2.36.0 S4Vectors_0.40.2 Biobase_2.62.0 BiocGenerics_0.48.1 DOSE_3.28.2
[8] clusterProfiler_4.10.0 stringr_1.5.1 ggplot2_3.4.4 data.table_1.14.10 aPEAR_1.0 dplyr_1.1.4 Seurat_5.0.1
[15] SeuratObject_5.0.1 sp_2.1-2 devtools_2.4.5 usethis_2.2.2
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.2 later_1.3.2 ggplotify_0.1.2 bitops_1.0-7 tibble_3.2.1 polyclip_1.10-6
[8] fastDummies_1.7.3 lifecycle_1.0.4 globals_0.16.2 lattice_0.21-9 MASS_7.3-60 SnowballC_0.7.1 magrittr_2.0.3
[15] plotly_4.10.3 remotes_2.4.2.1 httpuv_1.6.13 sctransform_0.4.1 spam_2.10-0 sessioninfo_1.2.2 pkgbuild_1.4.3
[22] spatstat.sparse_3.0-3 reticulate_1.34.0 cowplot_1.1.2 pbapply_1.7-2 DBI_1.2.0 RColorBrewer_1.1-3 abind_1.4-5
[29] pkgload_1.3.3 zlibbioc_1.48.0 expm_0.999-8 Rtsne_0.17 purrr_1.0.2 ggraph_2.1.0 RCurl_1.98-1.13
[36] yulab.utils_0.1.2 tweenr_2.0.2 GenomeInfoDbData_1.2.11 enrichplot_1.22.0 arules_1.7-7 ggrepel_0.9.4 irlba_2.3.5.1
[43] listenv_0.9.0 spatstat.utils_3.0-4 tidytree_0.4.6 goftest_1.2-3 RSpectra_0.16-1 spatstat.random_3.2-2 fitdistrplus_1.1-11
[50] parallelly_1.36.0 leiden_0.4.3.1 codetools_0.2-19 ggforce_0.4.1 tidyselect_1.2.0 aplot_0.2.2 farver_2.1.1
[57] viridis_0.6.4 matrixStats_1.2.0 spatstat.explore_3.2-5 jsonlite_1.8.8 tidygraph_1.3.0 ellipsis_0.3.2 progressr_0.14.0
[64] ggridges_0.5.5 survival_3.5-7 iterators_1.0.14 foreach_1.5.2 tools_4.3.2 treeio_1.26.0 ica_1.0-3
[71] Rcpp_1.0.11 glue_1.6.2 gridExtra_2.3 qvalue_2.34.0 GenomeInfoDb_1.38.2 withr_2.5.2 BiocManager_1.30.22
[78] fastmap_1.1.1 fansi_1.0.6 digest_0.6.33 gridGraphics_0.5-1 R6_2.5.1 mime_0.12 colorspace_2.1-0
[85] GO.db_3.18.0 scattermore_1.2 tensor_1.5 spatstat.data_3.0-3 RSQLite_2.3.4 utf8_1.2.4 tidyr_1.3.0
[92] generics_0.1.3 graphlayouts_1.0.2 httr_1.4.7 htmlwidgets_1.6.4 scatterpie_0.2.1 uwot_0.1.16 MCL_1.0
[99] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4 bayesbio_1.0.0 lmtest_0.9-40 XVector_0.42.0 shadowtext_0.1.2
[106] htmltools_0.5.7 fgsea_1.28.0 profvis_0.3.8 dotCall64_1.1-1 scales_1.3.0 png_0.1-8 ggfun_0.1.3
[113] rstudioapi_0.15.0 reshape2_1.4.4 nlme_3.1-163 cachem_1.0.8 zoo_1.8-12 KernSmooth_2.23-22 HDO.db_0.99.1
[120] parallel_4.3.2 miniUI_0.1.1.1 pillar_1.9.0 grid_4.3.2 vctrs_0.6.5 RANN_2.6.1 urlchecker_1.0.1
[127] lsa_0.73.3 promises_1.2.1 xtable_1.8-4 cluster_2.1.4 cli_3.6.2 compiler_4.3.2 rlang_1.1.2
[134] crayon_1.5.2 future.apply_1.11.1 plyr_1.8.9 fs_1.6.3 stringi_1.8.3 BiocParallel_1.36.0 viridisLite_0.4.2
[141] deldir_2.0-2 munsell_0.5.0 Biostrings_2.70.1 lazyeval_0.2.2 spatstat.geom_3.2-7 GOSemSim_2.28.0 Matrix_1.6-4
[148] RcppHNSW_0.5.0 patchwork_1.1.3 bit64_4.0.5 future_1.33.1 KEGGREST_1.42.0 shiny_1.8.0 ROCR_1.0-11
[155] igraph_1.6.0 memoise_2.0.1 ggtree_3.10.0 fastmatch_1.1-4 bit_4.0.5 gson_0.1.0 ape_5.7-1