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Posted to dev@arrow.apache.org by "Jonathan Keane (Jira)" <ji...@apache.org> on 2020/05/07 18:30:00 UTC
[jira] [Created] (ARROW-8734) [R] Compilation error on macOS
Jonathan Keane created ARROW-8734:
-------------------------------------
Summary: [R] Compilation error on macOS
Key: ARROW-8734
URL: https://issues.apache.org/jira/browse/ARROW-8734
Project: Apache Arrow
Issue Type: Bug
Components: R
Reporter: Jonathan Keane
I've tried to install / build from source (with from a git checkout and using the built-in `install_arrow()`) and when compiling I'm getting the following error reliably during the auto brew process:
{code:bash}
x System command 'R' failed, exit status: 1, stdout + stderr:
E> * checking for file ‘/Users/jkeane/Dropbox/arrow/r/DESCRIPTION’ ... OK
E> * preparing ‘arrow’:
E> * checking DESCRIPTION meta-information ... OK
E> * cleaning src
E> * running ‘cleanup’
E> * installing the package to build vignettes
E> -----------------------------------
E> * installing *source* package ‘arrow’ ...
E> ** using staged installation
E> *** Generating code with data-raw/codegen.R
E> There were 27 warnings (use warnings() to see them)
E> *** > 375 functions decorated with [[arrow|s3::export]]
E> *** > generated file `src/arrowExports.cpp`
E> *** > generated file `R/arrowExports.R`
E> *** Downloading apache-arrow
E> **** Using local manifest for apache-arrow
E> Thu May 7 13:13:42 CDT 2020: Auto-brewing apache-arrow in /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow...
E> ==> Tapping autobrew/core from https://github.com/autobrew/homebrew-core
E> Tapped 2 commands and 4639 formulae (4,888 files, 12.7MB).
E> lz4
E> openssl
E> thrift
E> snappy
E> ==> Downloading https://homebrew.bintray.com/bottles/lz4-1.8.3.mojave.bottle.tar.gz
E> Already downloaded: /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/downloads/b4158ef68d619dbf78935df6a42a70b8339a65bc8876cbb4446355ccd40fa5de--lz4-1.8.3.mojave.bottle.tar.gz
E> ==> Pouring lz4-1.8.3.mojave.bottle.tar.gz
E> ==> Skipping post_install step for autobrew...
E> 🍺 /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/Cellar/lz4/1.8.3: 22 files, 512.7KB
E> ==> Downloading https://homebrew.bintray.com/bottles/openssl-1.0.2p.mojave.bottle.tar.gz
E> Already downloaded: /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/downloads/fbb493745981c8b26c0fab115c76c2a70142bfde9e776c450277e9dfbbba0bb2--openssl-1.0.2p.mojave.bottle.tar.gz
E> ==> Pouring openssl-1.0.2p.mojave.bottle.tar.gz
E> ==> Skipping post_install step for autobrew...
E> ==> Caveats
E> openssl is keg-only, which means it was not symlinked into /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow,
E> because Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries.
E>
E> If you need to have openssl first in your PATH run:
E> echo 'export PATH="/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/bin:$PATH"' >> ~/.zshrc
E>
E> For compilers to find openssl you may need to set:
E> export LDFLAGS="-L/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/lib"
E> export CPPFLAGS="-I/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/include"
E>
E> For pkg-config to find openssl you may need to set:
E> export PKG_CONFIG_PATH="/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/lib/pkgconfig"
E>
E> ==> Summary
E> 🍺 /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/Cellar/openssl/1.0.2p: 1,793 files, 12MB
E> ==> Downloading https://homebrew.bintray.com/bottles/thrift-0.11.0.mojave.bottle.tar.gz
E> Already downloaded: /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/downloads/7e05ea11a9f7f924dd7f8f36252ec73a24958b7f214f71e3752a355e75e589bd--thrift-0.11.0.mojave.bottle.tar.gz
E> ==> Pouring thrift-0.11.0.mojave.bottle.tar.gz
E> ==> Skipping post_install step for autobrew...
E> ==> Caveats
E> To install Ruby binding:
E> gem install thrift
E> ==> Summary
E> 🍺 /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/Cellar/thrift/0.11.0: 102 files, 7MB
E> ==> Downloading https://homebrew.bintray.com/bottles/snappy-1.1.7_1.mojave.bottle.tar.gz
E> Already downloaded: /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/downloads/1f09938804055499d1dd951b13b26d80c56eae359aa051284bf4f51d109a9f73--snappy-1.1.7_1.mojave.bottle.tar.gz
E> ==> Pouring snappy-1.1.7_1.mojave.bottle.tar.gz
E> ==> Skipping post_install step for autobrew...
E> 🍺 /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/Cellar/snappy/1.1.7_1: 18 files, 115.8KB
E> ==> Downloading https://autobrew.github.io/bottles/apache-arrow-0.17.0.el_capitan.bottle.tar.gz
E> Already downloaded: /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/downloads/7dcf2302ba174a5efb32eaa5b8fe0ae874f4a4671f575e126c79a524830054ae--apache-arrow-0.17.0.el_capitan.bottle.tar.gz
E> ==> Pouring apache-arrow-0.17.0.el_capitan.bottle.tar.gz
E> ==> Skipping post_install step for autobrew...
E> 🍺 /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/Cellar/apache-arrow/0.17.0: 294 files, 49.7MB
E> ==> Caveats
E> ==> openssl
E> openssl is keg-only, which means it was not symlinked into /private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow,
E> because Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries.
E>
E> If you need to have openssl first in your PATH run:
E> echo 'export PATH="/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/bin:$PATH"' >> ~/.zshrc
E>
E> For compilers to find openssl you may need to set:
E> export LDFLAGS="-L/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/lib"
E> export CPPFLAGS="-I/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/include"
E>
E> For pkg-config to find openssl you may need to set:
E> export PKG_CONFIG_PATH="/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/build-apache-arrow/opt/openssl/lib/pkgconfig"
E>
E> ==> thrift
E> To install Ruby binding:
E> gem install thrift
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewarrow.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewarrow_dataset.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewparquet.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewlz4.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewcrypto.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewssl.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewsnappy.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewthrift.a
E> created /var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib/libbrewthriftz.a
E> PKG_CFLAGS=-I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW
E> PKG_LIBS=-L/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/lib -L/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/lib -lbrewparquet -lbrewarrow_dataset -lbrewarrow -lbrewthrift -lbrewlz4 -lbrewsnappy
E> ** libs
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c array.cpp -o array.o
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c array_from_vector.cpp -o array_from_vector.o
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c array_to_vector.cpp -o array_to_vector.o
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c arraydata.cpp -o arraydata.o
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T//build-apache-arrow/opt/apache-arrow/include -DARROW_R_WITH_ARROW -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c arrowExports.cpp -o arrowExports.o
E> arrowExports.cpp:1650:21: error: no member named 'CsvFileFormat' in namespace 'arrow::dataset'
E> std::shared_ptr<ds::CsvFileFormat> dataset___CsvFileFormat__Make(const std::shared_ptr<arrow::csv::ParseOptions>& parse_options);
E> ~~~~^
E> 1 error generated.
E> make: *** [arrowExports.o] Error 1
E> ERROR: compilation failed for package ‘arrow’
E> * removing ‘/private/var/folders/45/n5gfjjtn05j877spnpbnhqqw0000gn/T/RtmpNwJEKk/Rinstd9644c71dcbf/arrow’
E> -----------------------------------
E> ERROR: package installation failed
{code}
I'm sure I'm missing some setup step somewhere or I'm missing a necessary step to install from source. I've tried this both under R 3.6(.1) and 4.0 to see if upgrading helped and I get the same error
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