[
https://issues.apache.org/jira/browse/ARROW-12853?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17360286#comment-17360286
]
Neal Richardson commented on ARROW-12853:
-----------------------------------------
A PR would be great–especially if you have or know of a docker image that
reproduces the issue so we can add that to our continuous integration.
> [R] Install fails with LTO flags
> --------------------------------
>
> Key: ARROW-12853
> URL: https://issues.apache.org/jira/browse/ARROW-12853
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Affects Versions: 4.0.0
> Environment: R 4.1.0
> Reporter: Karl Dunkle Werner
> Priority: Major
> Labels: build
> Attachments: Makeconf_docker, Makeconf_local,
> arrow_install_local_4.1.0.log, arrow_install_rocker_4.1.0_with_system_deps.log
>
>
> 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:
> {noformat}
> 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=. -flto=auto
> -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
> -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chunkedarray.cpp -o chunkedarray.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 compression.cpp -o compression.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 compute.cpp -o compute.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 csv.cpp -o csv.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 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++ -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 feather.cpp -o feather.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 field.cpp -o field.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 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 -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 r_to_arrow.cpp -o r_to_arrow.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 recordbatch.cpp -o recordbatch.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 recordbatchreader.cpp -o
> recordbatchreader.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 recordbatchwriter.cpp -o
> recordbatchwriter.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 runtimeinfo.cpp -o runtimeinfo.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 scalar.cpp -o scalar.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 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’
> {noformat}
--
This message was sent by Atlassian Jira
(v8.3.4#803005)
