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elsherbini/dada2_devtools_install_output.txt

Created July 31, 2016 17:56
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Output from trying to install dada2 on cluster with old gcc
Raw
dada2_devtools_install_output.txt
> library("devtools")
> devtools::install_github("benjjneb/dada2")
Downloading GitHub repo benjjneb/dada2@master
from URL https://api.github.com/repos/benjjneb/dada2/zipball/master
Installing dada2
trying URL 'https://cran.rstudio.com/src/contrib/RcppParallel_4.3.19.tar.gz'
Content type 'application/x-gzip' length 1560737 bytes (1.5 MB)
==================================================
downloaded 1.5 MB
Installing RcppParallel
'/home/josephe/miniconda3/envs/dada2/lib64/R/bin/R' --no-site-file \
--no-environ --no-save --no-restore --quiet CMD INSTALL \
'/tmp/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel' \
--library='/home/josephe/.local/Rpackages' --install-tests
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** libs
mkdir -p ../inst/lib/; \
cd tbb/src; \
if [ -n "" ]; then \
make cpp0x=1 compiler=clang CXXFLAGS=-DTBB_NO_LEGACY=1 tbb_release tbbmalloc_release tbb_build_prefix=lib; \
elif [ -n "gcc -std=gnu99" ]; then \
make cpp0x=1 compiler=gcc CXXFLAGS=-DTBB_NO_LEGACY=1 tbb_release tbbmalloc_release tbb_build_prefix=lib; \
else \
make cpp0x=1 CXXFLAGS=-DTBB_NO_LEGACY=1 tbb_release tbbmalloc_release tbb_build_prefix=lib; \
fi; \
cd ../..; \
cp tbb/build/lib_release/libtbb*.* ../inst/lib/
make[1]: Entering directory `/tmp/RtmphrHw4w/devtoolsbf35792c369f/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/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel/src/tbb/build/lib_release'
../../build/Makefile.tbb:31: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc4.4.7_libc2.12_kernel2.6.32
g++ -o concurrent_hash_map.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_hash_map.cpp
g++ -o concurrent_queue.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_queue.cpp
g++ -o concurrent_vector.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_vector.cpp
g++ -o dynamic_link.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/dynamic_link.cpp
g++ -o itt_notify.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/itt_notify.cpp
g++ -o cache_aligned_allocator.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/cache_aligned_allocator.cpp
g++ -o pipeline.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/pipeline.cpp
g++ -o queuing_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/queuing_mutex.cpp
g++ -o queuing_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/queuing_rw_mutex.cpp
g++ -o reader_writer_lock.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/reader_writer_lock.cpp
g++ -o spin_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/spin_rw_mutex.cpp
g++ -o x86_rtm_rw_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/x86_rtm_rw_mutex.cpp
g++ -o spin_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/spin_mutex.cpp
g++ -o critical_section.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/critical_section.cpp
g++ -o mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/mutex.cpp
g++ -o recursive_mutex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/recursive_mutex.cpp
g++ -o condition_variable.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/condition_variable.cpp
g++ -o tbb_thread.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_thread.cpp
g++ -o concurrent_monitor.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/concurrent_monitor.cpp
g++ -o semaphore.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/semaphore.cpp
g++ -o private_server.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/private_server.cpp
g++ -o rml_tbb.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/rml/client/rml_tbb.cpp
sh ../../build/version_info_linux.sh g++ -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include -I. >version_string.ver
g++ -o tbb_misc.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include -I. ../../src/tbb/tbb_misc.cpp
g++ -o tbb_misc_ex.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_misc_ex.cpp
g++ -o task.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/task.cpp
g++ -o task_group_context.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/task_group_context.cpp
g++ -o governor.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/governor.cpp
g++ -o market.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/market.cpp
g++ -o arena.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/arena.cpp
g++ -o scheduler.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/scheduler.cpp
g++ -o observer_proxy.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/observer_proxy.cpp
g++ -o tbb_statistics.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_statistics.cpp
g++ -o tbb_main.o -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -std=c++0x -D_TBB_CPP0X -I../../src -I../../src/rml/include -I../../include ../../src/tbb/tbb_main.cpp
sh ../../build/generate_tbbvars.sh
echo "INPUT (libtbb.so.2)" > libtbb.so
g++ -E -x c++ ../../src/tbb/lin64-tbb-export.def -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -fPIC -D__TBB_BUILD=1 -Wall -Wno-parentheses -Wno-non-virtual-dtor -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include > tbb.def
g++ -fPIC -o libtbb.so.2 concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o spin_rw_mutex.o x86_rtm_rw_mutex.o spin_mutex.o critical_section.o mutex.o recursive_mutex.o condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o tbb_misc.o tbb_misc_ex.o task.o task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o tbb_main.o -ldl -lpthread -lrt -shared -Wl,-soname=libtbb.so.2 -m64 -Wl,--version-script,tbb.def
make[2]: Leaving directory `/tmp/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel/src/tbb/build/lib_release'
make -C "../build/lib_release" -r -f ../../build/Makefile.tbbmalloc cfg=release malloc
make[2]: Entering directory `/tmp/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel/src/tbb/build/lib_release'
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/backend.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/large_objects.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/backref.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/tbbmalloc.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -o itt_notify_malloc.o -I../../src -I../../src/rml/include -I../../include ../../src/tbb/itt_notify.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -Wno-parentheses -Wno-non-virtual-dtor -fPIC -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc -I. ../../src/tbbmalloc/frontend.cpp
echo "INPUT (libtbbmalloc.so.2)" > libtbbmalloc.so
g++ -E -x c++ ../../src/tbbmalloc/lin64-tbbmalloc-export.def -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -DTBB_NO_LEGACY=1 -fno-rtti -fno-exceptions -D__TBBMALLOC_BUILD=1 -I../../src -I../../src/rml/include -I../../include > tbbmalloc.def
gcc -fPIC -o libtbbmalloc.so.2 backend.o large_objects.o backref.o tbbmalloc.o itt_notify_malloc.o frontend.o -ldl -lpthread -lrt -shared -Wl,-soname=libtbbmalloc.so.2 -m64 -Wl,--version-script,tbbmalloc.def
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -Wall -DTBB_NO_LEGACY=1 -fPIC -D__TBBMALLOC_BUILD=1 -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/proxy.cpp
g++ -c -MMD -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -Wall -DTBB_NO_LEGACY=1 -fPIC -D__TBBMALLOC_BUILD=1 -I../../src -I../../src/rml/include -I../../include -I../../src/tbbmalloc -I../../src/tbbmalloc ../../src/tbbmalloc/tbb_function_replacement.cpp
echo "INPUT (libtbbmalloc_proxy.so.2)" > libtbbmalloc_proxy.so
g++ -E -x c++ ../../src/tbbmalloc/lin64-proxy-export.def -DDO_ITT_NOTIFY -g -O2 -DUSE_PTHREAD -m64 -Wall -DTBB_NO_LEGACY=1 -I../../src -I../../src/rml/include -I../../include > tbbmallocproxy.def
g++ -fPIC -o libtbbmalloc_proxy.so.2 proxy.o tbb_function_replacement.o -ldl -lpthread -lrt libtbbmalloc.so -shared -Wl,-soname=libtbbmalloc_proxy.so.2 -m64 -Wl,--version-script,tbbmallocproxy.def
make[2]: Leaving directory `/tmp/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel/src/tbb/build/lib_release'
make[1]: Leaving directory `/tmp/RtmphrHw4w/devtoolsbf35792c369f/RcppParallel/src/tbb/src'
g++ -I/home/josephe/miniconda3/envs/dada2/lib/R/include -DNDEBUG -std=c++11 -I../inst/include/ -DRCPP_PARALLEL_USE_TBB=1 -I/home/josephe/miniconda3/envs/dada2/include -I"/home/josephe/.local/Rpackages/BH/include" -fpic -I/home/josephe/miniconda3/envs/dada2/include -c options.cpp -o options.o
cc1plus: error: unrecognized command line option "-std=c++11"
make: *** [options.o] Error 1
ERROR: compilation failed for package ‘RcppParallel’
* removing ‘/home/josephe/.local/Rpackages/RcppParallel’
Error: Command failed (1)
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