plotBrowserTrack Error in .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), : Exiting See Error Above

[danli349]

Hello:

When I try to do plotBrowserTrack using a specific sample,

Samples <- projHeme$Sample
Samples2 <- Samples[!duplicated(Samples)]
for(i in 1:length(Samples2)){
    idxSample <- BiocGenerics::which(projHeme3$Sample %in% Samples2[i])
    cellsSample <- projHeme3$cellNames[idxSample]
    tmp <- projHeme3[cellsSample, ]
    p <- plotBrowserTrack(
        ArchRProj = tmp, 
        groupBy = "Clusters2", 
        geneSymbol = markerGenes, 
        upstream = 50000,
        downstream = 20000)
    for(j in 1:length(p)){
        pdf(paste0("plotBrowserTrack_",markerGenes[j],"_cluster_by_RNA_", Samples2[i], "_only.pdf",sep=""))
        grid::grid.newpage()
        grid::grid.draw(p[[j]])
        dev.off()
        }
    }

I got this error:

ArchR logging to : ArchRLogs/ArchR-plotBrowserTrack-8ec10712fc1-Date-2024-12-18_Time-17-22-06.038219.log
If there is an issue, please report to github with logFile!

2024-12-18 17:22:06.195084 : Validating Region, 0.003 mins elapsed.

GRanges object with 2 ranges and 2 metadata columns:
      seqnames            ranges strand |     gene_id      symbol
         <Rle>         <IRanges>  <Rle> | <character> <character>
  [1]     chr4 89274473-89294619      - |       12578      Cdkn2a
  [2]     chr7 89954654-89980976      - |       13626         Eed
  -------
  seqinfo: 21 sequences from mm10 genome
2024-12-18 17:22:06.258429 : Adding Bulk Tracks (1 of 2), 0.004 mins elapsed.

Getting Region From Arrow Files 1 of 1


************************************************************
2024-12-18 17:22:07.963247 : ERROR Found in .groupRegionSumArrows for PECN_POS_4 
LogFile = ArchRLogs/ArchR-plotBrowserTrack-8ec10712fc1-Date-2024-12-18_Time-17-22-06.038219.log

<subscriptOutOfBoundsError in `[<-`(`*tmp*`, , uniqueGroups[i], value = Matrix::rowSums(mat[,     which(cellGroups == uniqueGroups[i]), drop = FALSE])): subscript out of bounds>

************************************************************

Error in .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), : Exiting See Error Above
Traceback:

1. lapply(seq_along(region), function(x) {
 .     plotList <- list()
 .     if ("bulktrack" %in% tolower(plotSummary)) {
 .         .logDiffTime(sprintf("Adding Bulk Tracks (%s of %s)", 
 .             x, length(region)), t1 = tstart, verbose = verbose, 
 .             logFile = logFile)
 .         plotList$bulktrack <- .bulkTracks(ArchRProj = ArchRProj, 
 .             region = region[x], tileSize = tileSize, groupBy = groupBy, 
 .             threads = threads, minCells = minCells, pal = pal, 
 .             ylim = ylim, baseSize = baseSize, borderWidth = borderWidth, 
 .             tickWidth = tickWidth, facetbaseSize = facetbaseSize, 
 .             normMethod = normMethod, geneAnnotation = geneAnnotation, 
 .             title = title, useGroups = useGroups, tstart = tstart, 
 .             logFile = logFile) + theme(plot.margin = unit(c(0.35, 
 .             0.75, 0.35, 0.75), "cm"))
 .     }
 .     if ("sctrack" %in% tolower(plotSummary)) {
 .         .logDiffTime(sprintf("Adding SC Tracks (%s of %s)", x, 
 .             length(region)), t1 = tstart, verbose = verbose, 
 .             logFile = logFile)
 .         plotList$sctrack <- .scTracks(ArchRProj = ArchRProj, 
 .             region = region[x], tileSize = tileSize, groupBy = groupBy, 
 .             threads = threads, minCells = 5, maxCells = scCellsMax, 
 .             pal = pal, baseSize = baseSize, borderWidth = borderWidth, 
 .             tickWidth = tickWidth, scTileSize = scTileSize, facetbaseSize = facetbaseSize, 
 .             geneAnnotation = geneAnnotation, title = title, useGroups = useGroups, 
 .             tstart = tstart, logFile = logFile) + theme(plot.margin = unit(c(0.35, 
 .             0.75, 0.35, 0.75), "cm"))
 .     }
 .     if ("featuretrack" %in% tolower(plotSummary)) {
 .         if (!is.null(features)) {
 .             .logDiffTime(sprintf("Adding Feature Tracks (%s of %s)", 
 .                 x, length(region)), t1 = tstart, verbose = verbose, 
 .                 logFile = logFile)
 .             plotList$featuretrack <- .featureTracks(features = features, 
 .                 region = region[x], facetbaseSize = facetbaseSize, 
 .                 hideX = TRUE, title = "Peaks", logFile = logFile) + 
 .                 theme(plot.margin = unit(c(0.1, 0.75, 0.1, 0.75), 
 .                   "cm"))
 .         }
 .     }
 .     if ("looptrack" %in% tolower(plotSummary)) {
 .         if (!is.null(loops)) {
 .             .logDiffTime(sprintf("Adding Loop Tracks (%s of %s)", 
 .                 x, length(region)), t1 = tstart, verbose = verbose, 
 .                 logFile = logFile)
 .             plotList$looptrack <- .loopTracks(loops = loops, 
 .                 region = region[x], facetbaseSize = facetbaseSize, 
 .                 hideX = TRUE, hideY = TRUE, title = "Loops", 
 .                 logFile = logFile) + theme(plot.margin = unit(c(0.1, 
 .                 0.75, 0.1, 0.75), "cm"))
 .         }
 .     }
 .     if ("genetrack" %in% tolower(plotSummary)) {
 .         .logDiffTime(sprintf("Adding Gene Tracks (%s of %s)", 
 .             x, length(region)), t1 = tstart, verbose = verbose, 
 .             logFile = logFile)
 .         plotList$genetrack <- .geneTracks(geneAnnotation = geneAnnotation, 
 .             region = region[x], facetbaseSize = facetbaseSize, 
 .             title = "Genes", logFile = logFile) + theme(plot.margin = unit(c(0.1, 
 .             0.75, 0.1, 0.75), "cm"))
 .     }
 .     plotSummary <- tolower(plotSummary)
 .     names(sizes) <- plotSummary
 .     sizes <- sizes[order(plotSummary)]
 .     plotSummary <- plotSummary[order(plotSummary)]
 .     sizes <- sizes[tolower(names(plotList))]
 .     if (!is.null(useMatrix)) {
 .         suppressWarnings(.combinedFeaturePlot(plotList = plotList, 
 .             log2Norm = log2Norm, featureMat = featureMat, feature = region[x]$symbol[[1]], 
 .             useMatrix = useMatrix, pal = pal, sizes = sizes, 
 .             baseSize = baseSize, facetbaseSize = facetbaseSize, 
 .             borderWidth = borderWidth, tickWidth = tickWidth))
 .     }
 .     else {
 .         .logThis(names(plotList), sprintf("(%s of %s) names(plotList)", 
 .             x, length(region)), logFile = logFile)
 .         .logThis(sizes, sprintf("(%s of %s) sizes", x, length(region)), 
 .             logFile = logFile)
 .         .logDiffTime("Plotting", t1 = tstart, verbose = verbose, 
 .             logFile = logFile)
 .         tryCatch({
 .             suppressWarnings(ggAlignPlots(plotList = plotList, 
 .                 sizes = sizes, draw = FALSE))
 .         }, error = function(e) {
 .             .logMessage("Error with plotting, diagnosing each element", 
 .                 verbose = TRUE, logFile = logFile)
 .             for (i in seq_along(plotList)) {
 .                 tryCatch({
 .                   print(plotList[[i]])
 .                 }, error = function(f) {
 .                   .logError(f, fn = names(plotList)[i], info = "", 
 .                     errorList = NULL, logFile = logFile)
 .                 })
 .             }
 .             .logError(e, fn = "ggAlignPlots", info = "", errorList = NULL, 
 .                 logFile = logFile)
 .         })
 .     }
 . })
2. FUN(X[[i]], ...)
3. .bulkTracks(ArchRProj = ArchRProj, region = region[x], tileSize = tileSize, 
 .     groupBy = groupBy, threads = threads, minCells = minCells, 
 .     pal = pal, ylim = ylim, baseSize = baseSize, borderWidth = borderWidth, 
 .     tickWidth = tickWidth, facetbaseSize = facetbaseSize, normMethod = normMethod, 
 .     geneAnnotation = geneAnnotation, title = title, useGroups = useGroups, 
 .     tstart = tstart, logFile = logFile)
4. .groupRegionSumArrows(ArchRProj = ArchRProj, groupBy = groupBy, 
 .     normMethod = normMethod, useGroups = useGroups, minCells = minCells, 
 .     region = region, tileSize = tileSize, threads = threads, 
 .     verbose = verbose, logFile = logFile)
5. .safelapply(seq_along(ArrowFiles), function(i) {
 .     .logMessage(sprintf("Getting Region From Arrow Files %s of %s", 
 .         i, length(ArrowFiles)), logFile = logFile)
 .     tryCatch({
 .         .regionSumArrows(ArrowFile = ArrowFiles[i], region = region, 
 .             regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
 .             cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
 .             uniqueGroups = uniqueGroups)
 .     }, error = function(e) {
 .         errorList <- list(ArrowFile = ArrowFiles[i], region = region, 
 .             regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
 .             cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
 .             uniqueGroups = uniqueGroups)
 .         .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), 
 .             errorList = errorList, logFile = logFile)
 .     })
 . }, threads = threads) %>% Reduce("+", .)
6. Reduce("+", .)
7. .safelapply(seq_along(ArrowFiles), function(i) {
 .     .logMessage(sprintf("Getting Region From Arrow Files %s of %s", 
 .         i, length(ArrowFiles)), logFile = logFile)
 .     tryCatch({
 .         .regionSumArrows(ArrowFile = ArrowFiles[i], region = region, 
 .             regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
 .             cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
 .             uniqueGroups = uniqueGroups)
 .     }, error = function(e) {
 .         errorList <- list(ArrowFile = ArrowFiles[i], region = region, 
 .             regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
 .             cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
 .             uniqueGroups = uniqueGroups)
 .         .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), 
 .             errorList = errorList, logFile = logFile)
 .     })
 . }, threads = threads)
8. mclapply(..., mc.cores = threads, mc.preschedule = preschedule)
9. lapply(X = X, FUN = FUN, ...)
10. FUN(X[[i]], ...)
11. tryCatch({
  .     .regionSumArrows(ArrowFile = ArrowFiles[i], region = region, 
  .         regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
  .         cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
  .         uniqueGroups = uniqueGroups)
  . }, error = function(e) {
  .     errorList <- list(ArrowFile = ArrowFiles[i], region = region, 
  .         regionTiles = regionTiles, tileSize = tileSize, cellNames = cellsBySample[[names(ArrowFiles)[i]]], 
  .         cellGroups = groupsBySample[[names(ArrowFiles)[i]]], 
  .         uniqueGroups = uniqueGroups)
  .     .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), 
  .         errorList = errorList, logFile = logFile)
  . })
12. tryCatchList(expr, classes, parentenv, handlers)
13. tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. value[[3L]](cond)
15. .logError(e, fn = ".groupRegionSumArrows", info = .sampleName(ArrowFiles[i]), 
  .     errorList = errorList, logFile = logFile)
16. stop("Exiting See Error Above")
17. .handleSimpleError(function (cnd) 
  . {
  .     watcher$capture_plot_and_output()
  .     cnd <- sanitize_call(cnd)
  .     watcher$push(cnd)
  .     switch(on_error, continue = invokeRestart("eval_continue"), 
  .         stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error", 
  .             cnd))
  . }, "Exiting See Error Above", base::quote(.logError(e, fn = ".groupRegionSumArrows", 
  .     info = .sampleName(ArrowFiles[i]), errorList = errorList, 
  .     logFile = logFile)))

ArchR-plotBrowserTrack-8ec10712fc1-Date-2024-12-18_Time-17-22-06.038219.log

Could you please let me know how can I solve it?

Thanks a lot

[rcorces]

Hi @danli349! 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.