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gesistsa / rio

🐟 A Swiss-Army Knife for Data I/O
http://gesistsa.github.io/rio/
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Installing arrow format hung forever #387

Closed HamzaAhmedZia7 closed 6 months ago

HamzaAhmedZia7 commented 7 months ago

Using RStudio 2023.12.0 Build 369 , R 4.3.2 on 64 bit Arch Linux and installed rio 1.0.1 using install.packages('rio')

Then tried install_formats() which went on a for a long time installing various formats but hung on installing arrow for about 30 minutes.

Cancelled the command then searching this github issues I install.packages("rang") which went successfully but then again install_formats() hung on arrow

[ 49%] Building CXX object src/arrow/CMakeFiles/arrow_objlib.dir/compute/kernel.cc.o
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make[2]: *** Deleting file 'src/arrow/CMakeFiles/arrow_objlib.dir/compute/kernels/scalar_round.cc.o'
make[2]: *** Deleting file 'src/arrow/CMakeFiles/arrow_objlib.dir/compute/kernels/scalar_nested.cc.o'
make[2]: *** [src/arrow/CMakeFiles/arrow_objlib.dir/build.make:2512: src/arrow/CMakeFiles/arrow_objlib.dir/compute/kernels/scalar_nested.cc.o] Interrupt
make[2]: *** [src/arrow/CMakeFiles/arrow_objlib.dir/build.make:2540: src/arrow/CMakeFiles/arrow_objlib.dir/compute/kernels/scalar_round.cc.o] Interrupt
make[1]: *** [CMakeFiles/Makefile2:1314: src/arrow/CMakeFiles/arrow_objlib.dir/all] Interrupt
make: *** [Makefile:146: all] Interrupt
**** Complete build log may still be present at /tmp/RtmpZyqrjo/fileda1461fbfdb.log 
*** Failed to find Arrow C++ libraries.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
----------------------------------------------------------

Test compile error: <stdin>:1:10: fatal error: arrow/api.h: No such file or directory
compilation terminated.
Failing compile command: g++ -E -I/usr/local/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -std=gnu++17 -xc++ -
PKG_CFLAGS=
PKG_LIBS=
ERROR: configuration failed for package ‘arrow’
* removing ‘/home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3/arrow’
The downloaded source packages are in
    ‘/tmp/RtmpgZibII/downloaded_packages’
Warning message:
In utils::install.packages(to_install, ...) :
  installation of package ‘arrow’ had non-zero exit status
> install.packages("rang")
Installing package into ‘/home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘cachem’, ‘rprojroot’, ‘parsedate’, ‘fastmap’, ‘memoise’, ‘pkgsearch’, ‘remotes’, ‘renv’, ‘here’

trying URL 'https://cran.rstudio.com/src/contrib/cachem_1.0.8.tar.gz'
Content type 'application/x-gzip' length 26510 bytes (25 KB)
==================================================
downloaded 25 KB

trying URL 'https://cran.rstudio.com/src/contrib/rprojroot_2.0.4.tar.gz'
Content type 'application/x-gzip' length 59946 bytes (58 KB)
==================================================
downloaded 58 KB

trying URL 'https://cran.rstudio.com/src/contrib/parsedate_1.3.1.tar.gz'
Content type 'application/x-gzip' length 19800 bytes (19 KB)
==================================================
downloaded 19 KB

trying URL 'https://cran.rstudio.com/src/contrib/fastmap_1.1.1.tar.gz'
Content type 'application/x-gzip' length 46412 bytes (45 KB)
==================================================
downloaded 45 KB

trying URL 'https://cran.rstudio.com/src/contrib/memoise_2.0.1.tar.gz'
Content type 'application/x-gzip' length 17852 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cran.rstudio.com/src/contrib/pkgsearch_3.1.3.tar.gz'
Content type 'application/x-gzip' length 59217 bytes (57 KB)
==================================================
downloaded 57 KB

trying URL 'https://cran.rstudio.com/src/contrib/remotes_2.4.2.1.tar.gz'
Content type 'application/x-gzip' length 152560 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/src/contrib/renv_1.0.3.tar.gz'
Content type 'application/x-gzip' length 1140033 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/here_1.0.1.tar.gz'
Content type 'application/x-gzip' length 32954 bytes (32 KB)
==================================================
downloaded 32 KB

trying URL 'https://cran.rstudio.com/src/contrib/rang_0.3.0.tar.gz'
Content type 'application/x-gzip' length 536950 bytes (524 KB)
==================================================
downloaded 524 KB

begin installing package ‘rprojroot’
begin installing package ‘parsedate’
begin installing package ‘fastmap’
begin installing package ‘pkgsearch’
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rprojroot)
begin installing package ‘remotes’
* installing *source* package ‘pkgsearch’ ...
** package ‘pkgsearch’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgsearch)
begin installing package ‘renv’
* installing *source* package ‘parsedate’ ...
** package ‘parsedate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 13.2.1 20230801’
make[1]: Entering directory '/tmp/Rtmp6JrzDb/R.INSTALL41ec50e09bc9/parsedate/src'
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c date.c -o date.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c mingw.c -o mingw.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c rdate.c -o rdate.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto=auto -o parsedate.so date.o mingw.o rdate.o -L/usr/lib64/R/lib -lR
make[1]: Leaving directory '/tmp/Rtmp6JrzDb/R.INSTALL41ec50e09bc9/parsedate/src'
installing to /home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-parsedate/00new/parsedate/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (parsedate)
begin installing package ‘here’
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
* installing *source* package ‘here’ ...
** package ‘here’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (here)
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 13.2.1 20230801’
using C++ compiler: ‘g++ (GCC) 13.2.1 20230801’
make[1]: Entering directory '/tmp/Rtmpb7ib25/R.INSTALL41ed15f79522/fastmap/src'
g++ -std=gnu++17 -I"/usr/include/R/" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c fastmap.cpp -o fastmap.o
gcc -I"/usr/include/R/" -DNDEBUG -Ilib/  -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c init.c -o init.o
g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto=auto -o fastmap.so fastmap.o init.o -L/usr/lib64/R/lib -lR
make[1]: Leaving directory '/tmp/Rtmpb7ib25/R.INSTALL41ed15f79522/fastmap/src'
installing to /home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-fastmap/00new/fastmap/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fastmap)
begin installing package ‘cachem’
* installing *source* package ‘renv’ ...
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (renv)
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 13.2.1 20230801’
make[1]: Entering directory '/tmp/RtmpfWC9A8/R.INSTALL43422501dd2f/cachem/src'
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c cache.c -o cache.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c init.c -o init.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto=auto -o cachem.so cache.o init.o -L/usr/lib64/R/lib -lR
make[1]: Leaving directory '/tmp/RtmpfWC9A8/R.INSTALL43422501dd2f/cachem/src'
installing to /home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-cachem/00new/cachem/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cachem)
begin installing package ‘memoise’
* installing *source* package ‘memoise’ ...
** package ‘memoise’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (memoise)
begin installing package ‘rang’
* installing *source* package ‘rang’ ...
** package ‘rang’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rang)

The downloaded source packages are in
    ‘/tmp/RtmpgZibII/downloaded_packages’
> install_formats()
Installing package into ‘/home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/arrow_14.0.0.2.tar.gz'
Content type 'application/x-gzip' length 4263864 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** Disabling Arrow build with GCS on gcc-13.
*** Set ARROW_GCS=ON to explicitly enable.
*** pkg-config found.
*** Found local C++ source: 'tools/cpp'
*** Building libarrow from source
    For build options and troubleshooting, see the install guide:
    https://arrow.apache.org/docs/r/articles/install.html
**** cmake: /usr/bin/cmake
**** arrow 
**** Error building Arrow C++.
**** Printing contents of build log because the build failed while ARROW_R_DEV was set to FALSE
++ pwd
+ : /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow
+ : tools/cpp
+ : /tmp/RtmpdUzSTc/file452e29a35649
+ : libarrow/arrow-14.0.0
+ : /usr/bin/cmake
++ cd tools/cpp
++ pwd
+ SOURCE_DIR=/tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/tools/cpp
++ mkdir -p libarrow/arrow-14.0.0
++ cd libarrow/arrow-14.0.0
++ pwd
+ DEST_DIR=/tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/libarrow/arrow-14.0.0
+ '[' 2 = '' ']'
+ '[' '' '!=' '' ']'
+ '[' '' = false ']'
+ ARROW_DEFAULT_PARAM=OFF
+ case "$CXX" in
+ mkdir -p /tmp/RtmpdUzSTc/file452e29a35649
+ pushd /tmp/RtmpdUzSTc/file452e29a35649
/tmp/RtmpdUzSTc/file452e29a35649 /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow
+ /usr/bin/cmake -DARROW_BOOST_USE_SHARED=OFF -DARROW_BUILD_TESTS=OFF -DARROW_BUILD_SHARED=OFF -DARROW_BUILD_STATIC=ON -DARROW_ACERO=ON -DARROW_COMPUTE=ON -DARROW_CSV=ON -DARROW_DATASET=ON -DARROW_DEPENDENCY_SOURCE=AUTO -DAWSSDK_SOURCE= -DARROW_FILESYSTEM=ON -DARROW_GCS=OFF -DARROW_JEMALLOC=OFF -DARROW_MIMALLOC=ON -DARROW_JSON=ON -DARROW_PARQUET=ON -DARROW_S3=OFF -DARROW_WITH_BROTLI=OFF -DARROW_WITH_BZ2=OFF -DARROW_WITH_LZ4=ON -DARROW_WITH_RE2=ON -DARROW_WITH_SNAPPY=ON -DARROW_WITH_UTF8PROC=ON -DARROW_WITH_ZLIB=OFF -DARROW_WITH_ZSTD=OFF -DARROW_VERBOSE_THIRDPARTY_BUILD=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_DEBUG_MODE=OFF -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=/tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/libarrow/arrow-14.0.0 -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_UNITY_BUILD=OFF -Dxsimd_SOURCE= -Dzstd_SOURCE= -G 'Unix Makefiles' /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/tools/cpp
-- Building using CMake version: 3.28.1
-- The C compiler identification is GNU 13.2.1
-- The CXX compiler identification is GNU 13.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Arrow version: 14.0.0 (full: '14.0.0')
-- Arrow SO version: 1400 (full: 1400.0.0)
-- clang-tidy found, but version did not match "LLVM version 14"
-- clang-tidy 14 not found
-- clang-format found, but version did not match "clang-format version 14"
-- clang-format 14 not found
-- Could NOT find ClangTools (missing: CLANG_FORMAT_BIN CLANG_TIDY_BIN) 
-- infer not found
-- Found Python3: /usr/bin/python3.11 (found version "3.11.6") found components: Interpreter 
fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-- Found cpplint executable at /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/tools/cpp/build-support/cpplint.py
-- System processor: x86_64
-- Performing Test CXX_SUPPORTS_SSE4_2
-- Performing Test CXX_SUPPORTS_SSE4_2 - Success
-- Performing Test CXX_SUPPORTS_AVX2
-- Performing Test CXX_SUPPORTS_AVX2 - Success
-- Performing Test CXX_SUPPORTS_AVX512
-- Performing Test CXX_SUPPORTS_AVX512 - Success
-- Arrow build warning level: PRODUCTION
-- Using ld linker
-- Build Type: RELEASE
-- Performing Test CXX_LINKER_SUPPORTS_VERSION_SCRIPT
-- Performing Test CXX_LINKER_SUPPORTS_VERSION_SCRIPT - Success
-- Using AUTO approach to find dependencies
-- ARROW_ABSL_BUILD_VERSION: 20211102.0
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-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Looking for _M_ARM64
-- Looking for _M_ARM64 - not found
-- Looking for __SIZEOF_INT128__
-- Looking for __SIZEOF_INT128__ - found
-- Found Boost: /usr/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.58")  
-- Boost include dir: /usr/include
-- Providing CMake module for SnappyAlt as part of Arrow CMake package
-- Using pkg-config package for snappy that is used by arrow for static link
-- Building without OpenSSL support. Minimum OpenSSL version 1.0.2 required.
CMake Warning at cmake_modules/FindThriftAlt.cmake:56 (find_package):
  By not providing "FindThrift.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Thrift", but
  CMake did not find one.

  Could not find a package configuration file provided by "Thrift" (requested
  version 0.11.0) with any of the following names:

    ThriftConfig.cmake
    thrift-config.cmake

  Add the installation prefix of "Thrift" to CMAKE_PREFIX_PATH or set
  "Thrift_DIR" to a directory containing one of the above files.  If "Thrift"
  provides a separate development package or SDK, be sure it has been
  installed.
Call Stack (most recent call first):
  cmake_modules/ThirdpartyToolchain.cmake:277 (find_package)
  cmake_modules/ThirdpartyToolchain.cmake:1698 (resolve_dependency)
  CMakeLists.txt:542 (include)

-- Checking for module 'thrift'
--   Package 'thrift', required by 'virtual:world', not found
-- Could NOT find ThriftAlt: (Required is at least version "0.11.0") (found ThriftAlt_LIB-NOTFOUND)
-- Building Apache Thrift from source
-- Building (vendored) mimalloc from source
CMake Warning at cmake_modules/FindRapidJSONAlt.cmake:29 (find_package):
  By not providing "FindRapidJSON.cmake" in CMAKE_MODULE_PATH this project
  has asked CMake to find a package configuration file provided by
  "RapidJSON", but CMake did not find one.

  Could not find a package configuration file provided by "RapidJSON"
  (requested version 1.1.0) with any of the following names:

    RapidJSONConfig.cmake
    rapidjson-config.cmake

  Add the installation prefix of "RapidJSON" to CMAKE_PREFIX_PATH or set
  "RapidJSON_DIR" to a directory containing one of the above files.  If
  "RapidJSON" provides a separate development package or SDK, be sure it has
  been installed.
Call Stack (most recent call first):
  cmake_modules/ThirdpartyToolchain.cmake:277 (find_package)
  cmake_modules/ThirdpartyToolchain.cmake:2325 (resolve_dependency)
  CMakeLists.txt:542 (include)

-- Could NOT find RapidJSONAlt (missing: RAPIDJSON_INCLUDE_DIR) (Required is at least version "1.1.0")
-- Building RapidJSON from source
CMake Warning at cmake_modules/ThirdpartyToolchain.cmake:277 (find_package):
  By not providing "Findxsimd.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "xsimd", but
  CMake did not find one.

  Could not find a package configuration file provided by "xsimd" with any of
  the following names:

    xsimdConfig.cmake
    xsimd-config.cmake

  Add the installation prefix of "xsimd" to CMAKE_PREFIX_PATH or set
  "xsimd_DIR" to a directory containing one of the above files.  If "xsimd"
  provides a separate development package or SDK, be sure it has been
  installed.
Call Stack (most recent call first):
  cmake_modules/ThirdpartyToolchain.cmake:2377 (resolve_dependency)
  CMakeLists.txt:542 (include)

-- Building xsimd from source
CMake Warning at cmake_modules/Findlz4Alt.cmake:29 (find_package):
  By not providing "Findlz4.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "lz4", but
  CMake did not find one.

  Could not find a package configuration file provided by "lz4" with any of
  the following names:

    lz4Config.cmake
    lz4-config.cmake

  Add the installation prefix of "lz4" to CMAKE_PREFIX_PATH or set "lz4_DIR"
  to a directory containing one of the above files.  If "lz4" provides a
  separate development package or SDK, be sure it has been installed.
Call Stack (most recent call first):
  cmake_modules/ThirdpartyToolchain.cmake:277 (find_package)
  cmake_modules/ThirdpartyToolchain.cmake:2468 (resolve_dependency)
  CMakeLists.txt:542 (include)

-- Checking for module 'liblz4'
--   Found liblz4, version 1.9.4
-- Found lz4Alt: /usr/lib/liblz4.so  
-- Providing CMake module for lz4Alt as part of Arrow CMake package
-- Using pkg-config package for liblz4 that is used by arrow for static link
CMake Warning at cmake_modules/Findre2Alt.cmake:29 (find_package):
  By not providing "Findre2.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "re2", but
  CMake did not find one.

  Could not find a package configuration file provided by "re2" with any of
  the following names:

    re2Config.cmake
    re2-config.cmake

  Add the installation prefix of "re2" to CMAKE_PREFIX_PATH or set "re2_DIR"
  to a directory containing one of the above files.  If "re2" provides a
  separate development package or SDK, be sure it has been installed.
Call Stack (most recent call first):
  cmake_modules/ThirdpartyToolchain.cmake:277 (find_package)
  cmake_modules/ThirdpartyToolchain.cmake:2585 (resolve_dependency)
  CMakeLists.txt:542 (include)

-- Checking for module 're2'
--   Found re2, version 11.0.0
-- Found re2Alt: /usr/lib/libre2.so  
-- Providing CMake module for re2Alt as part of Arrow CMake package
-- Could NOT find utf8proc: (Required is at least version "2.2.0") (found utf8proc_LIB-NOTFOUND)
-- Building utf8proc from source
-- Found hdfs.h at: /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/tools/cpp/thirdparty/hadoop/include/hdfs.h
-- All bundled static libraries: thrift::thrift;mimalloc::mimalloc;utf8proc::utf8proc
-- CMAKE_C_FLAGS: -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -Wall -fno-semantic-interposition -msse4.2 
-- CMAKE_CXX_FLAGS:  -Wno-noexcept-type -Wno-self-move -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -fdiagnostics-color=always  -Wall -fno-semantic-interposition -msse4.2 
-- CMAKE_C_FLAGS_RELEASE: -O3 -DNDEBUG -O2 -ftree-vectorize 
-- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG -O2 -ftree-vectorize 
-- Creating bundled static library target arrow_bundled_dependencies at /tmp/RtmpdUzSTc/file452e29a35649/release/libarrow_bundled_dependencies.a
-- Looking for backtrace
-- Looking for backtrace - found
-- backtrace facility detected in default set of libraries
-- Found Backtrace: /usr/include  
-- ---------------------------------------------------------------------
-- Arrow version:                                 14.0.0
-- 
-- Build configuration summary:
--   Generator: Unix Makefiles
--   Build type: RELEASE
--   Source directory: /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/tools/cpp
--   Install prefix: /tmp/RtmpD8ahkN/R.INSTALL44385840a75a/arrow/libarrow/arrow-14.0.0
-- 
-- Compile and link options:
-- 
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--       Compiler flags to append when compiling Arrow
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--       Build static libraries
--   ARROW_BUILD_SHARED=OFF [default=ON]
--       Build shared libraries
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--       (for informational purposes)
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--       The Arrow git commit id (if any)
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--       The Arrow git commit description (if any)
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--       Exclude deprecated APIs from build
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--       Whether to create position-independent target
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--       Use ccache when compiling (if available)
--   ARROW_USE_SCCACHE=ON [default=ON]
--       Use sccache when compiling (if available),
--       takes precedence over ccache if a storage backend is configured
--   ARROW_USE_LD_GOLD=OFF [default=OFF]
--       Use ld.gold for linking on Linux (if available)
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--       Use precompiled headers when compiling
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--       Compile-time SIMD optimization level
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--       Max runtime SIMD optimization level
--   ARROW_ALTIVEC=ON [default=ON]
--       Build with Altivec if compiler has support
--   ARROW_RPATH_ORIGIN=OFF [default=OFF]
--       Build Arrow libraries with RATH set to $ORIGIN
--   ARROW_INSTALL_NAME_RPATH=ON [default=ON]
--       Build Arrow libraries with install_name set to @rpath
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--       Pass -ggdb flag to debug builds
--   ARROW_WITH_MUSL=OFF [default=OFF]
--       Whether the system libc is musl or not
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--       Enable threading in Arrow core
-- 
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-- 
--   ARROW_BUILD_EXAMPLES=OFF [default=OFF]
--       Build the Arrow examples
--   ARROW_BUILD_TESTS=OFF [default=OFF]
--       Build the Arrow googletest unit tests
--   ARROW_ENABLE_TIMING_TESTS=ON [default=ON]
--       Enable timing-sensitive tests
--   ARROW_BUILD_INTEGRATION=OFF [default=OFF]
--       Build the Arrow integration test executables
--   ARROW_BUILD_BENCHMARKS=OFF [default=OFF]
--       Build the Arrow micro benchmarks
--   ARROW_BUILD_BENCHMARKS_REFERENCE=OFF [default=OFF]
--       Build the Arrow micro reference benchmarks
--   ARROW_BUILD_OPENMP_BENCHMARKS=OFF [default=OFF]
--       Build the Arrow benchmarks that rely on OpenMP
--   ARROW_BUILD_DETAILED_BENCHMARKS=OFF [default=OFF]
--       Build benchmarks that do a longer exploration of performance
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--       Linkage of Arrow libraries with unit tests executables.
--   ARROW_FUZZING=OFF [default=OFF]
--       Build Arrow Fuzzing executables
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--       Enable unit tests which use large memory
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-- 
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--       Run the test suite using valgrind --tool=memcheck
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-- Project component options:
-- 
--   ARROW_ACERO=ON [default=OFF]
--       Build the Arrow Acero Engine Module
--   ARROW_AZURE=OFF [default=OFF]
--       Build Arrow with Azure support (requires the Azure SDK for C++)
--   ARROW_BUILD_UTILITIES=OFF [default=OFF]
--       Build Arrow commandline utilities
--   ARROW_COMPUTE=ON [default=OFF]
--       Build all Arrow Compute kernels
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--       Build the Arrow CSV Parser Module
--   ARROW_CUDA=OFF [default=OFF]
--       Build the Arrow CUDA extensions (requires CUDA toolkit)
--   ARROW_DATASET=ON [default=OFF]
--       Build the Arrow Dataset Modules
--   ARROW_FILESYSTEM=ON [default=OFF]
--       Build the Arrow Filesystem Layer
--   ARROW_FLIGHT=OFF [default=OFF]
--       Build the Arrow Flight RPC System (requires GRPC, Protocol Buffers)
--   ARROW_FLIGHT_SQL=OFF [default=OFF]
--       Build the Arrow Flight SQL extension
--   ARROW_GANDIVA=OFF [default=OFF]
--       Build the Gandiva libraries
--   ARROW_GCS=OFF [default=OFF]
--       Build Arrow with GCS support (requires the GCloud SDK for C++)
--   ARROW_HDFS=OFF [default=OFF]
--       Build the Arrow HDFS bridge
--   ARROW_IPC=ON [default=ON]
--       Build the Arrow IPC extensions
--   ARROW_JEMALLOC=OFF [default=ON]
--       Build the Arrow jemalloc-based allocator
--   ARROW_JSON=ON [default=OFF]
--       Build Arrow with JSON support (requires RapidJSON)
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--       Build the Arrow mimalloc-based allocator
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--       Build the Parquet libraries
--   ARROW_ORC=OFF [default=OFF]
--       Build the Arrow ORC adapter
--   ARROW_PYTHON=OFF [default=OFF]
--       Build some components needed by PyArrow.
--       (This is a deprecated option. Use CMake presets instead.)
--   ARROW_S3=OFF [default=OFF]
--       Build Arrow with S3 support (requires the AWS SDK for C++)
--   ARROW_SKYHOOK=OFF [default=OFF]
--       Build the Skyhook libraries
--   ARROW_SUBSTRAIT=OFF [default=OFF]
--       Build the Arrow Substrait Consumer Module
--   ARROW_TENSORFLOW=OFF [default=OFF]
--       Build Arrow with TensorFlow support enabled
--   ARROW_TESTING=OFF [default=OFF]
--       Build the Arrow testing libraries
-- 
-- Thirdparty toolchain options:
-- 
--   ARROW_DEPENDENCY_SOURCE=AUTO [default=AUTO|BUNDLED|SYSTEM|CONDA|VCPKG|BREW]
--       Method to use for acquiring arrow's build dependencies
--   ARROW_VERBOSE_THIRDPARTY_BUILD=OFF [default=OFF]
--       Show output from ExternalProjects rather than just logging to files
--   ARROW_DEPENDENCY_USE_SHARED=ON [default=ON]
--       Link to shared libraries
--   ARROW_BOOST_USE_SHARED=OFF [default=ON]
--       Rely on Boost shared libraries where relevant
--   ARROW_BROTLI_USE_SHARED=ON [default=ON]
--       Rely on Brotli shared libraries where relevant
--   ARROW_BZ2_USE_SHARED=ON [default=ON]
--       Rely on Bz2 shared libraries where relevant
--   ARROW_GFLAGS_USE_SHARED=ON [default=ON]
--       Rely on GFlags shared libraries where relevant
--   ARROW_GRPC_USE_SHARED=ON [default=ON]
--       Rely on gRPC shared libraries where relevant
--   ARROW_JEMALLOC_USE_SHARED=ON [default=ON]
--       Rely on jemalloc shared libraries where relevant
--   ARROW_LLVM_USE_SHARED=ON [default=ON]
--       Rely on LLVM shared libraries where relevant
--   ARROW_LZ4_USE_SHARED=ON [default=ON]
--       Rely on lz4 shared libraries where relevant
--   ARROW_OPENSSL_USE_SHARED=ON [default=ON]
--       Rely on OpenSSL shared libraries where relevant
--   ARROW_PROTOBUF_USE_SHARED=ON [default=ON]
--       Rely on Protocol Buffers shared libraries where relevant
--   ARROW_SNAPPY_USE_SHARED=ON [default=ON]
--       Rely on snappy shared libraries where relevant
--   ARROW_THRIFT_USE_SHARED=ON [default=ON]
--       Rely on thrift shared libraries where relevant
--   ARROW_UTF8PROC_USE_SHARED=ON [default=ON]
--       Rely on utf8proc shared libraries where relevant
--   ARROW_ZSTD_USE_SHARED=ON [default=ON]
--       Rely on zstd shared libraries where relevant
--   ARROW_USE_GLOG=OFF [default=OFF]
--       Build libraries with glog support for pluggable logging
--   ARROW_WITH_BACKTRACE=ON [default=ON]
--       Build with backtrace support
--   ARROW_WITH_OPENTELEMETRY=OFF [default=OFF]
--       Build libraries with OpenTelemetry support for distributed tracing
--   ARROW_WITH_BROTLI=OFF [default=OFF]
--       Build with Brotli compression
--   ARROW_WITH_BZ2=OFF [default=OFF]
--       Build with BZ2 compression
--   ARROW_WITH_LZ4=ON [default=OFF]
--       Build with lz4 compression
--   ARROW_WITH_SNAPPY=ON [default=OFF]
--       Build with Snappy compression
--   ARROW_WITH_ZLIB=OFF [default=OFF]
--       Build with zlib compression
--   ARROW_WITH_ZSTD=OFF [default=OFF]
--       Build with zstd compression
--   ARROW_WITH_UCX=OFF [default=OFF]
--       Build with UCX transport for Arrow Flight
--       (only used if ARROW_FLIGHT is ON)
--   ARROW_WITH_UTF8PROC=ON [default=ON]
--       Build with support for Unicode properties using the utf8proc library
--       (only used if ARROW_COMPUTE is ON or ARROW_GANDIVA is ON)
--   ARROW_WITH_RE2=ON [default=ON]
--       Build with support for regular expressions using the re2 library
--       (only used if ARROW_COMPUTE or ARROW_GANDIVA is ON)
-- 
-- Parquet options:
-- 
--   PARQUET_MINIMAL_DEPENDENCY=OFF [default=OFF]
--       Depend only on Thirdparty headers to build libparquet.
--       Always OFF if building binaries
--   PARQUET_BUILD_EXECUTABLES=OFF [default=OFF]
--       Build the Parquet executable CLI tools. Requires static libraries to be built.
--   PARQUET_BUILD_EXAMPLES=OFF [default=OFF]
--       Build the Parquet examples. Requires static libraries to be built.
--   PARQUET_REQUIRE_ENCRYPTION=OFF [default=OFF]
--       Build support for encryption. Fail if OpenSSL is not found
-- 
-- Gandiva options:
-- 
--   ARROW_GANDIVA_STATIC_LIBSTDCPP=OFF [default=OFF]
--       Include -static-libstdc++ -static-libgcc when linking with
--       Gandiva static libraries
--   ARROW_GANDIVA_PC_CXX_FLAGS="" [default=""]
--       Compiler flags to append when pre-compiling Gandiva operations
-- 
-- Advanced developer options:
-- 
--   ARROW_EXTRA_ERROR_CONTEXT=OFF [default=OFF]
--       Compile with extra error context (line numbers, code)
--   ARROW_OPTIONAL_INSTALL=OFF [default=OFF]
--       If enabled install ONLY targets that have already been built. Please be
--       advised that if this is enabled 'install' will fail silently on components
--       that have not been built
--   ARROW_GDB_INSTALL_DIR="" [default=""]
--       Use a custom install directory for GDB plugin.
--       In general, you don't need to specify this because the default
--       (CMAKE_INSTALL_FULL_BINDIR on Windows, CMAKE_INSTALL_FULL_LIBDIR otherwise)
--       is reasonable.
--   Outputting build configuration summary to /tmp/RtmpdUzSTc/file452e29a35649/cmake_summary.json
-- Configuring done (18.3s)
-- Generating done (0.1s)
-- Build files have been written to: /tmp/RtmpdUzSTc/file452e29a35649
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**** Complete build log may still be present at /tmp/RtmpdUzSTc/file452e5354868.log 
*** Failed to find Arrow C++ libraries.
------------------------- NOTE ---------------------------
There was an issue preparing the Arrow C++ libraries.
See https://arrow.apache.org/docs/r/articles/install.html
----------------------------------------------------------

Test compile error: <stdin>:1:10: fatal error: arrow/api.h: No such file or directory
compilation terminated.
Failing compile command: g++ -E -I/usr/local/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -std=gnu++17 -xc++ -
PKG_CFLAGS=
PKG_LIBS=
ERROR: configuration failed for package ‘arrow’
* removing ‘/home/hikmateustad/R/x86_64-pc-linux-gnu-library/4.3/arrow’
>

What should be done to resolve this?

chainsawriot commented 7 months ago

This is probably not an issue of rio. You probably will encounter the same issue with

install.packages("arrow")

I don't use Arch BTW, so I can't provide much help. You can either report this here; or try one of the methods listed here.

HamzaAhmedZia7 commented 7 months ago

You are right about installing arrow directly, I faced the same error.

So this error will not hamper the functionality of rio?

BTW I don't BTW ... seriously ;-)

chainsawriot commented 7 months ago

@HamzaAhmedZia7 Actually, as long as you don't use parquet and feather file formats; as well as you don't need to import data as arrow_table, you can use rio just fine without installing arrow the R package.