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Posted to issues@arrow.apache.org by "ALI Siavosh HAGHIGHI (Jira)" <ji...@apache.org> on 2022/09/01 19:34:00 UTC
[jira] [Created] (ARROW-17596) Installation on Redhat 7.9
ALI Siavosh HAGHIGHI created ARROW-17596:
---------------------------------------------
Summary: Installation on Redhat 7.9
Key: ARROW-17596
URL: https://issues.apache.org/jira/browse/ARROW-17596
Project: Apache Arrow
Issue Type: Bug
Components: C++
Environment: Redhat 7.9 (HPC cluster)
Reporter: ALI Siavosh HAGHIGHI
Hi,
Any method I choose To install I ran to some problem (R-4.1.1. and R-4.1.2):
# The normal install: - re2_ep download command succeeded. See also /tmp/RtmpRvCCWr/file3fbda77af639/re2_ep-prefix/src/re2_ep-stamp/re2_ep-download-*.log
[ 14%] No patch step for 're2_ep'
[ 14%] No update step for 're2_ep'
[ 14%] Performing configure step for 're2_ep'
-- re2_ep configure command succeeded. See also /tmp/RtmpRvCCWr/file3fbda77af639/re2_ep-prefix/src/re2_ep-stamp/re2_ep-configure-*.log
[ 14%] Performing build step for 're2_ep'
-- re2_ep build command succeeded. See also /tmp/RtmpRvCCWr/file3fbda77af639/re2_ep-prefix/src/re2_ep-stamp/re2_ep-build-*.log
[ 15%] Performing install step for 're2_ep'
-- re2_ep install command succeeded. See also /tmp/RtmpRvCCWr/file3fbda77af639/re2_ep-prefix/src/re2_ep-stamp/re2_ep-install-*.log
[ 15%] Completed 're2_ep'
[ 15%] Built target re2_ep
CMake Error at boost_ep-stamp/boost_ep-download-RELEASE.cmake:16 (message):
Command failed: 1
'/gpfs/share/apps/cmake/3.11.3/bin/cmake' '-Dmake=' '-Dconfig=' '-P' '/tmp/RtmpRvCCWr/file3fbda77af639/boost_ep-prefix/src/boost_ep-stamp/boost_ep-download-RELEASE-impl.cmake'
See also
/tmp/RtmpRvCCWr/file3fbda77af639/boost_ep-prefix/src/boost_ep-stamp/boost_ep-download-*.log
make[2]: *** [boost_ep-prefix/src/boost_ep-stamp/boost_ep-download] Error 1
make[1]: *** [CMakeFiles/boost_ep.dir/all] Error 2
gmake: *** [all] Error 2
**** Error building Arrow C++.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
---------------------------------------------------------
ERROR: configuration failed for package ‘arrow’
* removing ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
* restoring previous ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
The downloaded source packages are in
‘/tmp/RtmpiHuhIA/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'arrow', 'nloptr', 'Rfast', 'SeuratObject', 'Signac'
Update all/some/none? [a/s/n]:
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
installation of package ‘arrow’ had non-zero exit status
>
2. Using local boost 1.72.0:
> Sys.setenv("ARROW_R_DEV" = TRUE)
> install.packages("arrow")
————>
[ 50%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/options.cc.o
[ 50%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/parser.cc.o
[ 51%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/reader.cc.o
[ 51%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/writer.cc.o
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader]’:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/alloc_traits.h:455:4: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, _Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:520:39: required from ‘std::_Sp_counted_ptr_inplace<_Tp, _Alloc, _Lp>::_Sp_counted_ptr_inplace(_Alloc, _Args&& ...) [with _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:615:4: required from ‘std::__shared_count<_Lp>::__shared_count(std::_Sp_make_shared_tag, _Tp*, const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:1100:35: required from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:319:64: required from ‘std::shared_ptr<_Tp>::shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:619:14: required from ‘std::shared_ptr<_Tp1> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:635:39: required from ‘std::shared_ptr<_Tp1> std::make_shared(_Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:200:88: required from here
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:194:22: error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const std::unique_ptr<_Tp, _Dp>&) [with _Tp = arrow::Chunker; _Dp = std::default_delete<arrow::Chunker>]’
using BlockReader::BlockReader;
^~~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: declared here
unique_ptr(const unique_ptr&) = delete;
^~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/x86_64-pc-linux-gnu/bits/c++allocator.h:33:0,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/allocator.h:46,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:63,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/ext/new_allocator.h:120:4: note: synthesized method ‘arrow::csv::\{anonymous}::SerialBlockReader::SerialBlockReader(std::unique_ptr<arrow::Chunker>, std::shared_ptr<arrow::Buffer>, int64_t)’ first required here
{ ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader]’:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/alloc_traits.h:455:4: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, _Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:520:39: required from ‘std::_Sp_counted_ptr_inplace<_Tp, _Alloc, _Lp>::_Sp_counted_ptr_inplace(_Alloc, _Args&& ...) [with _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:615:4: required from ‘std::__shared_count<_Lp>::__shared_count(std::_Sp_make_shared_tag, _Tp*, const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:1100:35: required from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:319:64: required from ‘std::shared_ptr<_Tp>::shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:619:14: required from ‘std::shared_ptr<_Tp1> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:635:39: required from ‘std::shared_ptr<_Tp1> std::make_shared(_Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:290:86: required from here
/tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:283:22: error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const std::unique_ptr<_Tp, _Dp>&) [with _Tp = arrow::Chunker; _Dp = std::default_delete<arrow::Chunker>]’
using BlockReader::BlockReader;
^~~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: declared here
unique_ptr(const unique_ptr&) = delete;
^~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/x86_64-pc-linux-gnu/bits/c++allocator.h:33:0,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/allocator.h:46,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:63,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmpE0E9RB/R.INSTALL5feb21fc0c41/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/ext/new_allocator.h:120:4: note: synthesized method ‘arrow::csv::\{anonymous}::ThreadedBlockReader::ThreadedBlockReader(std::unique_ptr<arrow::Chunker>, std::shared_ptr<arrow::Buffer>, int64_t)’ first required here
{ ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [src/arrow/CMakeFiles/arrow_static.dir/csv/reader.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/arrow/CMakeFiles/arrow_static.dir/all] Error 2
gmake: *** [all] Error 2
**** Error building Arrow C++.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
---------------------------------------------------------
ERROR: configuration failed for package ‘arrow’
* removing ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
* restoring previous ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
The downloaded source packages are in
‘/tmp/RtmpnSpLOO/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("arrow") :
installation of package ‘arrow’ had non-zero exit status
3. rebuild from source:
with full rebuild:
[ 61%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/chunker.cc.o
[ 61%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/column_builder.cc.o
[ 61%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/column_decoder.cc.o
[ 61%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/options.cc.o
[ 62%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/parser.cc.o
[ 62%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/reader.cc.o
[ 62%] Building CXX object src/arrow/CMakeFiles/arrow_static.dir/csv/writer.cc.o
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader]’:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/alloc_traits.h:455:4: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, _Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:520:39: required from ‘std::_Sp_counted_ptr_inplace<_Tp, _Alloc, _Lp>::_Sp_counted_ptr_inplace(_Alloc, _Args&& ...) [with _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:615:4: required from ‘std::__shared_count<_Lp>::__shared_count(std::_Sp_make_shared_tag, _Tp*, const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:1100:35: required from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:319:64: required from ‘std::shared_ptr<_Tp>::shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::SerialBlockReader]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:619:14: required from ‘std::shared_ptr<_Tp1> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::SerialBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:635:39: required from ‘std::shared_ptr<_Tp1> std::make_shared(_Args&& ...) [with _Tp = arrow::csv::\{anonymous}::SerialBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:200:88: required from here
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:194:22: error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const std::unique_ptr<_Tp, _Dp>&) [with _Tp = arrow::Chunker; _Dp = std::default_delete<arrow::Chunker>]’
using BlockReader::BlockReader;
^~~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: declared here
unique_ptr(const unique_ptr&) = delete;
^~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/x86_64-pc-linux-gnu/bits/c++allocator.h:33:0,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/allocator.h:46,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:63,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/ext/new_allocator.h:120:4: note: synthesized method ‘arrow::csv::\{anonymous}::SerialBlockReader::SerialBlockReader(std::unique_ptr<arrow::Chunker>, std::shared_ptr<arrow::Buffer>, int64_t)’ first required here
{ ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader]’:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/alloc_traits.h:455:4: required from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(std::allocator_traits<std::allocator<_Tp1> >::allocator_type&, _Up*, _Args&& ...) [with _Up = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; std::allocator_traits<std::allocator<_Tp1> >::allocator_type = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:520:39: required from ‘std::_Sp_counted_ptr_inplace<_Tp, _Alloc, _Lp>::_Sp_counted_ptr_inplace(_Alloc, _Args&& ...) [with _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:615:4: required from ‘std::__shared_count<_Lp>::__shared_count(std::_Sp_make_shared_tag, _Tp*, const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr_base.h:1100:35: required from ‘std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; __gnu_cxx::_Lock_policy _Lp = (__gnu_cxx::_Lock_policy)2u]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:319:64: required from ‘std::shared_ptr<_Tp>::shared_ptr(std::_Sp_make_shared_tag, const _Alloc&, _Args&& ...) [with _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}; _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:619:14: required from ‘std::shared_ptr<_Tp1> std::allocate_shared(const _Alloc&, _Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Alloc = std::allocator<arrow::csv::\{anonymous}::ThreadedBlockReader>; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/shared_ptr.h:635:39: required from ‘std::shared_ptr<_Tp1> std::make_shared(_Args&& ...) [with _Tp = arrow::csv::\{anonymous}::ThreadedBlockReader; _Args = \{std::unique_ptr<arrow::Chunker, std::default_delete<arrow::Chunker> >, std::shared_ptr<arrow::Buffer>&, long int&}]’
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:290:86: required from here
/tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:283:22: error: use of deleted function ‘std::unique_ptr<_Tp, _Dp>::unique_ptr(const std::unique_ptr<_Tp, _Dp>&) [with _Tp = arrow::Chunker; _Dp = std::default_delete<arrow::Chunker>]’
using BlockReader::BlockReader;
^~~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:356:7: note: declared here
unique_ptr(const unique_ptr&) = delete;
^~~~~~~~~~
In file included from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/x86_64-pc-linux-gnu/bits/c++allocator.h:33:0,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/bits/allocator.h:46,
from /gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/memory:63,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.h:20,
from /tmp/RtmptS0JtL/R.INSTALL1278d7b12d1a2/arrow/tools/cpp/src/arrow/csv/reader.cc:18:
/gpfs/share/apps/gcc/6.1.0/include/c++/6.1.0/ext/new_allocator.h:120:4: note: synthesized method ‘arrow::csv::\{anonymous}::ThreadedBlockReader::ThreadedBlockReader(std::unique_ptr<arrow::Chunker>, std::shared_ptr<arrow::Buffer>, int64_t)’ first required here
{ ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [src/arrow/CMakeFiles/arrow_static.dir/csv/reader.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/arrow/CMakeFiles/arrow_static.dir/all] Error 2
gmake: *** [all] Error 2
**** Error building Arrow C++.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
---------------------------------------------------------
ERROR: configuration failed for package ‘arrow’
* removing ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
* restoring previous ‘/gpfs/share/apps/R/4.1.1/lib64/R/library/arrow’
The downloaded source packages are in
‘/tmp/RtmpnSpLOO/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("arrow") :
installation of package ‘arrow’ had non-zero exit status
>
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