Error in findPathClusters(enrich, cluster = "hier", minClusterSize = 3) : could not find function "findPathClusters"

[MANZHAOHUI]

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

[xyzheng123]

Hi, I ran into the same issue. It seems the cran version (v1.0.0) has the function that you were looking for, but the same function was not contained in the github version (v1.0).