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Posted to jira@arrow.apache.org by "Sindre Froyn (Jira)" <ji...@apache.org> on 2021/01/14 07:59:00 UTC
[jira] [Created] (ARROW-11249) [R] installation failure on CentOS 7
Sindre Froyn created ARROW-11249:
------------------------------------
Summary: [R] installation failure on CentOS 7
Key: ARROW-11249
URL: https://issues.apache.org/jira/browse/ARROW-11249
Project: Apache Arrow
Issue Type: Bug
Components: R
Affects Versions: 2.0.0
Environment: CentOS 7
Reporter: Sindre Froyn
I am experiencing some problems with installing the 'arrow' package on my Red Hat linux server. It looks like my issues and setup are very closely related to the ones described in this ticket:
https://issues.apache.org/jira/browse/ARROW-8586
However, even if the issue is marked as resolved, and I tried installing arrow package version 0.17.0 with the fixes mentioned, it still doesn't work. Any advice would be greatly appreciated!
Here are the environment variables I have set:
{code:java}
g020029@~ $ echo $CC
/usr/bin/gcc
g020029@~ $ echo $CXX
/usr/bin/g++
g020029@~ $ echo $LIBARROW_BINARY
centos-7
g020029@~ $ echo $ARROW_R_DEV
true{code}
I am not using devtools-8, which was reported as a possible issue in the other ticket.
{code:java}
g020029@~ $ which gcc
/usr/bin/gcc
g020029@~ $ /usr/bin/gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
g020029@~ $ which g++
/usr/bin/g++
g020029@~ $ /usr/bin/g++ --version
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
{code}
If it is important, here is the lsb version.
{code:java}
g020029@~ $ lsb_release -rs
7.5{code}
Finally, here is the output from the installation with a test-run afterwards. (Looks like the output isn't more verbose even if ARROW_R_DEV is set to true).
{code:java}
> install.packages("arrow", repos="https://cran.uib.no/")
Installing package into ‘/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 315k 100 315k 0 0 292k 0 0:00:01 0:00:01 --:--:-- 292k
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 33 0 33 0 0 49 0 --:--:-- --:--:-- --:--:-- 49
*** Successfully retrieved C++ binaries for centos-7
Warning message:
In unzip(bin_file, exdir = dst_dir) : error 1 in extracting from zip file
------------------------- NOTE ---------------------------
After installation, please run arrow::install_arrow()
for help installing required runtime libraries
---------------------------------------------------------
** libs
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shar ed/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPL EMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c array.cpp -o array.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shar ed/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPL EMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c array_from_vector.cpp -o array_from_vector.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shar ed/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPL EMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c array_to_vector.cpp -o a rray_to_vector.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_ 64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATIO N -g -O2 -c arraydata.cpp -o arraydata.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_ 64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATIO N -g -O2 -c arrowExports.cpp -o arrowExports.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_ 64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATIO N -g -O2 -c buffer.cpp -o buffer.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c chunkedarray.cpp -o chunkedarray.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c compression.cpp -o compression.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c compute.cpp -o compute.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c csv.cpp -o csv.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c dataset.cpp -o dataset.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c datatype.cpp -o datatype.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pcENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c expression.cpp -o expression.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c feather.cpp -o feather.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c field.cpp -o field.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c filesystem.cpp -o filesystem.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c imports.cpp -o imports.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c io.cpp -o io.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c json.cpp -o json.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c memorypool.cpp -o memorypool.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c message.cpp -o message.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c parquet.cpp -o parquet.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c py-to-r.cpp -o py-to-r.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c recordbatch.cpp -o recordbatch.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c recordbatchreader.cpp -o recordbatchreader.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c recordbatchwriter.cpp -o recordbatchwriter.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c scalar.cpp -o scalar.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c schema.cpp -o schema.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c symbols.cpp -o symbols.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c table.cpp -o table.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.1/lib64/R/include -DNDEBUG -I"/shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/cpp11/include" -DU_STATIC_IMPLEMENTATION -fpic -DU_STATIC_IMPLEMENTATION -g -O2 -c threadpool.cpp -o threadpool.o
g++ -std=gnu++11 -shared -L/opt/microsoft/ropen/3.5.1/lib64/R/lib -o arrow.so array.o array_from_vector.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 recordbatch.o recordbatchreader.o recordbatchwriter.o scalar.o schema.o symbols.o table.o threadpool.o -L/opt/microsoft/ropen/3.5.1/lib64/R/lib -lR
installing to /shared/home/G020029/R/x86_64-pc-linux-gnu-library/3.5/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
* DONE (arrow)
The downloaded source packages are in
‘/tmp/RtmpXNtt3z/downloaded_packages’
> library("arrow")
Attaching package: ‘arrow’
The following object is masked from ‘package:utils’:
timestamp
> tt2 = read_parquet(file = "/mnt_g/GF_Prising/G020029/test2.parquet")
Error in io___MemoryMappedFile__Open(path, mode) :
Cannot call io___MemoryMappedFile__Open(). Please use arrow::install_arrow() to install required runtime libraries.
{code}
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