Details
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Bug
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Status: Resolved
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Major
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Resolution: Fixed
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4.0.0
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None
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R 4.1.0
Description
Hi,
I noticed my installation failed after updating R to the newly released 4.1.0. Arrow compiles without error, but installation fails with a segfault when R tests whether the package can be loaded.
Here are the relevant environment variables I've set:
LIBARROW_MINIMAL: false
LIBARROW_BINARY: ubuntu-20.04 (also fails with false)
ARROW_R_DEV: true
Let me know if there are other configurations you'd like me to test.
Related: ARROW-12824
The install log:
install.packages("arrow") Installing package into ‘/home/karl/.R/4.1’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/arrow_4.0.0.1.tar.gz' Content type 'application/x-gzip' length 426715 bytes (416 KB) ================================================== downloaded 416 KB * installing *source* package ‘arrow’ ... ** package ‘arrow’ successfully unpacked and MD5 sums checked ** using staged installation *** Using ubuntu-18.04 binary for ubuntu-20.04 trying URL 'https://arrow-r-nightly.s3.amazonaws.com/libarrow/bin/ubuntu-18.04/arrow-4.0.0.1.zip' Content type 'binary/octet-stream' length 16007220 bytes (15.3 MB) ================================================== downloaded 15.3 MB *** Successfully retrieved C++ binaries for ubuntu-18.04 **** Binary package requires libcurl and openssl **** If installation fails, retry after installing those system requirements PKG_CFLAGS=-I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 PKG_LIBS=-L/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/lib -larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet -lssl -lcrypto -lcurl ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array.cpp -o array.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c array_to_vector.cpp -o array_to_vector.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arraydata.cpp -o arraydata.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c arrowExports.cpp -o arrowExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c buffer.cpp -o buffer.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. 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-D_FORTIFY_SOURCE=2 -g -c dataset.cpp -o dataset.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c datatype.cpp -o datatype.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c expression.cpp -o expression.o g++ 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-I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c filesystem.cpp -o filesystem.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c imports.cpp -o imports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.cpp -o io.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c json.cpp -o json.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c memorypool.cpp -o memorypool.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c message.cpp -o message.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parquet.cpp -o parquet.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c py-to-r.cpp -o py-to-r.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 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-flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c schema.cpp -o schema.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c symbols.cpp -o symbols.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c table.cpp -o table.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c threadpool.cpp -o threadpool.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_S3 -I'/home/karl/.R/4.1/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-aXXzqd/r-base-4.1.0=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c type_infer.cpp -o type_infer.o g++ -std=gnu++11 -Wl,--strip-debug -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o arrow.so array.o array_to_vector.o arraydata.o arrowExports.o buffer.o chunkedarray.o compression.o compute.o csv.o dataset.o datatype.o expression.o feather.o field.o filesystem.o imports.o io.o json.o memorypool.o message.o parquet.o py-to-r.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o runtimeinfo.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/tmp/RtmpGwVvlP/R.INSTALL106e64cdb5ef7/arrow/libarrow/arrow-4.0.0.1/lib -larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet -lssl -lcrypto -lcurl -L/usr/lib/R/lib -lR installing to /home/karl/.R/4.1/00LOCK-arrow/00new/arrow/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location *** caught segfault *** address (nil), cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(package, lib.loc) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 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) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)}) 8: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) 9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 10: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)) 11: doTryCatch(return(expr), name, parentenv, handler) 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 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)[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))}) 15: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))) 16: tools:::.test_load_package("arrow", "/home/karl/.R/4.1/00LOCK-arrow/00new") An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped) ERROR: loading failed * removing ‘/home/karl/.R/4.1/arrow’
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- is duplicated by
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ARROW-13255 [R] Unable to install on Ubuntu 21.04
- Closed