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Posted to issues@arrow.apache.org by "barracuda156 (via GitHub)" <gi...@apache.org> on 2023/05/31 04:36:50 UTC
[GitHub] [arrow] barracuda156 opened a new issue, #35832: [R] arrow segfaults on macOS 13 on loading: address 0xdde0, cause 'memory not mapped'
barracuda156 opened a new issue, #35832:
URL: https://github.com/apache/arrow/issues/35832
### Describe the bug, including details regarding any error messages, version, and platform.
```
2023-05-31T03:29:22.4399840Z /opt/local/bin/clang++-mp-15 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -arch x86_64 -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o compute.o config.o csv.o dataset.o datatype.o expression.o extension-impl.o feather.o field.o filesystem.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o safe-call-into-r-impl.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/opt/local/lib -larrow_acero -larrow_dataset -lparquet -larrow -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framewo
rk -Wl,CoreFoundation
2023-05-31T03:29:22.8237900Z installing to /opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new/arrow/libs
2023-05-31T03:29:22.8277300Z ** R
2023-05-31T03:29:22.9261840Z ** inst
2023-05-31T03:29:22.9289340Z ** byte-compile and prepare package for lazy loading
2023-05-31T03:29:59.2771540Z ** help
2023-05-31T03:29:59.7237560Z *** installing help indices
2023-05-31T03:29:59.9384780Z ** building package indices
2023-05-31T03:30:00.3599180Z ** testing if installed package can be loaded from temporary location
2023-05-31T03:30:00.9878060Z sh: line 1: 19545 Segmentation fault: 11 R_TESTS= '/opt/local/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/.tmp/RtmpKStuJb/file44c3339fb0e8'
2023-05-31T03:30:00.9889470Z
2023-05-31T03:30:00.9896130Z *** caught segfault ***
2023-05-31T03:30:00.9910800Z address 0xdde0, cause 'memory not mapped'
2023-05-31T03:30:00.9921710Z
2023-05-31T03:30:00.9924050Z Traceback:
2023-05-31T03:30:00.9925820Z 1: dyn.load(file, DLLpath = DLLpath, ...)
2023-05-31T03:30:00.9927140Z 2: library.dynam(lib, package, package.lib)
2023-05-31T03:30:00.9927470Z 3: loadNamespace(package, lib.loc)
2023-05-31T03:30:00.9929450Z 4: doTryCatch(return(expr), name, parentenv, handler)
2023-05-31T03:30:00.9936220Z 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
2023-05-31T03:30:00.9940000Z 6: tryCatchList(expr, classes, parentenv, handlers)
2023-05-31T03:30:00.9946880Z 7: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
2023-05-31T03:30:00.9953400Z 8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
2023-05-31T03:30:00.9955010Z 9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
2023-05-31T03:30:00.9955650Z 10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))
2023-05-31T03:30:00.9956260Z 11: doTryCatch(return(expr), name, parentenv, handler)
2023-05-31T03:30:00.9957250Z 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
2023-05-31T03:30:00.9957680Z 13: tryCatchList(expr, classes, parentenv, handlers)
2023-05-31T03:30:00.9962850Z 14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
2023-05-31T03:30:00.9966480Z 15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)))
2023-05-31T03:30:00.9971950Z 16: tools:::.test_load_package("arrow", "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-arrow/00new")
2023-05-31T03:30:00.9990930Z An irrecoverable exception occurred. R is aborting now ...
2023-05-31T03:30:00.9992930Z ERROR: loading failed
2023-05-31T03:30:00.9995650Z * removing ‘/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/arrow’
2023-05-31T03:30:01.0077230Z Command failed: cd "/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/arrow" && /opt/local/bin/R CMD INSTALL . --library=/opt/local/var/macports/build/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
2023-05-31T03:30:01.0086660Z Error: Failed to destroot R-arrow: command execution failed
2023-05-31T03:30:01.0086940Z Exit code: 1
2023-05-31T03:30:01.0091130Z DEBUG: Error code: CHILDSTATUS 17599 1
2023-05-31T03:30:01.0093680Z DEBUG: Backtrace: command execution failed
2023-05-31T03:30:01.0097430Z while executing
2023-05-31T03:30:01.0100960Z "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
2023-05-31T03:30:01.0102490Z invoked from within
2023-05-31T03:30:01.0103960Z "command_exec -callback portprogress::target_progress_callback destroot"
2023-05-31T03:30:01.0105130Z (procedure "portdestroot::destroot_main" line 2)
2023-05-31T03:30:01.0106180Z invoked from within
2023-05-31T03:30:01.0107190Z "$procedure $targetname"
2023-05-31T03:30:01.0109770Z Error: See /opt/local/var/macports/logs/_Users_runner_work_macports-ports_macports-ports_ports_R_R-arrow/R-arrow/main.log for details.
2023-05-31T03:30:01.0157460Z Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
2023-05-31T03:30:01.0159380Z Error: Processing of port R-arrow failed
2023-05-31T03:30:01.0826290Z Build of 'R-arrow' failed.
```
Both `apache-arrow` and `R-arrow` are at 12.0.0. Ironically, build on old macOS 10.6 with GCC is perfectly fine. New macOS with Clang fails.
[R-arrow_macOS_13_log.txt](https://github.com/apache/arrow/files/11608652/R-arrow_macOS_13_log.txt)
### Component(s)
R
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[GitHub] [arrow] barracuda156 commented on issue #35832: [R] arrow segfaults on macOS 13 on loading: address 0xdde0, cause 'memory not mapped'
Posted by "barracuda156 (via GitHub)" <gi...@apache.org>.
barracuda156 commented on issue #35832:
URL: https://github.com/apache/arrow/issues/35832#issuecomment-1597821560
@paleolimbot Those are unrelated in a sense of what and why is broken.
Here, with R package, it is new macOS with clangs are failing, while archaic systems with gcc are building it without a problem. I do not think this is Macports-specific. May be reproducible on macOS 13 with clang 15, if not other.
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[GitHub] [arrow] paleolimbot commented on issue #35832: [R] arrow segfaults on macOS 13 on loading: address 0xdde0, cause 'memory not mapped'
Posted by "paleolimbot (via GitHub)" <gi...@apache.org>.
paleolimbot commented on issue #35832:
URL: https://github.com/apache/arrow/issues/35832#issuecomment-1597682997
I'm not familiar with MacPorts or its packaging of Arrow or R. I see a linked ticket here about mimalloc...did that end up solving the issue?
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