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Build package with compilers without OpenMP support #61

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MarcusKlik opened this issue May 13, 2017 · 8 comments
Closed

Build package with compilers without OpenMP support #61

MarcusKlik opened this issue May 13, 2017 · 8 comments
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@MarcusKlik
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bug
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Fst package v0.8.0

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@MarcusKlik
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MarcusKlik commented May 13, 2017 •
edited

Currently, fst can't be build on OSX systems that don't have manually installed OpenMP (for example using these instructions). Without OpenMP support, fst should still be able to built and use single-threaded mode only. The same issue applies to the data.table package (see Rdatatable/data.table#2161).
@MarcusKlik MarcusKlik self-assigned this May 13, 2017
@MarcusKlik MarcusKlik added the bug label May 13, 2017
@MarcusKlik MarcusKlik added this to the Format complete milestone May 13, 2017
@MarcusKlik
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MarcusKlik commented Jul 1, 2017 •
edited

This issue seems to be fixed for package xgboost as documented here. They use a configure script to detect OSX and set the OpenMP flags accordingly.

@MarcusKlik
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CRAN OS X binaries are now build using OpenMP, so that should solve the OpenMP problem for most Mac users. The same applies to the data.table package, which uses OpenMP for it's fwrite method for example. Some Mac users have reported problems with data.table's October release, so I will keep track of any developments there..

@robocop-bob
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Hi Mark ,

Package "fst" starting on my mac with single core support. OpenMP is installed and declared .
Package data.table compilation with OpenMP ends with success and data.table working with 8 cores data.table::getDTthreads() 8

Can you help ?

sessionInfo()

Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.3/lib/libopenblasp-r0.3.3.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] fst_0.8.8
loaded via a namespace (and not attached):
[1] compiler_3.5.1 parallel_3.5.1 tools_3.5.1    yaml_2.2.0     Rcpp_1.0.0.1

~/.R/.Makevar
LLVM_LOC = /usr/local/opt/llvm
#CC=$(LLVM_LOC)/bin/clang
#CXX=$(LLVM_LOC)/bin/clang++
CC=$(LLVM_LOC)/bin/clang -fopenmp
CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
MAKEFLAGS = -j8

Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/fst_0.8.8.tar.gz'
Content type 'application/x-gzip' length 622658 bytes (608 KB)
==================================================
downloaded 608 KB

* installing *source* package ‘fst’ ...
** package ‘fst’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c flex_store.cpp -o flex_store.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c flex_store_v1.cpp -o flex_store_v1.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fst_blockrunner_char.cpp -o fst_blockrunner_char.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fst_compress.cpp -o fst_compress.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fst_error.cpp -o fst_error.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fst_table.cpp -o fst_table.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c openmp.cpp -o openmp.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/LZ4/lz4.c -o fstcore/LZ4/lz4.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/LZ4/xxhash.c -o fstcore/LZ4/xxhash.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/entropy_common.c -o fstcore/ZSTD/common/entropy_common.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/error_private.c -o fstcore/ZSTD/common/error_private.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/fse_decompress.c -o fstcore/ZSTD/common/fse_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/fse_compress.c -o fstcore/ZSTD/compress/fse_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/decompress/huf_decompress.c -o fstcore/ZSTD/decompress/huf_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/huf_compress.c -o fstcore/ZSTD/compress/huf_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/decompress/zstd_decompress.c -o fstcore/ZSTD/decompress/zstd_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/zstd_common.c -o fstcore/ZSTD/common/zstd_common.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_compress.c -o fstcore/ZSTD/compress/zstd_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/cover.c -o fstcore/ZSTD/dictBuilder/cover.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/divsufsort.c -o fstcore/ZSTD/dictBuilder/divsufsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_fast.c -o fstcore/ZSTD/compress/zstd_fast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_lazy.c -o fstcore/ZSTD/compress/zstd_lazy.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_ldm.c -o fstcore/ZSTD/compress/zstd_ldm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/pool.c -o fstcore/ZSTD/common/pool.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_opt.c -o fstcore/ZSTD/compress/zstd_opt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/zdict.c -o fstcore/ZSTD/dictBuilder/zdict.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_double_fast.c -o fstcore/ZSTD/compress/zstd_double_fast.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/compression/compression.cpp -o fstcore/compression/compression.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/compression/compressor.cpp -o fstcore/compression/compressor.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/interface/openmphelper.cpp -o fstcore/interface/openmphelper.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/interface/fststore.cpp -o fstcore/interface/fststore.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/logical/logical_v4.cpp -o fstcore_v1/logical/logical_v4.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/logical/logical_v10.cpp -o fstcore/logical/logical_v10.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/integer/integer_v2.cpp -o fstcore_v1/integer/integer_v2.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/integer/integer_v8.cpp -o fstcore/integer/integer_v8.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/byte/byte_v12.cpp -o fstcore/byte/byte_v12.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/double/double_v3.cpp -o fstcore_v1/double/double_v3.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/double/double_v9.cpp -o fstcore/double/double_v9.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/character/character_v1.cpp -o fstcore_v1/character/character_v1.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/character/character_v6.cpp -o fstcore/character/character_v6.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/factor/factor_v5.cpp -o fstcore_v1/factor/factor_v5.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/factor/factor_v7.cpp -o fstcore/factor/factor_v7.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/blockstreamer/blockstreamer_v2.cpp -o fstcore/blockstreamer/blockstreamer_v2.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore_v1/blockstreamer/blockstreamer_v1.cpp -o fstcore_v1/blockstreamer/blockstreamer_v1.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC  -g -O2 -c fstcore/integer64/integer64_v11.cpp -o fstcore/integer64/integer64_v11.o
ar rcs libLZ4.a fstcore/LZ4/lz4.o fstcore/LZ4/xxhash.o
ar rcs libZSTD.a fstcore/ZSTD/common/entropy_common.o fstcore/ZSTD/common/error_private.o fstcore/ZSTD/common/fse_decompress.o fstcore/ZSTD/compress/fse_compress.o fstcore/ZSTD/decompress/huf_decompress.o fstcore/ZSTD/compress/huf_compress.o fstcore/ZSTD/decompress/zstd_decompress.o fstcore/ZSTD/common/zstd_common.o fstcore/ZSTD/compress/zstd_compress.o fstcore/ZSTD/dictBuilder/cover.o fstcore/ZSTD/dictBuilder/divsufsort.o fstcore/ZSTD/compress/zstd_fast.o fstcore/ZSTD/compress/zstd_lazy.o fstcore/ZSTD/compress/zstd_ldm.o fstcore/ZSTD/common/pool.o fstcore/ZSTD/compress/zstd_opt.o fstcore/ZSTD/dictBuilder/zdict.o fstcore/ZSTD/compress/zstd_double_fast.o
ar rcs libCOMPRESSION.a fstcore/compression/compression.o fstcore/compression/compressor.o
ar rcs libFRAME.a fstcore/interface/openmphelper.o fstcore/interface/fststore.o fstcore_v1/logical/logical_v4.o fstcore/logical/logical_v10.o fstcore_v1/integer/integer_v2.o fstcore/integer/integer_v8.o fstcore/byte/byte_v12.o fstcore_v1/double/double_v3.o fstcore/double/double_v9.o fstcore_v1/character/character_v1.o fstcore/character/character_v6.o fstcore_v1/factor/factor_v5.o fstcore/factor/factor_v7.o fstcore/blockstreamer/blockstreamer_v2.o fstcore_v1/blockstreamer/blockstreamer_v1.o fstcore/integer64/integer64_v11.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.5.1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o fst.so RcppExports.o flex_store.o flex_store_v1.o fst_blockrunner_char.o fst_compress.o fst_error.o fst_table.o init.o openmp.o -L. -lFRAME -lCOMPRESSION -lLZ4 -lZSTD -L/usr/local/Cellar/r/3.5.1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.5/site-library/fst/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fst)

The downloaded source packages are in
	‘/private/var/folders/wp/mvnk6n2j1hvg7y9_ws6356wh0000gn/T/Rtmp9B9aK9/downloaded_packages’
> library(fst)
fst package v0.8.8
(OpenMP was not detected, using single threaded mode)

@MarcusKlik
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MarcusKlik commented Nov 22, 2018 •
edited

Hi @robbig2871, thanks for posting your question.

From your build output I can see that the .c files (the bundled LZ4 and ZSTD compressors) are compiled with the new llvm compiler, but the .cpp files (the fstlib C++ library) are still using the default compiler.

I think you can fix that by adding the following line to your ~/.R/.Makevars:

CXX11 = $(LLVM_LOC)/bin/clang++ -fopenmp

you could also change the CPPFLAGS line into:

CPPFLAGS = -I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -g -O3 -Wall -pedantic

that should trigger the new clang++ compiler and add the -openmp and -g -O3 -Wall -pedantic options.

By the way, with the Travis continuous integration build for fst, I recently fixed OpenMP problems by installing llvm and setting some globals (see also the .travis.yml file):

brew install llvm
export PATH="/usr/local/opt/llvm/bin:$PATH"
export LDFLAGS="-L/usr/local/opt/llvm/lib"
export CPPFLAGS="-I/usr/local/opt/llvm/include"
export PKG_CXXFLAGS="-O3 -Wall -pedantic"

(and there is no ~/.R/.Makevars file). On the Travis machine, these settings are enough for fst to build with OpenMP enabled.

I would be interested to see if one of these options will work for your setup, please let me know!

@robocop-bob
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robocop-bob commented Nov 25, 2018 •
edited

Hi @MarcusKlik .

Regarding Makevar - after changes and reinstallation fst see 8 threads !
Thank you for you help.

Regarding travis ... R from cmd line ... some issue found.

export PATH="/usr/local/opt/llvm/bin:$PATH"
export LDFLAGS="-L/usr/local/opt/llvm/lib"
export CPPFLAGS="-I/usr/local/opt/llvm/include"
export PKG_CXXFLAGS="-O3 -Wall -pedantic"

$ R

R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("fst")
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.usthb.dz/src/contrib/fst_0.8.8.tar.gz'
Content type 'application/x-gzip' length 622658 bytes (608 KB)
==================================================
downloaded 608 KB

* installing *source* package ‘fst’ ...
** package ‘fst’ successfully unpacked and MD5 sums checked
** libs
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c flex_store.cpp -o flex_store.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c flex_store_v1.cpp -o flex_store_v1.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fst_blockrunner_char.cpp -o fst_blockrunner_char.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fst_compress.cpp -o fst_compress.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fst_error.cpp -o fst_error.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fst_table.cpp -o fst_table.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c openmp.cpp -o openmp.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/LZ4/lz4.c -o fstcore/LZ4/lz4.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/LZ4/xxhash.c -o fstcore/LZ4/xxhash.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/entropy_common.c -o fstcore/ZSTD/common/entropy_common.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/error_private.c -o fstcore/ZSTD/common/error_private.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/fse_decompress.c -o fstcore/ZSTD/common/fse_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/fse_compress.c -o fstcore/ZSTD/compress/fse_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/decompress/huf_decompress.c -o fstcore/ZSTD/decompress/huf_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/huf_compress.c -o fstcore/ZSTD/compress/huf_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/decompress/zstd_decompress.c -o fstcore/ZSTD/decompress/zstd_decompress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/zstd_common.c -o fstcore/ZSTD/common/zstd_common.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_compress.c -o fstcore/ZSTD/compress/zstd_compress.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/cover.c -o fstcore/ZSTD/dictBuilder/cover.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/divsufsort.c -o fstcore/ZSTD/dictBuilder/divsufsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_fast.c -o fstcore/ZSTD/compress/zstd_fast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_lazy.c -o fstcore/ZSTD/compress/zstd_lazy.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_ldm.c -o fstcore/ZSTD/compress/zstd_ldm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/common/pool.c -o fstcore/ZSTD/common/pool.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_opt.c -o fstcore/ZSTD/compress/zstd_opt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/dictBuilder/zdict.c -o fstcore/ZSTD/dictBuilder/zdict.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fstcore/ZSTD/compress/zstd_double_fast.c -o fstcore/ZSTD/compress/zstd_double_fast.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/compression/compression.cpp -o fstcore/compression/compression.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/compression/compressor.cpp -o fstcore/compression/compressor.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/interface/openmphelper.cpp -o fstcore/interface/openmphelper.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/interface/fststore.cpp -o fstcore/interface/fststore.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/logical/logical_v4.cpp -o fstcore_v1/logical/logical_v4.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/logical/logical_v10.cpp -o fstcore/logical/logical_v10.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/integer/integer_v2.cpp -o fstcore_v1/integer/integer_v2.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/integer/integer_v8.cpp -o fstcore/integer/integer_v8.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/byte/byte_v12.cpp -o fstcore/byte/byte_v12.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/double/double_v3.cpp -o fstcore_v1/double/double_v3.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/double/double_v9.cpp -o fstcore/double/double_v9.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/character/character_v1.cpp -o fstcore_v1/character/character_v1.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/character/character_v6.cpp -o fstcore/character/character_v6.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/factor/factor_v5.cpp -o fstcore_v1/factor/factor_v5.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/factor/factor_v7.cpp -o fstcore/factor/factor_v7.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/blockstreamer/blockstreamer_v2.cpp -o fstcore/blockstreamer/blockstreamer_v2.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore_v1/blockstreamer/blockstreamer_v1.cpp -o fstcore_v1/blockstreamer/blockstreamer_v1.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG  -I. -Ifstcore -Ifstcore_v1 -Ifstcore/LZ4 -Ifstcore/ZSTD -Ifstcore/ZSTD/common -Ifstcore/ZSTD/decompress -Ifstcore/ZSTD/compress -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -g -O3 -Wall -pedantic  -O3 -Wall -pedantic -fPIC  -g -O2 -c fstcore/integer64/integer64_v11.cpp -o fstcore/integer64/integer64_v11.o
ar rcs libLZ4.a fstcore/LZ4/lz4.o fstcore/LZ4/xxhash.o
ar rcs libZSTD.a fstcore/ZSTD/common/entropy_common.o fstcore/ZSTD/common/error_private.o fstcore/ZSTD/common/fse_decompress.o fstcore/ZSTD/compress/fse_compress.o fstcore/ZSTD/decompress/huf_decompress.o fstcore/ZSTD/compress/huf_compress.o fstcore/ZSTD/decompress/zstd_decompress.o fstcore/ZSTD/common/zstd_common.o fstcore/ZSTD/compress/zstd_compress.o fstcore/ZSTD/dictBuilder/cover.o fstcore/ZSTD/dictBuilder/divsufsort.o fstcore/ZSTD/compress/zstd_fast.o fstcore/ZSTD/compress/zstd_lazy.o fstcore/ZSTD/compress/zstd_ldm.o fstcore/ZSTD/common/pool.o fstcore/ZSTD/compress/zstd_opt.o fstcore/ZSTD/dictBuilder/zdict.o fstcore/ZSTD/compress/zstd_double_fast.o
ar rcs libCOMPRESSION.a fstcore/compression/compression.o fstcore/compression/compressor.o
ar rcs libFRAME.a fstcore/interface/openmphelper.o fstcore/interface/fststore.o fstcore_v1/logical/logical_v4.o fstcore/logical/logical_v10.o fstcore_v1/integer/integer_v2.o fstcore/integer/integer_v8.o fstcore/byte/byte_v12.o fstcore_v1/double/double_v3.o fstcore/double/double_v9.o fstcore_v1/character/character_v1.o fstcore/character/character_v6.o fstcore_v1/factor/factor_v5.o fstcore/factor/factor_v7.o fstcore/blockstreamer/blockstreamer_v2.o fstcore_v1/blockstreamer/blockstreamer_v1.o fstcore/integer64/integer64_v11.o
/usr/local/opt/llvm/bin/clang++ -fopenmp -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.5.1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o fst.so RcppExports.o flex_store.o flex_store_v1.o fst_blockrunner_char.o fst_compress.o fst_error.o fst_table.o init.o openmp.o -L. -lFRAME -lCOMPRESSION -lLZ4 -lZSTD -L/usr/local/Cellar/r/3.5.1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring file ./libCOMPRESSION.a, file was built for archive which is not the architecture being linked (x86_64): ./libCOMPRESSION.ald: warning: ld: warning: ignoring file ./libZSTD.a, file was built for archive which is not the architecture being linked (x86_64): ./libZSTD.ald: warning: ignoring file ./libLZ4.a, file was built for archive which is not the architecture being linked (x86_64): ./libLZ4.a


ignoring file ./libFRAME.a, file was built for archive which is not the architecture being linked (x86_64): ./libFRAME.a
installing to /usr/local/lib/R/3.5/site-library/fst/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘fst’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/3.5/site-library/fst/libs/fst.so':
  dlopen(/usr/local/lib/R/3.5/site-library/fst/libs/fst.so, 6): Symbol not found: _XXH32
  Referenced from: /usr/local/lib/R/3.5/site-library/fst/libs/fst.so
  Expected in: flat namespace
 in /usr/local/lib/R/3.5/site-library/fst/libs/fst.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/3.5/site-library/fst’
* restoring previous ‘/usr/local/lib/R/3.5/site-library/fst’

The downloaded source packages are in
	‘/private/var/folders/wp/mvnk6n2j1hvg7y9_ws6356wh0000gn/T/RtmpDWAYeF/downloaded_packages’
Warning message:
In install.packages("fst") :
  installation of package ‘fst’ had non-zero exit status

@fstpackage
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Hi @robbig2871, thanks for testing both options!

The method used on Travis appears to result in some linker problems, I will have to take a closer look to see what's going on. But it's good to hear that the updated Makevars does the trick!

@brendanf brendanf mentioned this issue Dec 2, 2019
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@domq
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domq commented Oct 21, 2020

Still happening today (latest R, no OpenMP installed)

Error: package or namespace load failed for ‘fst’ in dyn.load(file, DLLpath = DLLpath, ...):
 impossible de charger l'objet partagé '/usr/local/Cellar/r/4.0.3/lib/R/library/00LOCK-fst/00new/fst/libs/fst.so':
  dlopen(/usr/local/Cellar/r/4.0.3/lib/R/library/00LOCK-fst/00new/fst/libs/fst.so, 6): Symbol not found: _XXH32
  Referenced from: /usr/local/Cellar/r/4.0.3/lib/R/library/00LOCK-fst/00new/fst/libs/fst.so
  Expected in: flat namespace
 in /usr/local/Cellar/r/4.0.3/lib/R/library/00LOCK-fst/00new/fst/libs/fst.so
Erreur : le chargement a échoué
Exécution arrêtée
ERROR: loading failed
* removing ‘/usr/local/Cellar/r/4.0.3/lib/R/library/fst’

Les packages source téléchargés sont dans
	‘/private/var/folders/g3/0p9ww9716jj42dj45gn7bxnc0000gp/T/RtmpCVTxjJ/downloaded_packages’
mise à jour de la liste HTML des packages dans '.Library'
Making 'packages.html' ... Terminé.
Warning message:
In install.packages("fst") :
  l'installation du package ‘fst’ a eu un statut de sortie non nul

(If you'll pardon my French — Mac OS X is weird, at least R doesn't seem to care about environment variables when setting locale)

@MarcusKlik
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Hi, @domq, thanks for your question, fst does not use a configure script to detect the missing OpenMP libraries. If you want, you can install llvm using homebrew and then use the flags as described here to get things working?

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