Skip to content

installation of package 'RcppParallel' had non-zero exit status #198

@theo-allnutt-bioinformatics

Description

install.packages('RcppParallel')

trying URL 'https://cloud.r-project.org/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 '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
../build/linux.inc:31: "Unknown Intel compiler"
OS: linux
arch=intel64
compiler=icc
runtime=cc8.5.0_libc2.28_kernel4.18.0
tbb_build_prefix=linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0
work_dir=/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/build/linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0_release
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
make[1]: Entering directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
../build/linux.inc:31: "Unknown Intel compiler"
Created ../build/lib_release directory
make -C "../build/lib_release"  -r -f ../../build/Makefile.tbb cfg=release
make[2]: Entering directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/build/lib_release'
/bin/sh: icc: command not found
/bin/sh: icc: command not found
/bin/sh: icc: command not found
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=icc target=linux runtime=cc8.5.0_libc2.28_kernel4.18.0
/bin/sh: icc: command not found
icpc -I../inst/include  -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -strict-ansi -D_FORTIFY_SOURCE=2 -fpic  -D__TBB_BUILD=1 -w1  -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
make[2]: icpc: Command not found
make[2]: *** [../../build/common_rules.inc:76: concurrent_hash_map.o] Error 127
make[2]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [Makefile:100: tbb_release] Error 2
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmpVAGh4q/R.INSTALL2e156974684a7d/RcppParallel/src/tbb/src'
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/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
/bin/sh: icpc: command not found
make: *** [/apps/R/4.2.2/lib64/R/etc/Makeconf:178: init.o] Error 127
ERROR: compilation failed for package 'RcppParallel'
* removing '/home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel'

The downloaded source packages are in
        '/scratch/nm31/ta0341/tmp/Rtmp5zVBSH/downloaded_packages'
Warning message:
In install.packages("RcppParallel") :
  installation of package 'RcppParallel' had non-zero exit status

Activity

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 15, 2023

@theo-allnutt-bioinformatics
Author

After installing Rcpp, which worked ok, tried intel-compiler/2021.6.0:

Selection: 1
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.10.tar.gz'
Content type 'application/x-gzip' length 2936173 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package 'Rcpp' ...
** package 'Rcpp' successfully unpacked and MD5 sums checked
** using staged installation
** libs
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c api.cpp -o api.o
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c attributes.cpp -o attributes.o
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c barrier.cpp -o barrier.o
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c date.cpp -o date.o
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c module.cpp -o module.o
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c rcpp_init.cpp -o rcpp_init.o
icpc -std=gnu++14 -shared -L/apps/R/4.2.2/lib64/R/lib -L/usr/local/lib64 -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/apps/R/4.2.2/lib64/R/lib -lR
installing to /home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-Rcpp/00new/Rcpp/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
** 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 (Rcpp)

The downloaded source packages are in
        '/scratch/nm31/ta0341/tmp/RtmpOvYcGT/downloaded_packages'
> install.packages('RcppParallel')
Installing package into '/home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/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 '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/tbb/src'
OS: linux
arch=intel64
compiler=icc
runtime=cc8.5.0_libc2.28_kernel4.18.0
tbb_build_prefix=linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0
work_dir=/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/build/linux_intel64_icc_cc8.5.0_libc2.28_kernel4.18.0_release
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/tbb/src'
make[1]: Entering directory '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/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 '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/tbb/build/lib_release'
../../build/Makefile.tbb:28: CONFIG: cfg=release arch=intel64 compiler=icc target=linux runtime=cc8.5.0_libc2.28_kernel4.18.0
icpc -I../inst/include  -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -O2 -DUSE_PTHREAD -strict-ansi -D_FORTIFY_SOURCE=2 -fpic  -D__TBB_BUILD=1 -w1  -g -O2 -DTBB_NO_LEGACY=1   -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1233): error: argument list for class template "tbb::interface5::concurrent_hash_map" is missing
  concurrent_hash_map(I, I, Args...)
  ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1233): error: expected a ")"
  concurrent_hash_map(I, I, Args...)
                       ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1233): error: template parameter "I" may not be redeclared in this scope
  concurrent_hash_map(I, I, Args...)
                      ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1234): error: expected a ";"
  -> internal::hash_map_t<concurrent_hash_map, internal::iterator_key_t<I>,internal::iterator_mapped_t<I>, Args...>;
  ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1239): error: argument list for class template "tbb::interface5::concurrent_hash_map" is missing
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
  ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1239): error: expected a ")"
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
                                                                    ^

In file included from ../../src/tbb/concurrent_hash_map.cpp(17):
../../include/tbb/concurrent_hash_map.h(1239): error: "initializer_list" is not a function or static data member
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
                           ^

compilation aborted for ../../src/tbb/concurrent_hash_map.cpp (code 2)
make[2]: *** [../../build/common_rules.inc:76: concurrent_hash_map.o] Error 2
make[2]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/tbb/build/lib_release'
make[1]: *** [Makefile:100: tbb_release] Error 2
make[1]: Leaving directory '/scratch/nm31/ta0341/tmp/RtmphhBioH/R.INSTALL2ee38811ae0dfe/RcppParallel/src/tbb/src'
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/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
icpc -std=gnu++14 -I"/apps/R/4.2.2/lib64/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
In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1163): error: argument list for class template "tbb::concurrent_vector" is missing
  > concurrent_vector(I, I, const A& = A())
    ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1163): error: expected a ")"
  > concurrent_vector(I, I, const A& = A())
                       ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1163): error: "I" is not a function or static data member
  > concurrent_vector(I, I, const A& = A())
                      ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1168): error: argument list for class template "tbb::concurrent_vector" is missing
  concurrent_vector(const concurrent_vector<T, A1> &, const A2 &)
  ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1168): warning #945: type qualifier ignored
  concurrent_vector(const concurrent_vector<T, A1> &, const A2 &)
                    ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1168): error: an explicit template argument list is not allowed on this declaration
  concurrent_vector(const concurrent_vector<T, A1> &, const A2 &)
                          ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1168): error: expected a ")"
  concurrent_vector(const concurrent_vector<T, A1> &, const A2 &)
                                                   ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1173): error: argument list for class template "tbb::concurrent_vector" is missing
  > concurrent_vector(std::initializer_list<T>, const A& = A())
    ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1173): error: an explicit template argument list is not allowed on this declaration
  > concurrent_vector(std::initializer_list<T>, const A& = A())
                      ^

In file included from ../inst/include/tbb/enumerable_thread_specific.h(23),
                 from ../inst/include/tbb/combinable.h(20),
                 from ../inst/include/tbb/tbb.h(40),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_vector.h(1173): error: expected a ")"
  > concurrent_vector(std::initializer_list<T>, const A& = A())
                                              ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1224): error: namespace "std" has no member "conditional_t"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
           ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1224): error: expected a ">"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                        ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1224): error: expected a ";"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                                                                                              ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1233): error: argument list for class template "tbb::interface5::concurrent_hash_map" is missing
  concurrent_hash_map(I, I, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1233): error: expected a ")"
  concurrent_hash_map(I, I, Args...)
                       ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1233): error: "I" is not a function or static data member
  concurrent_hash_map(I, I, Args...)
                      ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1239): error: argument list for class template "tbb::interface5::concurrent_hash_map" is missing
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
  ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1239): error: an explicit template argument list is not allowed on this declaration
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
                      ^

In file included from ../inst/include/tbb/tbb.h(41),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_hash_map.h(1239): error: expected a ")"
  concurrent_hash_map(std::initializer_list<std::pair<const Key, T>>, CompareOrAllocator)
                                                                    ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(521): error: namespace "std" has no member "conditional_t"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
           ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(521): error: expected a ">"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                        ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(521): error: expected a ";"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                                                                                              ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(532): error: argument list for class template "tbb::interface5::concurrent_priority_queue" is missing
  > concurrent_priority_queue(InputIterator, InputIterator, Args...)
    ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(532): error: expected a ")"
  > concurrent_priority_queue(InputIterator, InputIterator, Args...)
                                           ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(532): error: "InputIterator" is not a function or static data member
  > concurrent_priority_queue(InputIterator, InputIterator, Args...)
                              ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(536): error: argument list for class template "tbb::interface5::concurrent_priority_queue" is missing
  concurrent_priority_queue(std::initializer_list<T> init_list, CompareOrAllocalor)
  ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(536): error: an explicit template argument list is not allowed on this declaration
  concurrent_priority_queue(std::initializer_list<T> init_list, CompareOrAllocalor)
                            ^

In file included from ../inst/include/tbb/tbb.h(45),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_priority_queue.h(536): error: expected a ")"
  concurrent_priority_queue(std::initializer_list<T> init_list, CompareOrAllocalor)
                                                     ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(182): error: argument list for class template "tbb::strict_ppl::concurrent_queue" is missing
  > concurrent_queue(InputIterator, InputIterator, const A& = A())
    ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(182): error: expected a ")"
  > concurrent_queue(InputIterator, InputIterator, const A& = A())
                                  ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(182): error: "InputIterator" is not a function or static data member
  > concurrent_queue(InputIterator, InputIterator, const A& = A())
                     ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(453): error: argument list for class template "tbb::concurrent_bounded_queue" is missing
  > concurrent_bounded_queue(InputIterator, InputIterator, const A& = A())
    ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(453): error: expected a ")"
  > concurrent_bounded_queue(InputIterator, InputIterator, const A& = A())
                                          ^

In file included from ../inst/include/tbb/tbb.h(46),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_queue.h(453): error: "InputIterator" is not a function or static data member
  > concurrent_bounded_queue(InputIterator, InputIterator, const A& = A())
                             ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(267): error: namespace "std" has no member "conditional_t"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
           ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(267): error: expected a ">"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                        ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(267): error: expected a ";"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                                                                                              ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(278): error: argument list for class template "tbb::interface5::concurrent_unordered_map" is missing
  concurrent_unordered_map (I, I)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(278): error: expected a ")"
  concurrent_unordered_map (I, I)
                             ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(278): error: "I" is not a function or static data member
  concurrent_unordered_map (I, I)
                            ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(283): error: argument list for class template "tbb::interface5::concurrent_unordered_map" is missing
  concurrent_unordered_map(I, I, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(283): error: expected a ")"
  concurrent_unordered_map(I, I, size_t, Args...)
                            ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(283): error: "I" is not a function or static data member
  concurrent_unordered_map(I, I, size_t, Args...)
                           ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(288): error: argument list for class template "tbb::interface5::concurrent_unordered_map" is missing
  concurrent_unordered_map(std::initializer_list<std::pair<const Key, Element>>)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(288): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_map(std::initializer_list<std::pair<const Key, Element>>)
                           ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(293): error: argument list for class template "tbb::interface5::concurrent_unordered_map" is missing
  concurrent_unordered_map(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(293): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_map(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
                           ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(293): error: expected a ")"
  concurrent_unordered_map(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
                                                                               ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(460): error: argument list for class template "tbb::interface5::concurrent_unordered_multimap" is missing
  concurrent_unordered_multimap (I, I)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(460): error: expected a ")"
  concurrent_unordered_multimap (I, I)
                                  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(460): error: "I" is not a function or static data member
  concurrent_unordered_multimap (I, I)
                                 ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(465): error: argument list for class template "tbb::interface5::concurrent_unordered_multimap" is missing
  concurrent_unordered_multimap(I, I, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(465): error: expected a ")"
  concurrent_unordered_multimap(I, I, size_t, Args...)
                                 ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(465): error: "I" is not a function or static data member
  concurrent_unordered_multimap(I, I, size_t, Args...)
                                ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(470): error: argument list for class template "tbb::interface5::concurrent_unordered_multimap" is missing
  concurrent_unordered_multimap(std::initializer_list<std::pair<const Key, Element>>)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(470): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_multimap(std::initializer_list<std::pair<const Key, Element>>)
                                ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(475): error: argument list for class template "tbb::interface5::concurrent_unordered_multimap" is missing
  concurrent_unordered_multimap(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(475): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_multimap(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
                                ^

In file included from ../inst/include/tbb/tbb.h(47),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_map.h(475): error: expected a ")"
  concurrent_unordered_multimap(std::initializer_list<std::pair<const Key, Element>>, size_t, Args...)
                                                                                    ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(220): error: namespace "std" has no member "conditional_t"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
           ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(220): error: expected a ">"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                        ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(220): error: expected a ";"
      std::conditional_t< (sizeof...(Args)>0) && !is_allocator_v< pack_element_t<0, Args...> >,
                                                                                              ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(231): error: argument list for class template "tbb::interface5::concurrent_unordered_set" is missing
  concurrent_unordered_set(I, I)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(231): error: expected a ")"
  concurrent_unordered_set(I, I)
                            ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(231): error: "I" is not a function or static data member
  concurrent_unordered_set(I, I)
                           ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(236): error: argument list for class template "tbb::interface5::concurrent_unordered_set" is missing
  concurrent_unordered_set(I, I, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(236): error: expected a ")"
  concurrent_unordered_set(I, I, size_t, Args...)
                            ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(236): error: "I" is not a function or static data member
  concurrent_unordered_set(I, I, size_t, Args...)
                           ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(241): error: argument list for class template "tbb::interface5::concurrent_unordered_set" is missing
  concurrent_unordered_set(std::initializer_list<T>)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(241): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_set(std::initializer_list<T>)
                           ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(246): error: argument list for class template "tbb::interface5::concurrent_unordered_set" is missing
  concurrent_unordered_set(std::initializer_list<T>, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(246): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_set(std::initializer_list<T>, size_t, Args...)
                           ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(246): error: expected a ")"
  concurrent_unordered_set(std::initializer_list<T>, size_t, Args...)
                                                   ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(416): error: argument list for class template "tbb::interface5::concurrent_unordered_multiset" is missing
  concurrent_unordered_multiset(I, I)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(416): error: expected a ")"
  concurrent_unordered_multiset(I, I)
                                 ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(416): error: "I" is not a function or static data member
  concurrent_unordered_multiset(I, I)
                                ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(421): error: argument list for class template "tbb::interface5::concurrent_unordered_multiset" is missing
  concurrent_unordered_multiset(I, I, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(421): error: expected a ")"
  concurrent_unordered_multiset(I, I, size_t, Args...)
                                 ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(421): error: "I" is not a function or static data member
  concurrent_unordered_multiset(I, I, size_t, Args...)
                                ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(426): error: argument list for class template "tbb::interface5::concurrent_unordered_multiset" is missing
  concurrent_unordered_multiset(std::initializer_list<T>)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(426): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_multiset(std::initializer_list<T>)
                                ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(431): error: argument list for class template "tbb::interface5::concurrent_unordered_multiset" is missing
  concurrent_unordered_multiset(std::initializer_list<T>, size_t, Args...)
  ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(431): error: an explicit template argument list is not allowed on this declaration
  concurrent_unordered_multiset(std::initializer_list<T>, size_t, Args...)
                                ^

In file included from ../inst/include/tbb/tbb.h(48),
                 from ../inst/include/RcppParallel/TBB.h(10),
                 from ../inst/include/RcppParallel.h(21),
                 from options.cpp(2):
../inst/include/tbb/concurrent_unordered_set.h(431): error: expected a ")"
  concurrent_unordered_multiset(std::initializer_list<T>, size_t, Args...)
                                                        ^

compilation aborted for options.cpp (code 2)
make: *** [/apps/R/4.2.2/lib64/R/etc/Makeconf:178: options.o] Error 2
ERROR: compilation failed for package 'RcppParallel'
* removing '/home/554/ta0341/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel'

The downloaded source packages are in
        '/scratch/nm31/ta0341/tmp/RtmpOvYcGT/downloaded_packages'
Warning message:
In install.packages("RcppParallel") :
  installation of package 'RcppParallel' had non-zero exit status
eddelbuettel

eddelbuettel commented on Mar 15, 2023

@eddelbuettel
Member

Could you share some pertinent details about your OS, version, compiler versions etc? In a nutshell, if it is too non-standard it may be hard for anyone to help you.

kevinushey

kevinushey commented on Mar 15, 2023

@kevinushey
Contributor

My only guess is that your version of icpc is too old, or you need to install a newer one. I don't use it, so the amount of help I can provide is pretty low.

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 15, 2023

@theo-allnutt-bioinformatics
Author

Hi,

OS info:
NAME="Rocky Linux"
VERSION="8.7 (Green Obsidian)"
ID="rocky"
ID_LIKE="rhel centos fedora"
VERSION_ID="8.7"
PLATFORM_ID="platform:el8"
PRETTY_NAME="Rocky Linux 8.7 (Green Obsidian)"
ANSI_COLOR="0;32"
LOGO="fedora-logo-icon"
CPE_NAME="cpe:/o:rocky:rocky:8:GA"
HOME_URL="https://rockylinux.org/"
BUG_REPORT_URL="https://bugs.rockylinux.org/"
ROCKY_SUPPORT_PRODUCT="Rocky-Linux-8"
ROCKY_SUPPORT_PRODUCT_VERSION="8.7"
REDHAT_SUPPORT_PRODUCT="Rocky Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="8.7"

I am working on an HPC login node (don't need many resources for script I need to run which uses 'rbiom' of which rcppParallel is a dependency. In turn, rbiom is used by calculate_diversity.R here: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4)

I am not sure which compiler R is using, but I normally have to load this module for R installs to work:
module load intel-compiler/2021.6.0

Thanks.

eddelbuettel

eddelbuettel commented on Mar 16, 2023

@eddelbuettel
Member

R can tell you:

edd@rob:~$ R CMD config CC
ccache gcc
edd@rob:~$ R CMD config CXX
ccache g++
edd@rob:~$ 

That is my system here where ~/.R/Makevars takes over. Otherwise in a clean(er) Docker setup:

root@f14f94c099bd:/#  R CMD config CC
gcc
root@f14f94c099bd:/#  R CMD config CXX
g++ -std=gnu++14
root@f14f94c099bd:/# 

(from today's rocker/r-base with R 4.2.3)

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 16, 2023

@theo-allnutt-bioinformatics
Author

As above - using icc

R CMD config CC
icc

eddelbuettel

eddelbuettel commented on Mar 16, 2023

@eddelbuettel
Member

What does icc --version (or alike, not an icc user myself) say?

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 16, 2023

@theo-allnutt-bioinformatics
Author

As above, the module used is:
icc (ICC) 2021.6.0 20220226
Copyright (C) 1985-2022 Intel Corporation. All rights reserved.

But can also use 2021.8.0

There is no ~/.R on my system so do not know how to change to gcc. If I unload icc I get the first set of errors above.

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 16, 2023

@theo-allnutt-bioinformatics
Author

Thanks. Can't do that on my system as far as I know so I'll just leave it... Happens a lot with R.

eddelbuettel

eddelbuettel commented on Mar 16, 2023

@eddelbuettel
Member

We'll probably close this then as the issue appears to be more related to your specific setup than a general actionable item for all users of RcppParallel. I know this can be frustrating for you but there simply is not much for us here.

theo-allnutt-bioinformatics

theo-allnutt-bioinformatics commented on Mar 16, 2023

@theo-allnutt-bioinformatics
Author

Yes, no problem. Thanks for your help.

eddelbuettel

eddelbuettel commented on Mar 16, 2023

@eddelbuettel
Member

On RHEL/CentOS/Rockly/... one often needs devtoolset to access a recent enough compiler. That is known to work for building current CRAN packages on these OS variants with their somewhat dated default tool stacks.

Switching to yet another compiler is likely tricky. Sorry.

eddelbuettel

eddelbuettel commented on Aug 18, 2023

@eddelbuettel
Member

Closing as duplicate of #184

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions

      installation of package 'RcppParallel' had non-zero exit status · Issue #198 · RcppCore/RcppParallel