addMonocleTrajectory is throwing an error - Error in .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj")) : could not find function ".validInput"

Open susrinivasan opened this issue 1 year ago • 1 comments

Attach your log file I am unable to get a log file for this call.

Describe the bug THis used to work before but now it says could not find function .validInput, Am I missing a package?

**Context ** processPartialTrajectoriesForEntireSet <- function(object, useGps, trajName, principalGpName) { archRproj = object

head(archRproj$trajName[!is.na(archRproj$trajName)])

traj_cds <- getMonocleTrajectories( ArchRProj = archRproj, name = trajName, groupBy = "ClustersHar", clusterParams = list(k = 50), useGroups = useGps, principalGroup = principalGpName, embedding = "Harmony_Combined", graphParams = list("use_partition"=FALSE,"close_loop"=FALSE), ) print ("Done with getTrajectories") archRproj <- addMonocleTrajectory( ArchRProj = object, name = trajName, useGroups = useGps, groupBy = "ClustersHar", monocleCDS = traj_cds, force = TRUE )

return(archRproj) }

test4Gps = c("ML.adult", "ML.w8") projBaTP_coverage = processPartialTrajectoriesForEntireSet(projBaTP_coverage,test4Gps, "Test4_Traj", "ML.w8")

******************* error happens ********

projBaTP_coverage = processPartialTrajectoriesForEntireSet(projBaTP_coverage,test4Gps, "Test4_Traj", "ML.w8") Running Monocole3 Trajectory Infrastructure! Adding Embedding Clustering Embedding Learning Graphs Getting Principal Node Ordering Cells Plotting Results - /home/sumana/Salk_project/BasalTransplant_scMultiome/ArchR_new/projBaTP_integrated/Monocole3/Plot-Results-Test4_Traj.pdf [1] "Done with getTrajectories" Error in .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj")) : could not find function ".validInput" In addition: Warning message: In igraph::graph.dfs(stree_ori, root = root_cell, neimode = "all", : Argument neimode' is deprecated; use mode' instead

Session Info

sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Rocky Linux 8.10 (Green Obsidian)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.so

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

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] parallel stats4 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] decoupleR_2.2.2 readxl_1.4.1 RColorBrewer_1.1-3 pathview_1.3.5 org.Hs.eg.db_3.15.0
[6] AnnotationDbi_1.58.0 KEGGgraph_1.56.0 STRINGdb_2.8.4 Biostrings_2.64.1 XVector_0.36.0
[11] hexbin_1.28.2 circlize_0.4.15 ComplexHeatmap_2.12.1 presto_1.0.0 SeuratWrappers_0.3.0
[16] garnett_0.2.19 patchwork_1.1.2 enrichR_3.1 sp_1.5-0 SeuratObject_4.1.2
[21] Seurat_4.2.0 ggvenn_0.1.9 forcats_0.5.2 purrr_0.3.4 readr_2.1.2
[26] tidyr_1.2.1 tibble_3.1.8 tidyverse_1.3.2 textshape_1.7.3 dorothea_1.8.0
[31] reshape2_1.4.4 nabor_0.5.0 ReactomePA_1.40.0 enrichplot_1.16.2 clusterProfiler_4.4.4
[36] msigdbr_7.5.1 ggpubr_0.4.0 monocle3_1.2.9 SingleCellExperiment_1.18.0 dplyr_1.0.10
[41] rhdf5_2.40.0 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1 Rcpp_1.0.9
[46] Matrix_1.5-1 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0
[51] BiocGenerics_0.42.0 matrixStats_0.62.0 data.table_1.14.2 stringr_1.4.1 plyr_1.8.7
[56] magrittr_2.0.3 ggplot2_3.3.6 gtable_0.3.1 gtools_3.9.3 gridExtra_2.3
[61] ArchR_1.0.2 TFBSTools_1.34.0

loaded via [1] rsvd_1.0.5 [6] crayon_1.5.1 [11] backports_1.4.1 [16] irlba_2.3.5 [21] bcellViper_1.32.0 [26] poweRlaw_0.70.6 [31] spatstat.geom_2.4-0 [36] zoo_1.8-11 [41] zlibbioc_1.42.0 [46] treeio_1.20.2 [51] caTools_1.18.2 [56] listenv_0.8.0 [61] bitops_1.0-7 [66] gplots_3.1.3 [71] graphite_1.42.0 [76] gsubfn_0.7 [81] proxy_0.4-27 [86] abind_1.4-5 [91] GenomeInfoDbData_1.2.8 [96] jsonlite_1.8.0 [101] carData_3.0-5 [106] R.utils_2.12.0 [111] Rtsne_0.16 [116] survival_3.4-0 [121] BiocIO_1.6.0 [126] mime_0.12 [131] future.apply_1.9.1 [136] splines_4.2.0 [141] broom_1.0.1 [146] ggbeeswarm_0.6.0 [151] fansi_1.0.3 [156] lifecycle_1.0.2 [161] leiden_0.4.3 [166] htmlwidgets_1.5.4 [171] terra_1.6-18 [176] spatstat.random_2.2-0 [181] dbplyr_2.2.1 [186] httr_1.4.4 [191] viridis_0.6.2 [196] lme4_1.1-30 [201] scatterpie_0.1.8 [206] gargle_1.2.1 a namespace (and not attached): ica_1.0-3 Rsamtools_2.12.0 foreach_1.5.2 lmtest_0.9-40
spatstat.core_2.4-4 MASS_7.3-58.1 rhdf5filters_1.8.0 nlme_3.1-160
reprex_2.0.2 GOSemSim_2.22.0 rlang_1.0.5 ROCR_1.0-11
nloptr_2.0.3 proto_1.0.0 BiocParallel_1.30.3 rjson_0.2.21
CNEr_1.32.0 bit64_4.0.5 glue_1.6.2 pheatmap_1.0.12
sctransform_0.3.5 vipor_0.4.5 spatstat.sparse_2.1-1 DOSE_3.22.1
haven_2.5.1 tidyselect_1.1.2 fitdistrplus_1.1-8 XML_3.99-0.10
GenomicAlignments_1.32.1 chron_2.3-61 xtable_1.8-4 cli_3.4.0
rstudioapi_0.14 miniUI_0.1.1.1 rpart_4.1.19 fastmatch_1.1-3
shiny_1.7.3 leidenbase_0.1.11 clue_0.3-61 cluster_2.1.4
tidygraph_1.2.2 KEGGREST_1.36.3 ggrepel_0.9.1 ape_5.6-2
TFMPvalue_0.0.8 png_0.1-7 future_1.28.0 withr_2.5.0
ggforce_0.3.4 cellranger_1.1.0 pracma_2.4.2 pillar_1.8.1
GlobalOptions_0.1.2 cachem_1.0.6 fs_1.5.2 GetoptLong_1.0.5
hash_2.2.6.3 vctrs_0.4.1 ellipsis_0.3.2 generics_0.1.3
tools_4.2.0 beeswarm_0.4.0 munsell_0.5.0 tweenr_2.0.2
fgsea_1.22.0 DelayedArray_0.22.0 fastmap_1.1.0 compiler_4.2.0
httpuv_1.6.6 rtracklayer_1.56.1 plotly_4.10.0 rgeos_0.5-9
lattice_0.20-45 deldir_1.0-6 utf8_1.2.2 later_1.3.0
scales_1.2.1 graph_1.74.0 tidytree_0.4.0 pbapply_1.5-0
lazyeval_0.2.2 promises_1.2.0.1 car_3.1-0 doParallel_1.0.17
goftest_1.2-3 spatstat.utils_2.3-1 reticulate_1.26 cowplot_1.1.1
downloader_0.4 BSgenome_1.64.0 uwot_0.1.14 igraph_1.3.4
yaml_2.3.5 plotrix_3.8-2 htmltools_0.5.3 memoise_2.0.1
graphlayouts_0.8.1 viridisLite_0.4.1 digest_0.6.29 assertthat_0.2.1
rappdirs_0.3.3 RSQLite_2.2.17 sqldf_0.4-11 yulab.utils_0.0.5
remotes_2.4.2 blob_1.2.3 R.oo_1.25.0 labeling_0.4.2
Rhdf5lib_1.18.2 Cairo_1.6-0 googledrive_2.0.0 RCurl_1.98-1.8
hms_1.1.2 modelr_0.1.9 colorspace_2.0-3 BiocManager_1.30.18
shape_1.4.6 aplot_0.1.7 ggrastr_1.0.1 RANN_2.6.1
tzdb_0.3.0 parallelly_1.32.1 R6_2.5.1 ggridges_0.5.3
curl_4.3.2 ggsignif_0.6.3 googlesheets4_1.0.1 minqa_1.2.4
DO.db_2.9 qvalue_2.28.0 RcppAnnoy_0.0.19 iterators_1.0.14
polyclip_1.10-0 shadowtext_0.1.2 gridGraphics_0.5-1 seqLogo_1.62.0
reactome.db_1.81.0 rvest_1.0.3 mgcv_1.8-41 globals_0.16.1
progressr_0.11.0 codetools_0.2-18 lubridate_1.8.0 GO.db_3.15.0
R.methodsS3_1.8.2 DBI_1.1.3 ggfun_0.0.7 tensor_1.5
KernSmooth_2.23-20 stringi_1.7.8 farver_2.1.1 annotate_1.74.0
Rgraphviz_2.40.0 ggtree_3.4.2 xml2_1.3.3 boot_1.3-28.1
restfulr_0.0.15 ggplotify_0.1.0 scattermore_0.8 bit_4.0.4
spatstat.data_2.2-0 ggraph_2.0.6 pkgconfig_2.0.3 babelgene_22.9
DirichletMultinomial_1.38.0 rstatix_0.7.0

Additional context Add any other context about the problem here.

Jul 30 '24 18:07 susrinivasan

Hi @susrinivasan! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

Jul 30 '24 18:07 rcorces