addGroupCoverages: Error in rawToChar(bytes): embedded nul in string

[danli349]

Hello

How should I solve this problem?

projHeme4 <- addGroupCoverages(ArchRProj = projHeme3, groupBy = "Clusters")

ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-18c6270fa3c2-Date-2024-12-19_Time-11-39-24.379498.log
If there is an issue, please report to github with logFile!

C1 (1 of 15) : CellGroups N = 3

C2 (2 of 15) : CellGroups N = 2

C3 (3 of 15) : CellGroups N = 5

C4 (4 of 15) : CellGroups N = 4

C5 (5 of 15) : CellGroups N = 2

C6 (6 of 15) : CellGroups N = 4

C7 (7 of 15) : CellGroups N = 5

C8 (8 of 15) : CellGroups N = 5

C9 (9 of 15) : CellGroups N = 5

C10 (10 of 15) : CellGroups N = 5

C11 (11 of 15) : CellGroups N = 5

C12 (12 of 15) : CellGroups N = 5

C13 (13 of 15) : CellGroups N = 5

C14 (14 of 15) : CellGroups N = 5

C15 (15 of 15) : CellGroups N = 5

2024-12-19 11:39:30.054384 : Creating Coverage Files!, 0.094 mins elapsed.

2024-12-19 11:39:30.059389 : Batch Execution w/ safelapply!, 0.094 mins elapsed.

Error in rawToChar(bytes): embedded nul in string: 'R_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\nR_zmq_msg_send errno: 4 strerr
Traceback:

1. .batchlapply(args)
2. do.call(.safelapply, args)
3. (function (..., threads = 1, preschedule = FALSE) 
 . {
 .     if (tolower(.Platform$OS.type) == "windows") {
 .         threads <- 1
 .     }
 .     if (threads > 1) {
 .         .requirePackage("parallel", source = "cran")
 .         o <- mclapply(..., mc.cores = threads, mc.preschedule = preschedule)
 .         errorMsg <- list()
 .         for (i in seq_along(o)) {
 .             if (inherits(o[[i]], "try-error")) {
 .                 capOut <- utils::capture.output(o[[i]])
 .                 capOut <- capOut[!grepl("attr\\(\\,|try-error", 
 .                   capOut)]
 .                 capOut <- head(capOut, 10)
 .                 capOut <- unlist(lapply(capOut, function(x) substr(x, 
 .                   1, 250)))
 .                 capOut <- paste0("\t", capOut)
 .                 errorMsg[[length(errorMsg) + 1]] <- paste0(c(paste0("Error Found Iteration ", 
 .                   i, " : "), capOut), "\n")
 .             }
 .         }
 .         if (length(errorMsg) != 0) {
 .             errorMsg <- unlist(errorMsg)
 .             errorMsg <- head(errorMsg, 50)
 .             errorMsg[1] <- paste0("\n", errorMsg[1])
 .             stop(errorMsg)
 .         }
 .     }
 .     else {
 .         o <- lapply(...)
 .     }
 .     o
 . })(X = 1:65, FUN = function (i = NULL, cellGroups, kmerBias = NULL, 
 .     kmerLength = 6, genome = NULL, ArrowFiles = NULL, cellsInArrow = NULL, 
 .     availableChr = NULL, chromLengths = NULL, covDir = NULL, 
 .     tstart = NULL, subThreads = 1, verbose = TRUE, logFile = NULL) 
 . {
 .     prefix <- sprintf("Group %s (%s of %s) :", names(cellGroups)[i], 
 .         i, length(cellGroups))
 .     cellGroupi <- cellGroups[[i]]
 .     namei <- make.names(names(cellGroups)[i])
 .     covFile <- file.path(covDir, paste0(namei, ".insertions.coverage.h5"))
 .     rmf <- .suppressAll(file.remove(covFile))
 .     .logDiffTime(sprintf("%s Creating Group Coverage File : %s", 
 .         prefix, basename(covFile)), tstart, verbose = verbose, 
 .         logFile = logFile)
 .     tableGroupi <- table(cellGroupi)
 .     .logThis(cellGroupi, paste0(prefix, " cellGroupi"), logFile = logFile)
 .     .logMessage(paste0("Number of Cells = ", length(cellGroups[[i]])), 
 .         logFile = logFile)
 .     o <- tryCatch({
 .         o <- h5closeAll()
 .         o <- h5createFile(covFile)
 .     }, error = function(e) {
 .         rmf <- .suppressAll(file.remove(covFile))
 .         o <- h5closeAll()
 .         o <- h5createFile(covFile)
 .     })
 .     if (file.exists(covFile)) {
 .         .logMessage("Coverage File Exists!", logFile = logFile)
 .     }
 .     else {
 .         .logMessage("Coverage File Does Not Exist!", logFile = logFile)
 .     }
 .     o <- h5closeAll()
 .     o <- h5createGroup(covFile, paste0("Coverage"))
 .     .logMessage("Added Coverage Group", logFile = logFile)
 .     o <- h5closeAll()
 .     o <- h5createGroup(covFile, paste0("Metadata"))
 .     .logMessage("Added Metadata Group", logFile = logFile)
 .     o <- h5closeAll()
 .     o <- h5write(obj = "ArrowCoverage", file = covFile, name = "Class")
 .     .logMessage("Added ArrowCoverage Class", logFile = logFile)
 .     o <- h5closeAll()
 .     o <- h5createGroup(covFile, paste0("Coverage/Info"))
 .     .logMessage("Added Coverage/Info", logFile = logFile)
 .     o <- h5closeAll()
 .     o <- h5write(as.character(cellGroupi), covFile, "Coverage/Info/CellNames")
 .     .logMessage("Added Coverage/Info/CellNames", logFile = logFile)
 .     nFragDump <- 0
 .     nCells <- c()
 .     for (k in seq_along(availableChr)) {
 .         .logDiffTime(sprintf("%s Processed Fragments Chr (%s of %s)", 
 .             prefix, k, length(availableChr)), tstart, verbose = FALSE, 
 .             logFile = logFile)
 .         it <- 0
 .         for (j in seq_along(ArrowFiles)) {
 .             cellsInI <- sum(cellsInArrow[[names(ArrowFiles)[j]]] %in% 
 .                 cellGroupi)
 .             if (cellsInI > 0) {
 .                 it <- it + 1
 .                 if (it == 1) {
 .                   fragik <- .getFragsFromArrow(ArrowFiles[j], 
 .                     chr = availableChr[k], out = "GRanges", cellNames = cellGroupi)
 .                 }
 .                 else {
 .                   fragik <- c(fragik, .getFragsFromArrow(ArrowFiles[j], 
 .                     chr = availableChr[k], out = "GRanges", cellNames = cellGroupi))
 .                 }
 .             }
 .         }
 .         matchRG <- as.vector(S4Vectors::match(mcols(fragik)$RG, 
 .             names(tableGroupi)))
 .         fragik <- rep(fragik, tableGroupi[matchRG])
 .         nCells <- c(nCells, unique(mcols(fragik)$RG))
 .         covk <- coverage(IRanges(start = c(start(fragik), end(fragik)), 
 .             width = 1), width = chromLengths[availableChr[k]])
 .         nFragDump <- nFragDump + length(fragik)
 .         rm(fragik)
 .         chrLengths <- paste0("Coverage/", availableChr[k], "/Lengths")
 .         chrValues <- paste0("Coverage/", availableChr[k], "/Values")
 .         lengthRle <- length(covk@lengths)
 .         o <- h5createGroup(covFile, paste0("Coverage/", availableChr[k]))
 .         o <- .suppressAll(h5createDataset(covFile, chrLengths, 
 .             storage.mode = "integer", dims = c(lengthRle, 1), 
 .             level = 0))
 .         o <- .suppressAll(h5createDataset(covFile, chrValues, 
 .             storage.mode = "integer", dims = c(lengthRle, 1), 
 .             level = 0))
 .         o <- h5write(obj = covk@lengths, file = covFile, name = chrLengths)
 .         o <- h5write(obj = covk@values, file = covFile, name = chrValues)
 .         gc()
 .     }
 .     if (length(unique(cellGroupi)) != length(unique(nCells))) {
 .         .logMessage(paste0("Not all cells (", length(unique(cellGroupi)), 
 .             ") were found for coverage creation (", length(unique(nCells)), 
 .             ")!"), logFile = logFile)
 .         stop("Not all cells (", length(unique(cellGroupi)), ") were found for coverage creation (", 
 .             length(unique(nCells)), ")!")
 .     }
 .     out <- list(covFile = covFile, nCells = length(cellGroupi), 
 .         nFragments = nFragDump)
 .     return(out)
 . }, cellGroups = new("SimpleCharacterList", elementType = "character", 
 .     elementMetadata = NULL, metadata = list(), listData = list(
 .         C1._.PECN_NEG_5 = c("PECN_NEG_5#ACGCACGGTTCTTTAG-1", ...)), covDir = "/mnt/d/R/seurat/Amish_Juan_PECN/Save-ProjHeme4/GroupCoverages/Clusters", 
 .     threads = 10L, verbose = TRUE, tstart = structure(1734626364.39807, class = c("POSIXct", 
 .     "POSIXt")), logFile = "ArchRLogs/ArchR-addGroupCoverages-18c6270fa3c2-Date-2024-12-19_Time-11-39-24.379498.log", 
 .     subThreads = 1)
4. mclapply(..., mc.cores = threads, mc.preschedule = preschedule)
5. warning(gettextf("%d function calls resulted in an error", has.errors), 
 .     domain = NA)
6. .signalSimpleWarning("50 function calls resulted in an error", 
 .     base::quote(mclapply(..., mc.cores = threads, mc.preschedule = preschedule)))
7. withRestarts({
 .     .Internal(.signalCondition(simpleWarning(msg, call), msg, 
 .         call))
 .     .Internal(.dfltWarn(msg, call))
 . }, muffleWarning = function() NULL)
8. withOneRestart(expr, restarts[[1L]])
9. doWithOneRestart(return(expr), restart)
10. (function (cnd) 
  . {
  .     if (getOption("warn") >= 2 || getOption("warn") < 0) {
  .         return()
  .     }
  .     watcher$capture_plot_and_output()
  .     if (on_warning$capture) {
  .         cnd <- sanitize_call(cnd)
  .         watcher$push(cnd)
  .     }
  .     if (on_warning$silence) {
  .         invokeRestart("muffleWarning")
  .     }
  . })(structure(list(message = "50 function calls resulted in an error", 
  .     call = mclapply(..., mc.cores = threads, mc.preschedule = preschedule)), class = c("simpleWarning", 
  . "warning", "condition")))
11. watcher$capture_plot_and_output()
12. capture_output()
13. sink_con()
14. read_con(con)
15. rawToChar(bytes)
16. .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))
  . }, "embedded nul in string: 'R_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerror: Interrupted system call\\nR_zmq_msg_send errno: 4 strerr", 
  .     base::quote(rawToChar(bytes)))

ArchR-addGroupCoverages-18c6270fa3c2-Date-2024-12-19_Time-11-39-24.379498.log

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.

[danli349]

@rcorces
I solved this problem by reinstalling the new version ArchR

devtools::install_github("GreenleafLab/ArchR", ref="release_1.0.3", repos = BiocManager::repositories())

Thanks