[R] Crash on MacOS (x86) when running tests with homebrew apache-arrow also installed

paleolimbot commented 1 year ago

Describe the bug, including details regarding any error messages, version, and platform.

This is the second time this has happened...this is intermittent in the sense that it occurs only sometimes, but that "sometimes" depends on the commit that I've checked out. Once I check out a new commit, the problem goes away. That said, it's only happened for two commits, so maybe I'm reading into that too much.

This was actually reproduced with more than one commit checked out, and the error went away when I did brew uninstall gdal and brew uninstall apache-arrow. When I reinstall apache-arrow, I get the same segfault again.

I will take a closer look at the output of the buliding for both of those cases...I have a feeling there is one or more dependencies that get picked up from system when arrow is installed from homebrew that don't when it is not.

To reproduce...I do a clean rebuild and install of Arrow. .

CURRENT_WD=`pwd` export ARROW_HOME=/Users/dewey/.r-arrow-dev-build/dist export ARROW_SRC=/Users/dewey/Desktop/rscratch/arrow export ARROW_VIRTUALENV=/Users/dewey/Desktop/rscratch/pyarrow-dev rm -rf $ARROW_HOME mkdir -p $ARROW_HOME rm -rf $ARROW_HOME/../build mkdir $ARROW_HOME/../build pushd $ARROW_HOME/../build cmake \ -DCMAKE_INSTALL_PREFIX=$ARROW_HOME \ -DCMAKE_BUILD_TYPE=Debug \ -DCMAKE_INSTALL_LIBDIR=lib \ -DARROW_COMPUTE=ON \ -DARROW_CSV=ON \ -DARROW_DATASET=ON \ -DARROW_EXTRA_ERROR_CONTEXT=ON \ -DARROW_FILESYSTEM=ON \ -DARROW_INSTALL_NAME_RPATH=OFF \ -DARROW_JEMALLOC=ON \ -DARROW_JSON=ON \ -DARROW_PARQUET=ON \ -DARROW_WITH_SNAPPY=ON \ -DARROW_WITH_ZLIB=ON \ -DARROW_MIMALLOC=ON \ -DARROW_S3=ON \ -DARROW_WITH_BROTLI=ON \ -DARROW_WITH_BZ2=ON \ -DARROW_WITH_LZ4=ON \ -DARROW_WITH_SNAPPY=ON \ -DARROW_WITH_ZSTD=ON \ -DARROW_SUBSTRAIT=ON \ -DARROW_PYTHON=ON \ -DARROW_TESTING=ON \ "$ARROW_SRC/cpp" && make -j8 install && echo "Arrow built and installed to ARROW_HOME='$ARROW_HOME'" cd $CURRENT_WD

Then I do a clean reinstall of the R package: cd arrow/r && R CMD INSTALL . --preclean.

Then I run cd arrow/r && R -e 'devtools::test()'. I get a setfault in the same place every time ("altrep vectors from string arrays").

``` devtools::test() ℹ Testing arrow Some features are not enabled in this build of Arrow. Run `arrow_info()` for more information. ✔ | F W S OK | Context ⠹ | 73 | altrep *** caught segfault *** address 0x40, cause 'memory not mapped' Traceback: 1: .Call(`_arrow_vec_to_Array`, x, s_type) 2: vec_to_Array(x, type) 3: Array$create(c("one", NA, "three")) 4: eval(code, test_env) 5: eval(code, test_env) 6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 7: doTryCatch(return(expr), name, parentenv, handler) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 10: doTryCatch(return(expr), name, parentenv, handler) 11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 12: tryCatchList(expr, classes, parentenv, handlers) 13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 14: test_code(desc, code, env = parent.frame(), reporter = reporter) 15: test_that("altrep vectors from string arrays", { withr::local_options(list(arrow.use_altrep = TRUE)) v_chr <- Array$create(c("one", NA, "three")) c_chr <- ChunkedArray$create(c("one", NA, "three")) expect_true(is_arrow_altrep(as.vector(v_chr))) expect_true(is_arrow_altrep(as.vector(v_chr$Slice(1)))) expect_true(is_arrow_altrep(as.vector(c_chr))) expect_true(is_arrow_altrep(as.vector(c_chr$Slice(1)))) expect_true(is_arrow_altrep(as.vector(v_chr$Slice(2)))) expect_true(is_arrow_altrep(as.vector(c_chr$Slice(2)))) c_chr <- ChunkedArray$create("zero", c("one", NA, "three")) expect_equal(c_chr$num_chunks, 2L) expect_true(is_arrow_altrep(as.vector(c_chr))) expect_true(is_arrow_altrep(as.vector(c_chr$Slice(3))))}) 16: eval(code, test_env) 17: eval(code, test_env) 18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 19: doTryCatch(return(expr), name, parentenv, handler) 20: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 22: doTryCatch(return(expr), name, parentenv, handler) 23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 24: tryCatchList(expr, classes, parentenv, handlers) 25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 26: test_code(NULL, exprs, env) 27: source_file(path, child_env(env), wrap = wrap) 28: FUN(X[[i]], ...) 29: lapply(test_paths, test_one_file, env = env, wrap = wrap) 30: doTryCatch(return(expr), name, parentenv, handler) 31: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 32: tryCatchList(expr, classes, parentenv, handlers) 33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap)) 35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package) 36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel) 37: test_dir(test_path, package = package, reporter = reporter, ..., load_package = load_package) 38: testthat::test_local(pkg$path, filter = filter, stop_on_failure = stop_on_failure, load_package = load_package, ...) 39: devtools::test() An irrecoverable exception occurred. R is aborting now ... zsh: segmentation fault R -e "devtools::test()" ```

The backtrace is also consistent:

  arrow::Status Allocate(int64_t size, int64_t alignment, uint8_t** out) override {
    return GcAndTryAgain([&] { return pool_->Allocate(size, alignment, out); }); // Crash happens on this line
  }

The allocator is mimalloc.

Console is in 'commands' mode, prefix expressions with '?'. Attached to process 12660 Stop reason: EXC_BAD_ACCESS (code=1, address=0x40) bt * thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x40) * frame #0: 0x0000000107989fb2 libarrow.1000.dylib`arrow::(anonymous namespace)::MimallocAllocator::AllocateAligned(long long, unsigned char**) + 42 frame #1: 0x000000010798a25d libarrow.1000.dylib`arrow::BaseMemoryPoolImpl::Allocate(long long, unsigned char**) + 47 frame #2: 0x000000010628f5e2 arrow.so`arrow::Status GcMemoryPool::GcAndTryAgain(GcMemoryPool::Allocate(long long, long long, unsigned char**)::'lambda'() const&) [inlined] GcMemoryPool::Allocate(this=(0x00000001063499e8, 0x00007ffeeed2cb90, 0x00007ffeeed2cb98, 0x00007ffeeed2cba0))::'lambda'()::operator()() const at memorypool.cpp:31:46 [opt] frame #3: 0x000000010628f5bd arrow.so`arrow::Status GcMemoryPool::GcAndTryAgain(this=0x00000001063499e8, call=(0x00000001063499e8, 0x00007ffeeed2cb90, 0x00007ffeeed2cb98, 0x00007ffeeed2cba0))::'lambda'() const&) at memorypool.cpp:53:9 [opt] frame #4: 0x000000010628f4cd arrow.so`GcMemoryPool::Allocate(this=, size=, alignment=, out=) at memorypool.cpp:31:12 [opt] frame #5: 0x000000010cc75b7d libarrow.1100.dylib`arrow::PoolBuffer::Reserve(this=0x00007ffd715fff70, capacity=16) at memory_pool.cc:839:9 frame #6: 0x000000010cc75854 libarrow.1100.dylib`arrow::PoolBuffer::Resize(this=0x00007ffd715fff70, new_size=16, shrink_to_fit=true) at memory_pool.cc:863:7 frame #7: 0x000000010cc679bd libarrow.1100.dylib`arrow::Result>> arrow::(anonymous namespace)::ResizePoolBuffer>, std::__1::unique_ptr>>(buffer=arrow::PoolBuffer @ 0x00007ffd715fff70, size=16) at memory_pool.cc:903:3 frame #8: 0x000000010cc67949 libarrow.1100.dylib`arrow::AllocateResizableBuffer(size=16, alignment=64, pool=0x00000001063499e8) at memory_pool.cc:929:10 frame #9: 0x000000010628bf76 arrow.so`arrow::BufferBuilder::Resize(this=0x00007ffd715460d8, new_capacity=16, shrink_to_fit=) at buffer_builder.h:78:7 [opt] frame #10: 0x00000001062c2ff5 arrow.so`arrow::BaseBinaryBuilder::Resize(long long) [inlined] arrow::TypedBufferBuilder::Resize(this=0x00007ffd715460d8, new_capacity=4, shrink_to_fit=true) at buffer_builder.h:270:27 [opt] frame #11: 0x00000001062c2fd8 arrow.so`arrow::BaseBinaryBuilder::Resize(this=0x00007ffd71546048, capacity=3) at builder_binary.h:320:5 [opt] frame #12: 0x00000001062c26aa arrow.so`arrow::r::RPrimitiveConverter::UnsafeAppendUtf8Strings(cpp11::r_vector const&, long long, long long) [inlined] arrow::ArrayBuilder::Reserve(this=0x00007ffd71546048, additional_capacity=3) at builder_base.h:118:12 [opt] frame #13: 0x00000001062c267b arrow.so`arrow::r::RPrimitiveConverter::UnsafeAppendUtf8Strings(this=0x00007ffd715fed00, s=0x00007ffeeed2cea8, size=3, offset=0) at r_to_arrow.cpp:880:5 [opt] frame #14: 0x00000001062c242d arrow.so`arrow::r::RPrimitiveConverter::Extend(this=0x00007ffd715fed00, x=, size=3, offset=0) at r_to_arrow.cpp:869:12 [opt] frame #15: 0x0000000106299378 arrow.so`arrow::r::vec_to_arrow_ChunkedArray(x=0x00007ffd7bf309d8, type=, type_inferred=) at r_to_arrow.cpp:1329:26 [opt] frame #16: 0x0000000106299fe5 arrow.so`arrow::r::vec_to_arrow_Array(x=, type=, type_inferred=) at r_to_arrow.cpp:1335:24 [opt] frame #17: 0x000000010629c427 arrow.so`vec_to_Array(x=0x00007ffd7bf309d8, s_type=) at r_to_arrow.cpp:1593:23 [opt] frame #18: 0x00000001062183ed arrow.so`::_arrow_vec_to_Array(x_sexp=, s_type_sexp=) at arrowExports.cpp:4339:24 [opt] frame #19: 0x0000000100f3d8ed libR.dylib`R_doDotCall(ofun=, nargs=2, cargs=0x00007ffeeed2f530, call=0x00007ffd73af7f70) at dotcode.c:604:17 [opt] frame #20: 0x0000000100f3f28e libR.dylib`do_dotcall(call=0x00007ffd73af7f70, op=, args=, env=) at dotcode.c:1284:11 [opt] frame #21: 0x0000000100f6fe46 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e4c98) at eval.c:851:9 [opt] frame #22: 0x0000000100f9218e libR.dylib`do_begin(call=, op=0x00007ffd70816b20, args=0x00007ffd73af7de8, rho=0x00007ffd784e4c98) at eval.c:2539:10 [opt] frame #23: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e4c98) at eval.c:823:12 [opt] frame #24: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd74d00048, newrho=0x00007ffd784e4c98, sysparent=, rho=0x00007ffd784e5d70, arglist=, op=) at eval.c:0 [opt] frame #25: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd74d00048, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #26: 0x0000000100f6febb libR.dylib`Rf_eval(e=, rho=0x00007ffd784e5d70) at eval.c:871:12 [opt] frame #27: 0x0000000100f9224c libR.dylib`do_return(call=, op=, args=, rho=0x00007ffd784e5d70) at eval.c:2557:6 [opt] frame #28: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e5d70) at eval.c:823:12 [opt] frame #29: 0x0000000100f9218e libR.dylib`do_begin(call=, op=0x00007ffd70816b20, args=0x00007ffd74d002e8, rho=0x00007ffd784e5d70) at eval.c:2539:10 [opt] frame #30: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e5d70) at eval.c:823:12 [opt] frame #31: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e5d70) at eval.c:823:12 [opt] frame #32: 0x0000000100f9218e libR.dylib`do_begin(call=, op=0x00007ffd70816b20, args=0x00007ffd74d00630, rho=0x00007ffd784e5d70) at eval.c:2539:10 [opt] frame #33: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784e5d70) at eval.c:823:12 [opt] frame #34: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d05e0a8, newrho=0x00007ffd784e5d70, sysparent=, rho=0x00007ffd784b0950, arglist=, op=) at eval.c:0 [opt] frame #35: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d05e0a8, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #36: 0x0000000100f6febb libR.dylib`Rf_eval(e=, rho=0x00007ffd784b0950) at eval.c:871:12 [opt] frame #37: 0x0000000100f92eb6 libR.dylib`do_set(call=, op=0x00007ffd7080b608, args=0x00007ffd7d05e038, rho=0x00007ffd784b0950) at eval.c:2991:8 [opt] frame #38: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784b0950) at eval.c:823:12 [opt] frame #39: 0x0000000100f9218e libR.dylib`do_begin(call=, op=0x00007ffd70816b20, args=0x00007ffd7d05df20, rho=0x00007ffd784b0950) at eval.c:2539:10 [opt] frame #40: 0x0000000100f6fbf7 libR.dylib`Rf_eval(e=, rho=0x00007ffd784b0950) at eval.c:823:12 [opt] frame #41: 0x0000000100f93821 libR.dylib`do_eval(call=, op=, args=, rho=0x00007ffd784cf478) at eval.c:3366:13 [opt] frame #42: 0x0000000100f77035 libR.dylib`bcEval(body=0x00007ffd7086a208, rho=0x00007ffd784cf478, useCache=) at eval.c:7136:14 [opt] frame #43: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #44: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9320, newrho=0x00007ffd784cf478, sysparent=, rho=0x00007ffd780aef50, arglist=, op=) at eval.c:0 [opt] frame #45: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9320, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #46: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d0f0910, rho=0x00007ffd780aef50, useCache=) at eval.c:7104:12 [opt] frame #47: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #48: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784d0010) at eval.c:568:8 [opt] frame #49: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784d0010, symbol=0x00007ffd7085d350, rho=0x00007ffd784cfbe8, keepmiss=) at eval.c:5157:15 [opt] frame #50: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cfbe8, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #51: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd72d076d0, rho=0x00007ffd784cfbe8, useCache=) at eval.c:6888:20 [opt] frame #52: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #53: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9400, newrho=0x00007ffd784cfbe8, sysparent=, rho=0x00007ffd780aef50, arglist=, op=) at eval.c:0 [opt] frame #54: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9400, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #55: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d0f0948, rho=0x00007ffd780aef50, useCache=) at eval.c:7104:12 [opt] frame #56: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #57: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784cc0f0) at eval.c:568:8 [opt] frame #58: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784cc0f0, symbol=0x00007ffd7085d350, rho=0x00007ffd784cbe88, keepmiss=) at eval.c:5157:15 [opt] frame #59: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cbe88, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #60: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a4d8, rho=0x00007ffd784cbe88, useCache=) at eval.c:6888:20 [opt] frame #61: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #62: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784cba28) at eval.c:568:8 [opt] frame #63: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784cba28, symbol=0x00007ffd7085d350, rho=0x00007ffd784cb788, keepmiss=) at eval.c:5157:15 [opt] frame #64: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cb788, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #65: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd71956680, rho=0x00007ffd784cb788, useCache=) at eval.c:6888:20 [opt] frame #66: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #67: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784cade8) at eval.c:568:8 [opt] frame #68: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784cade8, symbol=0x00007ffd7085d350, rho=0x00007ffd784cab48, keepmiss=) at eval.c:5157:15 [opt] frame #69: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cab48, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #70: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd71956338, rho=0x00007ffd784cab48, useCache=) at eval.c:6888:20 [opt] frame #71: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #72: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784caa30) at eval.c:568:8 [opt] frame #73: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784caa30, symbol=0x00007ffd7085d350, rho=0x00007ffd784ca790, keepmiss=) at eval.c:5157:15 [opt] frame #74: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784ca790, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #75: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a820, rho=0x00007ffd784ca790, useCache=) at eval.c:6888:20 [opt] frame #76: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #77: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784ca6e8) at eval.c:568:8 [opt] frame #78: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784ca6e8, symbol=0x00007ffd7085d350, rho=0x00007ffd784d0358, keepmiss=) at eval.c:5157:15 [opt] frame #79: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784d0358, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #80: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195aba0, rho=0x00007ffd784d0358, useCache=) at eval.c:6888:20 [opt] frame #81: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #82: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7195be70, newrho=0x00007ffd784d0358, sysparent=, rho=0x00007ffd784ca790, arglist=, op=) at eval.c:0 [opt] frame #83: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7195be70, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #84: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71956060, rho=0x00007ffd784ca790, useCache=) at eval.c:7104:12 [opt] frame #85: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #86: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd719568b0, newrho=0x00007ffd784ca790, sysparent=, rho=0x00007ffd784cab48, arglist=, op=) at eval.c:0 [opt] frame #87: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd719568b0, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #88: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71957330, rho=0x00007ffd784cab48, useCache=) at eval.c:7104:12 [opt] frame #89: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #90: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71956f78, newrho=0x00007ffd784cab48, sysparent=, rho=0x00007ffd784cb788, arglist=, op=) at eval.c:0 [opt] frame #91: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71956f78, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #92: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd719566b8, rho=0x00007ffd784cb788, useCache=) at eval.c:7104:12 [opt] frame #93: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #94: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784cb6e0) at eval.c:568:8 [opt] frame #95: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784cb6e0, symbol=0x00007ffd7085d350, rho=0x00007ffd784cb440, keepmiss=) at eval.c:5157:15 [opt] frame #96: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cb440, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #97: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a820, rho=0x00007ffd784cb440, useCache=) at eval.c:6888:20 [opt] frame #98: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #99: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd784cb398) at eval.c:568:8 [opt] frame #100: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd784cb398, symbol=0x00007ffd7085d350, rho=0x00007ffd784cb0f8, keepmiss=) at eval.c:5157:15 [opt] frame #101: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd784cb0f8, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #102: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195aba0, rho=0x00007ffd784cb0f8, useCache=) at eval.c:6888:20 [opt] frame #103: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #104: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7195be70, newrho=0x00007ffd784cb0f8, sysparent=, rho=0x00007ffd784cb440, arglist=, op=) at eval.c:0 [opt] frame #105: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7195be70, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #106: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71956060, rho=0x00007ffd784cb440, useCache=) at eval.c:7104:12 [opt] frame #107: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #108: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71956fe8, newrho=0x00007ffd784cb440, sysparent=, rho=0x00007ffd784cb788, arglist=, op=) at eval.c:0 [opt] frame #109: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71956fe8, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #110: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71957330, rho=0x00007ffd784cb788, useCache=) at eval.c:7104:12 [opt] frame #111: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #112: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71957528, newrho=0x00007ffd784cb788, sysparent=, rho=0x00007ffd784cbe88, arglist=, op=) at eval.c:0 [opt] frame #113: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71957528, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #114: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7194a698, rho=0x00007ffd784cbe88, useCache=) at eval.c:7104:12 [opt] frame #115: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #116: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9470, newrho=0x00007ffd784cbe88, sysparent=, rho=0x00007ffd780aef50, arglist=, op=) at eval.c:0 [opt] frame #117: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9470, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #118: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d0e06e0, rho=0x00007ffd780aef50, useCache=) at eval.c:7104:12 [opt] frame #119: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #120: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d122710, newrho=0x00007ffd780aef50, sysparent=, rho=0x00007ffd71e878e0, arglist=, op=) at eval.c:0 [opt] frame #121: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d122710, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #122: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d11f788, rho=0x00007ffd71e878e0, useCache=) at eval.c:7104:12 [opt] frame #123: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #124: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d05e208, newrho=0x00007ffd71e878e0, sysparent=, rho=0x00007ffd7d0f32b0, arglist=, op=) at eval.c:0 [opt] frame #125: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d05e208, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #126: 0x0000000100f6febb libR.dylib`Rf_eval(e=, rho=0x00007ffd7d0f32b0) at eval.c:871:12 [opt] frame #127: 0x0000000100f93cfd libR.dylib`do_eval(call=, op=, args=, rho=) at eval.c:3389:9 [opt] frame #128: 0x0000000100f77035 libR.dylib`bcEval(body=0x00007ffd7086a208, rho=0x00007ffd7d107080, useCache=) at eval.c:7136:14 [opt] frame #129: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #130: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9320, newrho=0x00007ffd7d107080, sysparent=, rho=0x00007ffd7d0f0088, arglist=, op=) at eval.c:0 [opt] frame #131: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9320, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #132: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d0f0910, rho=0x00007ffd7d0f0088, useCache=) at eval.c:7104:12 [opt] frame #133: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #134: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d0ffd78) at eval.c:568:8 [opt] frame #135: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d0ffd78, symbol=0x00007ffd7085d350, rho=0x00007ffd7d0ff950, keepmiss=) at eval.c:5157:15 [opt] frame #136: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d0ff950, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #137: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd72d076d0, rho=0x00007ffd7d0ff950, useCache=) at eval.c:6888:20 [opt] frame #138: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #139: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9400, newrho=0x00007ffd7d0ff950, sysparent=, rho=0x00007ffd7d0f0088, arglist=, op=) at eval.c:0 [opt] frame #140: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9400, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #141: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7d0f0948, rho=0x00007ffd7d0f0088, useCache=) at eval.c:7104:12 [opt] frame #142: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #143: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d0fdec8) at eval.c:568:8 [opt] frame #144: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d0fdec8, symbol=0x00007ffd7085d350, rho=0x00007ffd7d0fdc60, keepmiss=) at eval.c:5157:15 [opt] frame #145: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d0fdc60, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #146: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a4d8, rho=0x00007ffd7d0fdc60, useCache=) at eval.c:6888:20 [opt] frame #147: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #148: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d0fd800) at eval.c:568:8 [opt] frame #149: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d0fd800, symbol=0x00007ffd7085d350, rho=0x00007ffd7d101470, keepmiss=) at eval.c:5157:15 [opt] frame #150: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d101470, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #151: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd71956680, rho=0x00007ffd7d101470, useCache=) at eval.c:6888:20 [opt] frame #152: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #153: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d100a60) at eval.c:568:8 [opt] frame #154: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d100a60, symbol=0x00007ffd7085d350, rho=0x00007ffd7d1007c0, keepmiss=) at eval.c:5157:15 [opt] frame #155: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d1007c0, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #156: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd71956338, rho=0x00007ffd7d1007c0, useCache=) at eval.c:6888:20 [opt] frame #157: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #158: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d1006a8) at eval.c:568:8 [opt] frame #159: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d1006a8, symbol=0x00007ffd7085d350, rho=0x00007ffd7d100408, keepmiss=) at eval.c:5157:15 [opt] frame #160: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d100408, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #161: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a820, rho=0x00007ffd7d100408, useCache=) at eval.c:6888:20 [opt] frame #162: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #163: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d100360) at eval.c:568:8 [opt] frame #164: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d100360, symbol=0x00007ffd7085d350, rho=0x00007ffd7d1000c0, keepmiss=) at eval.c:5157:15 [opt] frame #165: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d1000c0, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #166: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195aba0, rho=0x00007ffd7d1000c0, useCache=) at eval.c:6888:20 [opt] frame #167: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #168: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7195be70, newrho=0x00007ffd7d1000c0, sysparent=, rho=0x00007ffd7d100408, arglist=, op=) at eval.c:0 [opt] frame #169: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7195be70, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #170: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71956060, rho=0x00007ffd7d100408, useCache=) at eval.c:7104:12 [opt] frame #171: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #172: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd719568b0, newrho=0x00007ffd7d100408, sysparent=, rho=0x00007ffd7d1007c0, arglist=, op=) at eval.c:0 [opt] frame #173: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd719568b0, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #174: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71957330, rho=0x00007ffd7d1007c0, useCache=) at eval.c:7104:12 [opt] frame #175: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #176: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71956f78, newrho=0x00007ffd7d1007c0, sysparent=, rho=0x00007ffd7d101470, arglist=, op=) at eval.c:0 [opt] frame #177: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71956f78, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #178: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd719566b8, rho=0x00007ffd7d101470, useCache=) at eval.c:7104:12 [opt] frame #179: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #180: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d1013c8) at eval.c:568:8 [opt] frame #181: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d1013c8, symbol=0x00007ffd7085d350, rho=0x00007ffd7d101128, keepmiss=) at eval.c:5157:15 [opt] frame #182: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d101128, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #183: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195a820, rho=0x00007ffd7d101128, useCache=) at eval.c:6888:20 [opt] frame #184: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #185: 0x0000000100f8dd3c libR.dylib`forcePromise(e=0x00007ffd7d101080) at eval.c:568:8 [opt] frame #186: 0x0000000100f9934a libR.dylib`getvar [inlined] FORCE_PROMISE(value=0x00007ffd7d101080, symbol=0x00007ffd7085d350, rho=0x00007ffd7d100de0, keepmiss=) at eval.c:5157:15 [opt] frame #187: 0x0000000100f99342 libR.dylib`getvar(symbol=0x00007ffd7085d350, rho=0x00007ffd7d100de0, dd=, keepmiss=, vcache=, sidx=) at eval.c:5198:14 [opt] frame #188: 0x0000000100f73b67 libR.dylib`bcEval(body=0x00007ffd7195aba0, rho=0x00007ffd7d100de0, useCache=) at eval.c:6888:20 [opt] frame #189: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #190: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7195be70, newrho=0x00007ffd7d100de0, sysparent=, rho=0x00007ffd7d101128, arglist=, op=) at eval.c:0 [opt] frame #191: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7195be70, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #192: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71956060, rho=0x00007ffd7d101128, useCache=) at eval.c:7104:12 [opt] frame #193: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #194: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71956fe8, newrho=0x00007ffd7d101128, sysparent=, rho=0x00007ffd7d101470, arglist=, op=) at eval.c:0 [opt] frame #195: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71956fe8, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #196: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd71957330, rho=0x00007ffd7d101470, useCache=) at eval.c:7104:12 [opt] frame #197: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #198: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd71957528, newrho=0x00007ffd7d101470, sysparent=, rho=0x00007ffd7d0fdc60, arglist=, op=) at eval.c:0 [opt] frame #199: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd71957528, op=, arglist=, rho=, suppliedvars=) at eval.c:1844:16 [opt] frame #200: 0x0000000100f7692e libR.dylib`bcEval(body=0x00007ffd7194a698, rho=0x00007ffd7d0fdc60, useCache=) at eval.c:7104:12 [opt] frame #201: 0x0000000100f6fa01 libR.dylib`Rf_eval(e=, rho=) at eval.c:748:8 [opt] frame #202: 0x0000000100f8f839 libR.dylib`R_execClosure(call=0x00007ffd7d0e9470, newrho=0x00007ffd7d0fdc60, sysparent=, rho=0x00007ffd7d0f0088, arglist=, op=) at eval.c:0 [opt] frame #203: 0x0000000100f8e627 libR.dylib`Rf_applyClosure(call=0x00007ffd7d0e9470, op=, arglist=, rho=, suppliedvars=

Component(s)

R

nealrichardson commented 1 year ago

I've never encountered this myself, but given all of the ways that using homebrew apache-arrow can conflict with the R package, I wonder if we should just remove the homebrew path in configure, or make it explicitly opt-in so that folks won't run into it accidentally.

nealrichardson commented 1 year ago

Can we call this resolved by #35147?

thisisnic commented 11 months ago

@paleolimbot Is this ticket resovled now?

paleolimbot commented 11 months ago

Yes!

apache / arrow

[R] Crash on MacOS (x86) when running tests with homebrew apache-arrow also installed #33903

Describe the bug, including details regarding any error messages, version, and platform.

Component(s)