Error in if (common.len == 1L) unlist(x, recursive = FALSE) else if (common.len > : argument is of length zero.

[VDD58]

Hello,
I have been using ArchR to analyze my 10x scATAC data.
I have been repetitively getting this error. As far as I understand it is due to my environment. I have reinstalled ArchR as previously suggested but I still get the same error. This is an error I get only when I add returnGR = TRUE
Does anybody have an idea what i can try?
Any suggestions will be highly appreciated.

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.so

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] presto_1.0.0 nabor_0.5.0
[3] pheatmap_1.0.12 rhdf5_2.40.0
[5] SummarizedExperiment_1.26.1 Biobase_2.56.0
[7] MatrixGenerics_1.8.1 Rcpp_1.0.9
[9] Matrix_1.4-1 GenomicRanges_1.48.0
[11] GenomeInfoDb_1.32.2 IRanges_2.30.0
[13] S4Vectors_0.34.0 BiocGenerics_0.42.0
[15] matrixStats_0.62.0 data.table_1.14.2
[17] stringr_1.4.0 plyr_1.8.7
[19] magrittr_2.0.3 ggplot2_3.3.6
[21] gtable_0.3.0 gtools_3.9.2.2
[23] gridExtra_2.3 ArchR_1.0.2
[25] sp_1.5-0 SeuratObject_4.1.0
[27] Seurat_4.1.1

loaded via a namespace (and not attached):
[1] uuid_1.1-0 igraph_1.3.2
[3] repr_1.1.4 lazyeval_0.2.2
[5] splines_4.0.1 BiocParallel_1.30.3
[7] listenv_0.8.0 scattermore_0.8
[9] digest_0.6.29 htmltools_0.5.3
[11] fansi_1.0.3 BSgenome_1.64.0
[13] tensor_1.5 cluster_2.1.0
[15] ROCR_1.0-11 Biostrings_2.64.0
[17] globals_0.15.1 spatstat.sparse_2.1-1
[19] colorspace_2.0-3 ggrepel_0.9.1
[21] dplyr_1.0.9 crayon_1.5.1
[23] RCurl_1.98-1.7 jsonlite_1.8.0
[25] progressr_0.10.1 spatstat.data_2.2-0
[27] survival_3.1-12 zoo_1.8-10
[29] glue_1.6.2 polyclip_1.10-0
[31] zlibbioc_1.42.0 XVector_0.36.0
[33] leiden_0.4.2 DelayedArray_0.22.0
[35] Rhdf5lib_1.18.2 future.apply_1.9.0
[37] abind_1.4-5 scales_1.2.0
[39] DBI_1.1.3 spatstat.random_2.2-0
[41] miniUI_0.1.1.1 viridisLite_0.4.0
[43] xtable_1.8-4 reticulate_1.25
[45] spatstat.core_2.4-4 htmlwidgets_1.5.4
[47] httr_1.4.3 RColorBrewer_1.1-3
[49] ellipsis_0.3.2 ica_1.0-3
[51] XML_3.99-0.10 pkgconfig_2.0.3
[53] uwot_0.1.11 deldir_1.0-6
[55] utf8_1.2.2 tidyselect_1.1.2
[57] rlang_1.0.3 reshape2_1.4.4
[59] later_1.3.0 munsell_0.5.0
[61] tools_4.0.1 cli_3.3.0
[63] generics_0.1.3 ggridges_0.5.3
[65] evaluate_0.15 fastmap_1.1.0
[67] yaml_2.3.5 goftest_1.2-3
[69] fitdistrplus_1.1-8 purrr_0.3.4
[71] RANN_2.6.1 pbapply_1.5-0
[73] future_1.26.1 nlme_3.1-158
[75] mime_0.12 compiler_4.0.1
[77] plotly_4.10.0 png_0.1-7
[79] spatstat.utils_2.3-1 tibble_3.1.8
[81] stringi_1.7.8 rgeos_0.5-9
[83] lattice_0.20-41 IRdisplay_1.1
[85] vctrs_0.4.1 pillar_1.8.0
[87] lifecycle_1.0.1 rhdf5filters_1.8.0
[89] spatstat.geom_2.4-0 lmtest_0.9-40
[91] RcppAnnoy_0.0.19 cowplot_1.1.1
[93] bitops_1.0-7 irlba_2.3.5
[95] rtracklayer_1.56.1 httpuv_1.6.5
[97] patchwork_1.1.1 BiocIO_1.6.0
[99] R6_2.5.1 promises_1.2.0.1
[101] KernSmooth_2.23-17 parallelly_1.32.1
[103] codetools_0.2-16 MASS_7.3-58
[105] assertthat_0.2.1 rjson_0.2.21
[107] withr_2.5.0 GenomicAlignments_1.32.0
[109] Rsamtools_2.12.0 sctransform_0.3.3
[111] GenomeInfoDbData_1.2.8 mgcv_1.8-31
[113] parallel_4.0.1 rpart_4.1-15
[115] IRkernel_1.3.0.9000 tidyr_1.2.0
[117] BSgenome.Hsapiens.UCSC.hg19_1.4.3 Rtsne_0.16
[119] pbdZMQ_0.3-7 shiny_1.7.2
[121] base64enc_0.1-3 restfulr_0.0.15

[rcorces]

I dont see an error message in your post. Also, errors are meant to be posted in Issues.

[VDD58]

Hi,
I am so sorry, I was sure I put the error in the title... sorry.
I am currently trying to plot my marker peaks in Browser Tracks but I every-time i am putting returnGR = TRUE, i get the following error:
markerList <- getMarkers(markersPeaks, cutOff = "FDR <= 0.01 & Log2FC >= 1", returnGR = TRUE)
Error in if (common.len == 1L) unlist(x, recursive = FALSE) else if (common.len > : argument is of length zero
Traceback:

1. getMarkers(markersPeaks, cutOff = "FDR <= 0.05 & Log2FC >= 1",
   . returnGR = TRUE)
2. lapply(seq_len(ncol(passMat)), function(x) {
   . idx <- which(passMat[, x])
   . rrx <- rr[idx]
   . rrx$Log2FC <- SummarizedExperiment::assays(seMarker[idx,
   . ])[["Log2FC"]][, x]
   . rrx$FDR <- SummarizedExperiment::assays(seMarker[idx, ])[["FDR"]][,
   . x]
   . if ("MeanDiff" %in% assayNames) {
   . rrx$MeanDiff <- SummarizedExperiment::assays(seMarker[idx,
   . ])[["MeanDiff"]][, x]
   . }
   . rrx <- rrx[order(rrx$FDR), , drop = FALSE]
   . if (!is.null(n)) {
   . if (n < nrow(rrx)) {
   . rrx <- rrx[seq_len(n), , drop = FALSE]
   . }
   . }
   . rrx
   . }) %>% SimpleList
3. SimpleList(.)
4. lapply(seq_len(ncol(passMat)), function(x) {
   . idx <- which(passMat[, x])
   . rrx <- rr[idx]
   . rrx$Log2FC <- SummarizedExperiment::assays(seMarker[idx,
   . ])[["Log2FC"]][, x]
   . rrx$FDR <- SummarizedExperiment::assays(seMarker[idx, ])[["FDR"]][,
   . x]
   . if ("MeanDiff" %in% assayNames) {
   . rrx$MeanDiff <- SummarizedExperiment::assays(seMarker[idx,
   . ])[["MeanDiff"]][, x]
   . }
   . rrx <- rrx[order(rrx$FDR), , drop = FALSE]
   . if (!is.null(n)) {
   . if (n < nrow(rrx)) {
   . rrx <- rrx[seq_len(n), , drop = FALSE]
   . }
   . }
   . rrx
   . })
5. FUN(X[[i]], ...)
6. $<-(tmp, Log2FC, value = c(1.44930142980843, 1.44699865424006,
   . 2.43710342858528, 2.41907599333148, 1.24409516167695, 1.43483749840799,
   . 1.27413740697967, 1.77830953612223, 1.18718873131247, 1.32587539944879,
   . 1.36603579669386, 1.02843882149065, 1.27020759155352, 1.20650523216843,
   . 1.89224684382123, 1.35314152731967, 1.69750086776501, 1.23231531222107,
   . 1.05943136702463, 1.24635378574012, 1.4912936293512, 1.04464598287467,
   . 1.60339949771058, 2.48349482433459, 3.03105537711964, 1.04513349008691,
   . 1.57472911098149, 2.04148220785651, 1.01640767065374, 1.01217597754628,
   . 1.38632630558414, 2.32616288400691, 1.43790351313235, 2.61123490477872,
   . 1.2425927836295, 1.22182800106868, 1.33942146226859, 1.05375438215196,
   . 1.77784990604465, 1.67495159258951, 1.13850867740225, 1.07973235703242,
   . 1.04934688622261, 1.10670778178779, 1.08341757549326, 1.11595804670766,
   . 1.22915819271981, 1.2231275890393, 1.08386629982699, 1.85792564335976,
   . 2.04634216611824, 1.18891360352884, 1.36632390578299, 1.23543851700314,
   . 1.01986358250508, 2.34948565810177, 1.07193459074847, 1.2816157909949,
   . 1.03892398073052, 3.70559621518396))
7. updateObject(x)
8. updateObject(x)
9. callNextMethod()
10. .nextMethod(object = object)
    [2:35 PM, 7/25/2022] Val: 11. updateObject(object@elementMetadata, ..., verbose = verbose)
11. validObject(result)
12. anyStrings(validityMethod(as(object, superClass)))
13. isTRUE(x)
14. validityMethod(as(object, superClass))
15. method(object)
16. .valid.SimpleList.listData(x)
17. sapply(as.list(x), function(xi) extends(class(xi), elementTypeX))
18. sapply(as.list(x), function(xi) extends(class(xi), elementTypeX))
19. simplify2array(answer, higher = (simplify == "array"))

Similar error was previously addressed in #938 and resolved after reinstalling ArchR. Unfortunately this is not my case.
Interestingly, I can load GenomicRanges.
Any suggestions will be more than appreciated

[rcorces]

I am not able to recapitulate this error with the tutorial data (see below). Are you getting this error on the tutorial data?

> markersPeaks <- getMarkerFeatures(
+     ArchRProj = projHeme5, 
+     useMatrix = "PeakMatrix", 
+     groupBy = "Clusters2",
+     bias = c("TSSEnrichment", "log10(nFrags)"),
+     testMethod = "wilcoxon"
+ )
ArchR logging to : ArchRLogs/ArchR-getMarkerFeatures-43075bcfdab2-Date-2022-07-26_Time-08-32-45.log
If there is an issue, please report to github with logFile!
2022-07-26 08:32:46 : Matching Known Biases, 0.008 mins elapsed.
###########
2022-07-26 08:33:13 : Completed Pairwise Tests, 0.466 mins elapsed.
###########
ArchR logging successful to : ArchRLogs/ArchR-getMarkerFeatures-43075bcfdab2-Date-2022-07-26_Time-08-32-45.log
> markerList <- getMarkers(markersPeaks, cutOff = "FDR <= 0.01 & Log2FC >= 1")
> markerList2 <- getMarkers(markersPeaks, cutOff = "FDR <= 0.01 & Log2FC >= 1", returnGR = TRUE)
> markerList2
List of length 11
names(11): B CD4.M CD4.N CLP Erythroid GMP Mono NK pDC PreB Progenitor

The code for getMarkers() is quite simple and it would be easy for you to step through it line by line to figure out why you're getting this error. Its failing within the lapply call but I'm not certain where. Either way, its probably something specific to your environment if you're getting this error on the tutorial data.

[VDD58]

Little update,
I can select a particular gene and get the Grange but not run getMarkers(markersPeaks, cutOff = "FDR <= 0.05 & Log2FC >= 1",
. returnGR = TRUE)

getGenes(ArchRProj = proj5, symbols = 'TP53')

GRanges object with 1 range and 2 metadata columns:
      seqnames          ranges strand |     gene_id      symbol
         <Rle>       <IRanges>  <Rle> | <character> <character>
  [1]    chr17 7565097-7590868      - |        7157        TP53
  -------
  seqinfo: 24 sequences from hg19 genome