RcppParallel Install Issues

[acwilsoncu]

Hi all, am attempting to install the RcppParallel package as root on a Centos 7 server running RStudio Workbench. Am a bit stuck on how to proceed and would appreciate any input you all have on how to get around this error:

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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> install.packages('RcppParallel', repos='https://cran.rstudio.com/')
trying URL 'https://cran.rstudio.com/src/contrib/RcppParallel_5.1.7.tar.gz'
Content type 'application/x-gzip' length 1629119 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'R/tbb-autodetected.R.in' => 'R/tbb-autodetected.R'
*** configured file: 'src/Makevars.in' => 'src/Makevars'
*** configured file: 'src/install.libs.R.in' => 'src/install.libs.R'
** finished configure for package 'RcppParallel'
** libs
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=gcc
runtime=cc4.8.5_libc2.17_kernel3.10.0
tbb_build_prefix=linux_intel64_gcc_cc4.8.5_libc2.17_kernel3.10.0
work_dir=/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/build/linux_intel64_gcc_cc4.8.5_libc2.17_kernel3.10.0_release
make[1]: Leaving directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/src'
make[1]: Entering directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/src'
Created ../build/lib_release directory
make -C "../build/lib_release"  -r -f ../../build/Makefile.tbb cfg=release
make[2]: Entering directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/build/lib_release'
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc4.8.5_libc2.17_kernel3.10.0
g++ -I../inst/include  -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -m64 -mrtm  -fpic  -D__TBB_BUILD=1 -Wall -Wextra  -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
In file included from ../../include/tbb/concurrent_hash_map.h:26:0,
                 from ../../src/tbb/concurrent_hash_map.cpp:17:
../../include/tbb/compat/iterator.h:19:11: error: expected nested-name-specifier before ‘iterator_category’
     using iterator_category = Category;
           ^
../../include/tbb/compat/iterator.h:19:11: error: using-declaration for non-member at class scope
../../include/tbb/compat/iterator.h:19:29: error: expected ‘;’ before ‘=’ token
     using iterator_category = Category;
                             ^
../../include/tbb/compat/iterator.h:19:29: error: expected unqualified-id before ‘=’ token
../../include/tbb/compat/iterator.h:20:11: error: expected nested-name-specifier before ‘value_type’
     using value_type = T;
           ^
../../include/tbb/compat/iterator.h:20:11: error: using-declaration for non-member at class scope
../../include/tbb/compat/iterator.h:20:22: error: expected ‘;’ before ‘=’ token
     using value_type = T;
                      ^
../../include/tbb/compat/iterator.h:20:22: error: expected unqualified-id before ‘=’ token
../../include/tbb/compat/iterator.h:21:11: error: expected nested-name-specifier before ‘difference_type’
     using difference_type = Distance;
           ^
../../include/tbb/compat/iterator.h:21:11: error: using-declaration for non-member at class scope
../../include/tbb/compat/iterator.h:21:27: error: expected ‘;’ before ‘=’ token
     using difference_type = Distance;
                           ^
../../include/tbb/compat/iterator.h:21:27: error: expected unqualified-id before ‘=’ token
../../include/tbb/compat/iterator.h:22:11: error: expected nested-name-specifier before ‘pointer’
     using pointer = Pointer;
           ^
../../include/tbb/compat/iterator.h:22:11: error: using-declaration for non-member at class scope
../../include/tbb/compat/iterator.h:22:19: error: expected ‘;’ before ‘=’ token
     using pointer = Pointer;
                   ^
../../include/tbb/compat/iterator.h:22:19: error: expected unqualified-id before ‘=’ token
../../include/tbb/compat/iterator.h:23:11: error: expected nested-name-specifier before ‘reference’
     using reference = Reference;
           ^
../../include/tbb/compat/iterator.h:23:11: error: using-declaration for non-member at class scope
../../include/tbb/compat/iterator.h:23:21: error: expected ‘;’ before ‘=’ token
     using reference = Reference;
                     ^
../../include/tbb/compat/iterator.h:23:21: error: expected unqualified-id before ‘=’ token
make[2]: *** [concurrent_hash_map.o] Error 1
make[2]: Leaving directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [tbb_release] Error 2
make[1]: Leaving directory `/tmp/RtmpReWVfG/R.INSTALL8ed30717eb6/RcppParallel/src/tbb/src'
g++ -std=gnu++11 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -c init.cpp -o init.o
g++ -std=gnu++11 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I../inst/include  -I/usr/local/include  -std=gnu++11 -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic  -g -O2  -c options.cpp -o options.o
g++ -std=gnu++11 -shared -L/opt/R/4.2.1/lib/R/lib -L/usr/local/lib -o RcppParallel.so init.o options.o -L/opt/R/4.2.1/lib/R/lib -lR
installing via 'install.libs.R' to /opt/R/4.2.1/lib/R/library/00LOCK-RcppParallel/00new/RcppParallel
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘RcppParallel’
    finding HTML links ... done
    RcppParallel-package                    html  
    RcppParallel.package.skeleton           html  
    flags                                   html  
    setThreadOptions                        html  
    tbbLibraryPath                          html  
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘RcppParallel’:
 .onLoad failed in loadNamespace() for 'RcppParallel', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/opt/R/4.2.1/lib/R/library/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so':
  /opt/R/4.2.1/lib/R/library/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so: undefined symbol: _ZN3tbb10interface58internal9task_base7destroyERNS_4taskE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/4.2.1/lib/R/library/RcppParallel’

The downloaded source packages are in
    ‘/tmp/RtmpeTViAn/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("RcppParallel", repos = "https://cran.rstudio.com/") :
  installation of package ‘RcppParallel’ had non-zero exit status
> 
> 

[eddelbuettel]

Please search the existing issues for 'CentOS 7' -- this has come up before, your toolchain is likely to old but there is a workaround / improvement via devtoolset.

Here is search for all 'centos' issues: https://github.com/RcppCore/RcppParallel/issues?q=is%3Aissue+centos -- please review and report back. This is most likely a duplicate issue.

[acwilsoncu]

Thanks for your input, @eddelbuettel

I was able to resolve this by creating the ~/.R/Makevars file and setting the CXX11 compiler to be the same as the CXX from the output of 'R CMD config --all'

[J-Kamp]

Thanks for your input, @eddelbuettel

I was able to resolve this by creating the ~/.R/Makevars file and setting the CXX11 compiler to be the same as the CXX from the output of 'R CMD config --all'

Can you be more specific on what you did? I have tried adding the Makevars file with: CXX11 = /gsc/software/linux-x86_64-centos7/gcc-7.2.0/bin/g++

Installing both with R CMD, in R with install.packages and with devtools directly.

None of it works and I end up with the same error as you posted in the top.