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Posted to jira@arrow.apache.org by "Nic Crane (Jira)" <ji...@apache.org> on 2021/05/25 22:41:00 UTC
[jira] [Commented] (ARROW-12860) [R] Error when installing R
package on Raspbian
[ https://issues.apache.org/jira/browse/ARROW-12860?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17351376#comment-17351376 ]
Nic Crane commented on ARROW-12860:
-----------------------------------
Resolved - needed to use additional build flags "{color:#000000}-DARROW_CXXFLAGS=-latomic{color}" as on Raspberry Pi linking with libatomic doesn't happen as it should (i.e. [https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81358]{color:#333333} and {color}[https://github.com/alexa/avs-device-sdk/issues/1404])
> [R] Error when installing R package on Raspbian
> -----------------------------------------------
>
> Key: ARROW-12860
> URL: https://issues.apache.org/jira/browse/ARROW-12860
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Reporter: Nic Crane
> Priority: Minor
>
> Posting this on behalf of a friend who has a slight allergy to Jira - he's installed the R package via install.packages, but is getting the following error:
> {code:java}
> * installing *source* package 'arrow' ...
> ** package 'arrow' successfully unpacked and MD5 sums checked
> ** using staged installation
> *** Successfully retrieved C++ source
> *** Building C++ libraries
> **** arrow
> PKG_CFLAGS=-I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET
> PKG_LIBS=-L/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/lib -larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet
> ** libs
> make[1]: Entering directory '/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/src'
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c array.cpp -o array.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c array_to_vector.cpp -o array_to_vector.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c arraydata.cpp -o arraydata.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c arrowExports.cpp -o arrowExports.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c buffer.cpp -o buffer.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c chunkedarray.cpp -o chunkedarray.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c compression.cpp -o compression.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c compute.cpp -o compute.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c csv.cpp -o csv.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c dataset.cpp -o dataset.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c datatype.cpp -o datatype.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c expression.cpp -o expression.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c feather.cpp -o feather.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c field.cpp -o field.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c filesystem.cpp -o filesystem.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c imports.cpp -o imports.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c io.cpp -o io.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c json.cpp -o json.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c memorypool.cpp -o memorypool.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c message.cpp -o message.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c parquet.cpp -o parquet.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c py-to-r.cpp -o py-to-r.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c r_to_arrow.cpp -o r_to_arrow.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c recordbatch.cpp -o recordbatch.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c recordbatchreader.cpp -o recordbatchreader.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c recordbatchwriter.cpp -o recordbatchwriter.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c runtimeinfo.cpp -o runtimeinfo.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c scalar.cpp -o scalar.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c schema.cpp -o schema.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c symbols.cpp -o symbols.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c table.cpp -o table.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c threadpool.cpp -o threadpool.o
> g++ -std=gnu++11 -I"/opt/R/release/lib/R/include" -DNDEBUG -I/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/include -DARROW_R_WITH_ARROW -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -I'/home/mds/R/r4pi/cpp11/include' -I/usr/local/include -fpic -g -O2 -c type_infer.cpp -o type_infer.o
> g++ -std=gnu++11 -shared -L/opt/R/release/lib/R/lib -L/usr/local/lib -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/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/libarrow/arrow-4.0.0.1/lib -larrow_dataset -lparquet -larrow -larrow -larrow_bundled_dependencies -larrow_dataset -lparquet -L/opt/R/release/lib/R/lib -lR
> make[1]: Leaving directory '/tmp/RtmpLeOMgI/R.INSTALL7a137b00b451/arrow/src'
> installing to /home/mds/R/r4pi/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
> Error: package or namespace load failed for 'arrow' in dyn.load(file, DLLpath = DLLpath, ...):
> unable to load shared object '/home/mds/R/r4pi/00LOCK-arrow/00new/arrow/libs/arrow.so':
> /home/mds/R/r4pi/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: __atomic_fetch_add_8
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/home/mds/R/r4pi/arrow'
> Error: Build of package failed
> {code}
>
> {code:java}
> > sessionInfo()
> R version 4.1.0 (2021-05-18)
> Platform: armv7l-unknown-linux-gnueabihf (32-bit)
> Running under: Raspbian GNU/Linux 10 (buster)Matrix products: default
> BLAS/LAPACK: /usr/lib/arm-linux-gnueabihf/libopenblas_armv6p-r0.3.5.solocale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:
> [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):
> [1] compiler_4.1.0
> {code}
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