[
https://issues.apache.org/jira/browse/ARROW-12853?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17352614#comment-17352614
]
Karl Dunkle Werner commented on ARROW-12853:
--------------------------------------------
With that environment variable set, the relevant parts of the log become:
{noformat}
+ /usr/bin/cmake -DARROW_BOOST_USE_SHARED=OFF -DARROW_BUILD_TESTS=OFF
-DARROW_BUILD_SHARED=OFF -DARROW_BUILD_STATIC=ON -DARROW_COMPUTE=ON
-DARROW_CSV=ON -DARROW_DATASET=ON -DARROW_DEPENDENCY_SOURCE=BUNDLED
-DARROW_FILESYSTEM=ON -DARROW_JEMALLOC=OFF -DARROW_MIMALLOC=OFF -DARROW_JSON=ON
-DARROW_PARQUET=ON -DARROW_S3=OFF -DARROW_WITH_BROTLI=OFF -DARROW_WITH_BZ2=OFF
-DARROW_WITH_LZ4=OFF -DARROW_WITH_RE2=ON -DARROW_WITH_SNAPPY=OFF
-DARROW_WITH_UTF8PROC=ON -DARROW_WITH_ZLIB=OFF -DARROW_WITH_ZSTD=OFF
-DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_LIBDIR=lib
-DCMAKE_INSTALL_PREFIX=/tmp/RtmpvaRJ9j/R.INSTALL3dfc55511a7e/arrow/libarrow/arrow-4.0.0.1
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_UNITY_BUILD=ON
'-DARROW_CXXFLAGS="-flto=auto' '-ffat-lto-objects"' -G 'Unix Makefiles'
/tmp/RtmphF0pgX/file3e221c541529/apache-arrow-4.0.0/cpp
...
-- CMAKE_C_FLAGS: -O3 -DNDEBUG -Wall -fno-semantic-interposition -msse4.2
"-flto=auto
-- CMAKE_CXX_FLAGS: -Wno-noexcept-type -Wno-subobject-linkage
-fdiagnostics-color=always -O3 -DNDEBUG -Wall -fno-semantic-interposition
-msse4.2 "-flto=auto
...
Scanning dependencies of target arrow_dataset_objlib
[ 44%] Building CXX object
src/arrow/dataset/CMakeFiles/arrow_dataset_objlib.dir/Unity/unity_1_cxx.cxx.o
/bin/sh: 1: Syntax error: Unterminated quoted string
make[2]: ***
[src/arrow/dataset/CMakeFiles/arrow_dataset_objlib.dir/build.make:82:
src/arrow/dataset/CMakeFiles/arrow_dataset_objlib.dir/Unity/unity_1_cxx.cxx.o]
Error 2
make[1]: *** [CMakeFiles/Makefile2:1450:
src/arrow/dataset/CMakeFiles/arrow_dataset_objlib.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
{noformat}
So it looks like the quoted string isn't getting parsed properly. (See
{{"-flto=auto}}.)
If I instead do {{EXTRA_CMAKE_FLAGS='-DARROW_CXXFLAGS=-flto=auto
-ffat-lto-objects'}}, the Arrow build only picks up the {{-flto=auto}} flag,
and the R compilation generates a bunch of {{-Wodr}} warnings before failing.
If I do {{EXTRA_CMAKE_FLAGS='-DARROW_CXXFLAGS=-flto=auto
-DARROW_CXXFLAGS=-ffat-lto-objects'}}, only the {{-ffat-lto-objects}} flag is
included. Both of those still end in a segfault.
Is there a better way to pass multiple flags?
{noformat}
g++ -std=gnu++11 -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/RtmpKRWweq/R.INSTALL2b7b181077e9/arrow/libarrow/arrow-4.0.0.1/lib
-larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies
-larrow_dataset -lparquet -L/usr/lib/R/lib -lR
/tmp/RtmpKRWweq/R.INSTALL2b7b181077e9/arrow/libarrow/arrow-4.0.0.1/include/arrow/io/interfaces.h:305:20:
warning: virtual table of type ‘struct WritableFile’ violates one definition
rule [-Wodr]
305 | class ARROW_EXPORT WritableFile : public OutputStream, public Seekable {
| ^
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/interfaces.h:305:
note: the conflicting type defined in another translation unit
<built-in>: note: virtual method ‘__cxa_pure_virtual’
/tmp/RtmpKRWweq/R.INSTALL2b7b181077e9/arrow/libarrow/arrow-4.0.0.1/include/arrow/io/interfaces.h:124:18:
note: ought to match virtual method ‘Abort’ but does not
124 | virtual Status Abort();
| ^
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/slow.h:51:
warning: virtual table of type ‘struct SlowInputStreamBase’ violates one
definition rule [-Wodr]
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/slow.h:51:
note: the conflicting type defined in another translation unit
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/interfaces.cc:91:
note: virtual method ‘io_context’
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does
not
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/concurrency.h:162:
warning: virtual table of type ‘struct RandomAccessFileConcurrencyWrapper’
violates one definition rule [-Wodr]
/tmp/RtmpKRWweq/R.INSTALL2b7b181077e9/arrow/libarrow/arrow-4.0.0.1/include/arrow/io/concurrency.h:162:20:
note: the conflicting type defined in another translation unit
162 | class ARROW_EXPORT RandomAccessFileConcurrencyWrapper : public
RandomAccessFile {
| ^
/tmp/RtmpsSjESj/file2ba1153cf93c/apache-arrow-4.0.0/cpp/src/arrow/io/interfaces.cc:91:
note: virtual method ‘io_context’
<built-in>: note: ought to match virtual method ‘__cxa_pure_virtual’ but does
not
** testing if installed package can be loaded from temporary location
*** caught segfault ***
address (nil), cause 'memory not mapped'
{noformat}
In ARROW-9616, you said "If CRAN decides that it LTO's everything, then we
wouldn't be able to turn that off." The [release
notes|https://cran.r-project.org/doc/manuals/r-release/NEWS.html] for R 4.1.0
say "Packages can opt in or out of LTO compilation via a {{UseLTO}} field in
the {{‘DESCRIPTION’}} file. (As usual this can be overridden by the
command-line flags.)" So it sounds like they're not going to force LTO, at
least for now.
> [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}
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