Error in subsetArchRProject

[jinbufan]

Hi, I encountered an error when I tried to subset project by sample names, here is the code:

dd=split(proj2@cellColData,proj2$Libname)
for (i in names(dd)){
subsetArchRProject(
ArchRProj = proj2,
cells = getCellNames(proj2[proj2$Libname==i,]),
outputDirectory = i,
dropCells = TRUE,
logFile = NULL,
threads = getArchRThreads(),
force = TRUE)}

Here is the logfile:
Copying ArchRProject to new outputDirectory : /data/work/01.human_brain/03.额叶/subGroup/sample/T599T600-1

Copying Arrow Files...

Copying Arrow Files (1 of 1)

Getting ImputeWeights

No imputeWeights found, returning NULL

Copying Other Files...

Copying Other Files (1 of 18): 00.peak_file

Copying Other Files (2 of 18): 01.clustering_har

Copying Other Files (3 of 18): addp2g.FineClust.qvalue.noFilter.rds

Copying Other Files (4 of 18): Annotations

Copying Other Files (5 of 18): ArchRLogs

Copying Other Files (6 of 18): Background-Peaks.rds

Copying Other Files (7 of 18): Embeddings

Copying Other Files (8 of 18): file_ArchRProject_addp2g.FineClust.qvalue.Filter.20240306.rds

Copying Other Files (9 of 18): file_Full_p2gGR_cCRE_not_merge_and_filter.rds

Copying Other Files (10 of 18): file_p2gGR_cCRE_merge_and_filter.rds

Copying Other Files (11 of 18): FineClust.rds

Copying Other Files (12 of 18): GroupCoverages

Copying Other Files (13 of 18): IterativeLSI

Copying Other Files (14 of 18): markerPeaks_FineClust.rds

Copying Other Files (15 of 18): Peak2GeneLinks

Copying Other Files (16 of 18): PeakCalls

Copying Other Files (17 of 18): Plots

Copying Other Files (18 of 18): RNAIntegration

Error in saveArchRProject(ArchRProj = ArchRProj[cells, ], outputDirectory = outputDirectory, : all(file.exists(zfiles)) is not TRUE
Traceback:

1. subsetArchRProject(ArchRProj = proj2, cells = getCellNames(proj2[proj2$Libname ==
   . i, ]), outputDirectory = i, dropCells = FALSE, logFile = NULL,
   . threads = getArchRThreads(), force = TRUE)
2. saveArchRProject(ArchRProj = ArchRProj[cells, ], outputDirectory = outputDirectory,
   . load = TRUE, dropCells = dropCells, logFile = logFile, threads = threads)
3. stopifnot(all(file.exists(zfiles)))

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

Matrix products: default
BLAS/LAPACK: /opt/conda/lib/libopenblasp-r0.3.23.so

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

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

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

other attached packages:
[1] rhdf5_2.42.1 SummarizedExperiment_1.28.0
[3] Biobase_2.58.0 MatrixGenerics_1.10.0
[5] Rcpp_1.0.10 Matrix_1.5-4.1
[7] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[9] IRanges_2.32.0 S4Vectors_0.36.2
[11] BiocGenerics_0.44.0 matrixStats_1.0.0
[13] data.table_1.14.8 stringr_1.5.0
[15] plyr_1.8.8 magrittr_2.0.3
[17] ggplot2_3.4.2 gtable_0.3.3
[19] gtools_3.9.4 gridExtra_2.3
[21] ArchR_1.0.2

loaded via a namespace (and not attached):
[1] lattice_0.21-8 listenv_0.9.0 digest_0.6.31
[4] utf8_1.2.3 parallelly_1.36.0 IRdisplay_1.1
[7] R6_2.5.1 repr_1.1.6 evaluate_0.21
[10] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.1
[13] uuid_1.1-0 RCurl_1.98-1.12 munsell_0.5.0
[16] DelayedArray_0.24.0 compiler_4.2.2 pkgconfig_2.0.3
[19] base64enc_0.1-3 globals_0.16.2 htmltools_0.5.5
[22] tidyselect_1.2.0 tibble_3.2.1 GenomeInfoDbData_1.2.9
[25] codetools_0.2-19 fansi_1.0.4 future_1.32.0
[28] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
[31] bitops_1.0-7 rhdf5filters_1.10.1 jsonlite_1.8.5
[34] lifecycle_1.0.3 scales_1.2.1 future.apply_1.11.0
[37] cli_3.6.1 stringi_1.7.12 XVector_0.38.0
[40] generics_0.1.3 vctrs_0.6.3 IRkernel_1.3.2
[43] Rhdf5lib_1.20.0 tools_4.2.2 glue_1.6.2
[46] parallel_4.2.2 fastmap_1.1.1 colorspace_2.1-0
[49] pbdZMQ_0.3-9

I also tried to change dropCells = FALSE but it still get error.

[rcorces]

Hi @jinbufan! 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.