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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2149/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TileDBArray 1.16.0  (landing page)
Aaron Lun
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/TileDBArray
git_branch: RELEASE_3_20
git_last_commit: f71c41f
git_last_commit_date: 2024-10-29 10:50:33 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


BUILD results for TileDBArray on merida1

To the developers/maintainers of the TileDBArray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TileDBArray.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: TileDBArray
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TileDBArray
StartedAt: 2024-12-19 22:40:20 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 22:41:18 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 58.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TileDBArray
###
##############################################################################
##############################################################################


* checking for file ‘TileDBArray/DESCRIPTION’ ... OK
* preparing ‘TileDBArray’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 35822 Illegal instruction: 4  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpRDaA5b/xshell8495395571b5' 2>&1
 ERROR
--- re-building ‘userguide.Rmd’ using rmarkdown

 *** caught illegal operation ***
address 0x1135d02f9, cause 'illegal opcode'

Traceback:
 1: libtiledb_array_open(ctx@ptr, uri, query_type)
 2: tiledb_array(sink@path, attrs = sink@attr, query_type = "WRITE")
 3: write_block(sink, viewport, block)
 4: write_block(sink, viewport, block)
 5: FUN(init, viewport, ...)
 6: FUN(viewport, init, ...)
 7: gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
 8: sinkApply(sink, FUN, x, verbose, verbose_read_block, grid = grid,     verbose = FALSE)
 9: BLOCK_write_to_sink(sink, x)
10: writeTileDBArray(X)
11: eval(expr, envir)
12: eval(expr, envir)
13: withVisible(eval(expr, envir))
14: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = 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")    }}, error = 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))})
15: eval(call)
16: eval(call)
17: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
18: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
20: withRestartList(expr, restarts[-nr])
21: doWithOneRestart(return(expr), restart)
22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
23: withRestartList(expr, restarts[-nr])
24: doWithOneRestart(return(expr), restart)
25: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
26: withRestartList(expr, restarts)
27: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE,     eval_error = function(cnd) {        signalCondition(cnd)        stop(cnd)    })
28: evaluate::evaluate(...)
29: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
30: in_dir(input_dir(), expr)
31: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
32: eng_r(options)
33: block_exec(params)
34: call_block(x)
35: process_group(group)
36: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
37: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
38: process_file(text, output)
39: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
40: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
41: vweave_rmarkdown(...)
42: engine$weave(file, quiet = quiet, encoding = enc)
43: doTryCatch(return(expr), name, parentenv, handler)
44: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
47: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...