Tried to upgrade to version 0.19.1, but got the message below. <stro

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Oh I see. Thanks <a class="user-mention notranslate" data-hovercard-type="user" data-h

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Update: qs install successful after reinstall of <cod

install.packages() error in RHEL,about traversc/qs

Comments (9)

traversc commented on May 30, 2024 1

It sounds like an issue with compiler version. g++ -std=c++0x Should probably be g++ -std=c++11.

Create a file ~/.R/Makevars and put in

CXXFLAGS = -O3  -std=c++11
CXX11FLAGS = -O3  -std=c++11

See if that helps. If not, you may have to update the compiler compiler which can be a bit tricky, do you have someone managing the system who can help?

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dipterix commented on May 30, 2024

I have similar problem. Trying to test my package on r-hub and got preperror. Here's original report.
https://builder.r-hub.io/status/original/dipsaus_0.0.2.tar.gz-2a07cfa0f31244dbbb9cf3bda0b0fb32

installation of package ‘qs’ had non-zero exit status

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traversc commented on May 30, 2024

Hi @dipterix, that is a bug with rhub. They are using outdated alt-rep header files on some of their platforms.

The error you receive in the rhub status log is:

/usr/local/lib/R/include/R_ext/Altrep.h:35:31: error: expected primary-expression before ‘class’
 R_new_altrep(R_altrep_class_t class, SEXP data1, SEXP data2);
...

But if you look in the R source code, you can see it doesn't match the latest R version:

SEXP
R_new_altrep(R_altrep_class_t aclass, SEXP data1, SEXP data2);

https://github.com/wch/r-source/blob/trunk/src/include/R_ext/Altrep.h#L38-L39

(The underlying issue was the "class" variable name which is a restricted keyword in C++; this was fixed in R 3.6. For earlier versions, I use pre-processor macros to fix the issue)

I filed an issue here:

r-hub/rhub#289

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dipterix commented on May 30, 2024

Oh I see. Thanks @traversc

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leungi commented on May 30, 2024

Thanks for the explanation and detailed answer @traversc 🙇‍♂️!

It really helps for someone like me, who has minimal Linux/C knowledge, and managing DIY-style.

Followed your guide and got it installed on one of the machines; hope it'll be successful as well on another machine coming later today 🤞.

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c qs_functions.cpp -o qs_functions.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/debug.c -o ZSTD/common/debug.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/entropy_common.c -o ZSTD/common/entropy_common.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/error_private.c -o ZSTD/common/error_private.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/fse_decompress.c -o ZSTD/common/fse_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/pool.c -o ZSTD/common/pool.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/threading.c -o ZSTD/common/threading.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/xxhash.c -o ZSTD/common/xxhash.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/zstd_common.c -o ZSTD/common/zstd_common.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/fse_compress.c -o ZSTD/compress/fse_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/hist.c -o ZSTD/compress/hist.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/huf_compress.c -o ZSTD/compress/huf_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_compress.c -o ZSTD/compress/zstd_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_double_fast.c -o ZSTD/compress/zstd_double_fast.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_fast.c -o ZSTD/compress/zstd_fast.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_lazy.c -o ZSTD/compress/zstd_lazy.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_ldm.c -o ZSTD/compress/zstd_ldm.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstdmt_compress.c -o ZSTD/compress/zstdmt_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_opt.c -o ZSTD/compress/zstd_opt.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/huf_decompress.c -o ZSTD/decompress/huf_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_ddict.c -o ZSTD/decompress/zstd_ddict.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_decompress_block.c -o ZSTD/decompress/zstd_decompress_block.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_decompress.c -o ZSTD/decompress/zstd_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/cover.c -o ZSTD/dictBuilder/cover.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/divsufsort.c -o ZSTD/dictBuilder/divsufsort.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/fastcover.c -o ZSTD/dictBuilder/fastcover.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/zdict.c -o ZSTD/dictBuilder/zdict.o
ar rcs libQSZSTD.a ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c LZ4/lz4.c -o LZ4/lz4.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
ar rcs libQSLZ4.a LZ4/lz4.o LZ4/lz4hc.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o qs.so RcppExports.o qs_functions.o -lpthread -L. -lQSZSTD -lQSLZ4 -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/00LOCK-qs/00new/qs/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package âqsâ
    finding HTML links ... done
    blosc_shuffle_raw                       html
    blosc_unshuffle_raw                     html
    convertToAlt                            html
    is_big_endian                           html
    lz4_compress_bound                      html
    lz4_compress_raw                        html
    lz4_decompress_raw                      html
    qdeserialize                            html
    qdump                                   html
    qread                                   html
    qread_fd                                html
    qread_handle                            html
    qread_ptr                               html
    qsave                                   html
    qsave_fd                                html
    qsave_handle                            html
    qserialize                              html
    randomStrings                           html
    starnames                               html
    zstd_compress_bound                     html
    zstd_compress_raw                       html
    zstd_decompress_raw                     html
** 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 (qs)
Making 'packages.html' ... done

The downloaded source packages are in
        â/tmp/RtmpVbpvaq/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

from qs.

leungi commented on May 30, 2024

@traversc: apologies to have to reopen this.

I tried the same trick with ~/.R/Makevars but faced the same issue on new machine.

I inspected the console message from the previous successful install, and tried various options for Makevars, but still no go.

Hope you may provide more guidance 🙇‍♂️

Trial 1

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (file.exists(M)) file.remove(M)
if (!file.exists(M)) file.create(M)
cat("\nCXX = g++",
"CXXFLAGS=-O3 -std=c++11",
"CXX11FLAGS =-O3 -std=c++11",
    file = M, sep = "\n", append = TRUE)

Trial 2

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (file.exists(M)) file.remove(M)
if (!file.exists(M)) file.create(M)
cat("\nCXX = g++",
"CXXFLAGS=-O3 -std=c++11 -fPIC",
"CXX11FLAGS =-O3 -std=c++11 -fPIC",
    file = M, sep = "\n", append = TRUE)

Trial 3

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (file.exists(M)) file.remove(M)
if (!file.exists(M)) file.create(M)
cat("\nCXX = g++",
"CXXFLAGS=-O2 -std=c++11 -fPIC",
"CXX11FLAGS =-O2 -std=c++11 -fPIC",
    file = M, sep = "\n", append = TRUE)

Trial 4

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (file.exists(M)) file.remove(M)
if (!file.exists(M)) file.create(M)
cat("\nCXX = g++",
"CXXFLAGS=-O3 -std=c++11",
"CXX11FLAGS =-O3 -std=c++11",
"CC = cc",
"CFLAGS = -std=gnu99",
    file = M, sep = "\n", append = TRUE)

Compiler info

[leungi@ohylpyt1-d ~]$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/local/gcc493/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.3/configure --prefix=/usr/local/gcc493 --program-suffix=49 --enable-languages=c,c++ --disable-libstdcxx-pch --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)

[leungi@ohylpyt1-d ~]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc493/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.3/configure --prefix=/usr/local/gcc493 --program-suffix=49 --enable-languages=c,c++ --disable-libstdcxx-pch --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)

from qs.

traversc commented on May 30, 2024

Could you post the error log when you install? Unsure what the issue could be. What is different about the machine?

from qs.

leungi commented on May 30, 2024

Thanks for prompt response!

The only difference I see is the gcc and g++ minor version.

System Info

[leungi@ohylpyt1-d ~]$ uname -a
Linux ohylpyt1-d 3.10.0-514.6.1.el7.x86_64 #1 SMP Sat Dec 10 11:15:38 EST 2016 x86_64 x86_64 x86_64 GNU/Linux

Trial 1

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -c qs_functions.cpp -o qs_functions.o
In file included from qs_functions.cpp:21:0:
qs_common.h: In member function âint fd_wrapper::ferror()â:
qs_common.h:457:40: error: âerrnoâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                        ^
qs_common.h:457:49: error: âEBADFâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                                 ^
qs_common.h: In function âuint32_t validate_data(const QsMetadata&, stream_reader&, uint32_t, uint32_t, uint64_t, bool)â:
qs_common.h:1157:34: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                  ^
qs_common.h:1157:72: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                                                        ^
qs_common.h: In member function âuint64_t zstd_decompress_env::decompress(void*, size_t, const void*, size_t)â:
qs_common.h:1528:124: error: âto_stringâ is not a member of âstdâ
     if(return_value > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize " + std::to_string(return_value));
                                                                                                                            ^
qs_common.h: In member function âuint64_t lz4_decompress_env::decompress(char*, int, const char*, int)â:
qs_common.h:1545:146: error: âto_stringâ is not a member of âstdâ
     if(static_cast<uint64_t>(return_value) > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize" + std::to_string(return_value));
                                                                                                                                                  ^
qs_functions.cpp: In function âRcpp::RObject c_qdump(const string&)â:
qs_functions.cpp:492:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:493:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:496:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:504:33: error: âto_stringâ is not a member of âstdâ
       outvec["computed_hash"] = std::to_string(computed_hash);
                                 ^
qs_functions.cpp:514:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:515:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:516:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(computed_hash);
                               ^
qs_functions.cpp:519:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:558:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:559:34: error: âto_stringâ is not a member of âstdâ
     outvec["number_of_blocks"] = std::to_string(totalsize);
                                  ^
qs_functions.cpp:562:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(xenv.digest());
                               ^
qs_functions.cpp:565:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp: In function âstd::string xxhash_raw(SEXP)â:
qs_functions.cpp:714:10: error: âto_stringâ is not a member of âstdâ
   return std::to_string(xenv.digest());
          ^
make: *** [qs_functions.o] Error 1
ERROR: compilation failed for package âqsâ
* removing â/usr/lib64/R/library/qsâ
* restoring previous â/usr/lib64/R/library/qsâ

The downloaded source packages are in
        â/tmp/RtmpL0cL3G/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("qs") :
  installation of package âqsâ had non-zero exit status

Trial 2

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -fPIC -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -fPIC -c qs_functions.cpp -o qs_functions.o
In file included from qs_functions.cpp:21:0:
qs_common.h: In member function âint fd_wrapper::ferror()â:
qs_common.h:457:40: error: âerrnoâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                        ^
qs_common.h:457:49: error: âEBADFâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                                 ^
qs_common.h: In function âuint32_t validate_data(const QsMetadata&, stream_reader&, uint32_t, uint32_t, uint64_t, bool)â:
qs_common.h:1157:34: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                  ^
qs_common.h:1157:72: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                                                        ^
qs_common.h: In member function âuint64_t zstd_decompress_env::decompress(void*, size_t, const void*, size_t)â:
qs_common.h:1528:124: error: âto_stringâ is not a member of âstdâ
     if(return_value > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize " + std::to_string(return_value));
                                                                                                                            ^
qs_common.h: In member function âuint64_t lz4_decompress_env::decompress(char*, int, const char*, int)â:
qs_common.h:1545:146: error: âto_stringâ is not a member of âstdâ
     if(static_cast<uint64_t>(return_value) > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize" + std::to_string(return_value));
                                                                                                                                                  ^
qs_functions.cpp: In function âRcpp::RObject c_qdump(const string&)â:
qs_functions.cpp:492:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:493:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:496:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:504:33: error: âto_stringâ is not a member of âstdâ
       outvec["computed_hash"] = std::to_string(computed_hash);
                                 ^
qs_functions.cpp:514:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:515:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:516:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(computed_hash);
                               ^
qs_functions.cpp:519:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:558:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:559:34: error: âto_stringâ is not a member of âstdâ
     outvec["number_of_blocks"] = std::to_string(totalsize);
                                  ^
qs_functions.cpp:562:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(xenv.digest());
                               ^
qs_functions.cpp:565:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp: In function âstd::string xxhash_raw(SEXP)â:
qs_functions.cpp:714:10: error: âto_stringâ is not a member of âstdâ
   return std::to_string(xenv.digest());
          ^
make: *** [qs_functions.o] Error 1
ERROR: compilation failed for package âqsâ
* removing â/usr/lib64/R/library/qsâ
* restoring previous â/usr/lib64/R/library/qsâ

The downloaded source packages are in
        â/tmp/RtmpL0cL3G/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("qs") :
  installation of package âqsâ had non-zero exit status

Trial 3

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -std=c++11 -fPIC -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -std=c++11 -fPIC -c qs_functions.cpp -o qs_functions.o
In file included from qs_functions.cpp:21:0:
qs_common.h: In member function âint fd_wrapper::ferror()â:
qs_common.h:457:40: error: âerrnoâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                        ^
qs_common.h:457:49: error: âEBADFâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                                 ^
qs_common.h: In function âuint32_t validate_data(const QsMetadata&, stream_reader&, uint32_t, uint32_t, uint64_t, bool)â:
qs_common.h:1157:34: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                  ^
qs_common.h:1157:72: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                                                        ^
qs_common.h: In member function âuint64_t zstd_decompress_env::decompress(void*, size_t, const void*, size_t)â:
qs_common.h:1528:124: error: âto_stringâ is not a member of âstdâ
     if(return_value > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize " + std::to_string(return_value));
                                                                                                                            ^
qs_common.h: In member function âuint64_t lz4_decompress_env::decompress(char*, int, const char*, int)â:
qs_common.h:1545:146: error: âto_stringâ is not a member of âstdâ
     if(static_cast<uint64_t>(return_value) > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize" + std::to_string(return_value));
                                                                                                                                                  ^
qs_functions.cpp: In function âRcpp::RObject c_qdump(const string&)â:
qs_functions.cpp:492:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:493:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:496:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:504:33: error: âto_stringâ is not a member of âstdâ
       outvec["computed_hash"] = std::to_string(computed_hash);
                                 ^
qs_functions.cpp:514:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:515:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:516:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(computed_hash);
                               ^
qs_functions.cpp:519:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:558:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:559:34: error: âto_stringâ is not a member of âstdâ
     outvec["number_of_blocks"] = std::to_string(totalsize);
                                  ^
qs_functions.cpp:562:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(xenv.digest());
                               ^
qs_functions.cpp:565:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp: In function âstd::string xxhash_raw(SEXP)â:
qs_functions.cpp:714:10: error: âto_stringâ is not a member of âstdâ
   return std::to_string(xenv.digest());
          ^
make: *** [qs_functions.o] Error 1
ERROR: compilation failed for package âqsâ
* removing â/usr/lib64/R/library/qsâ
* restoring previous â/usr/lib64/R/library/qsâ

The downloaded source packages are in
        â/tmp/RtmpL0cL3G/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("qs") :
  installation of package âqsâ had non-zero exit status

Trial 4

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O3 -std=c++11 -c qs_functions.cpp -o qs_functions.o
In file included from qs_functions.cpp:21:0:
qs_common.h: In member function âint fd_wrapper::ferror()â:
qs_common.h:457:40: error: âerrnoâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                        ^
qs_common.h:457:49: error: âEBADFâ was not declared in this scope
     return fcntl(fd, F_GETFD) == -1 || errno == EBADF;
                                                 ^
qs_common.h: In function âuint32_t validate_data(const QsMetadata&, stream_reader&, uint32_t, uint32_t, uint64_t, bool)â:
qs_common.h:1157:34: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                  ^
qs_common.h:1157:72: error: âto_stringâ is not a member of âstdâ
                                  std::to_string(recorded_hash) + "," + std::to_string(computed_hash) + "), data may be corrupted");
                                                                        ^
qs_common.h: In member function âuint64_t zstd_decompress_env::decompress(void*, size_t, const void*, size_t)â:
qs_common.h:1528:124: error: âto_stringâ is not a member of âstdâ
     if(return_value > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize " + std::to_string(return_value));
                                                                                                                            ^
qs_common.h: In member function âuint64_t lz4_decompress_env::decompress(char*, int, const char*, int)â:
qs_common.h:1545:146: error: âto_stringâ is not a member of âstdâ
     if(static_cast<uint64_t>(return_value) > BLOCKSIZE) throw std::runtime_error("Malformed compress block: decompressed size > max blocksize" + std::to_string(return_value));
                                                                                                                                                  ^
qs_functions.cpp: In function âRcpp::RObject c_qdump(const string&)â:
qs_functions.cpp:492:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:493:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:496:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:504:33: error: âto_stringâ is not a member of âstdâ
       outvec["computed_hash"] = std::to_string(computed_hash);
                                 ^
qs_functions.cpp:514:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:515:35: error: âto_stringâ is not a member of âstdâ
     outvec["decompressed_size"] = std::to_string(totalsize);
                                   ^
qs_functions.cpp:516:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(computed_hash);
                               ^
qs_functions.cpp:519:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp:558:32: error: âto_stringâ is not a member of âstdâ
     outvec["readable_bytes"] = std::to_string(readable_bytes);
                                ^
qs_functions.cpp:559:34: error: âto_stringâ is not a member of âstdâ
     outvec["number_of_blocks"] = std::to_string(totalsize);
                                  ^
qs_functions.cpp:562:31: error: âto_stringâ is not a member of âstdâ
     outvec["computed_hash"] = std::to_string(xenv.digest());
                               ^
qs_functions.cpp:565:33: error: âto_stringâ is not a member of âstdâ
       outvec["recorded_hash"] = std::to_string(recorded_hash);
                                 ^
qs_functions.cpp: In function âstd::string xxhash_raw(SEXP)â:
qs_functions.cpp:714:10: error: âto_stringâ is not a member of âstdâ
   return std::to_string(xenv.digest());
          ^
make: *** [qs_functions.o] Error 1
ERROR: compilation failed for package âqsâ
* removing â/usr/lib64/R/library/qsâ
* restoring previous â/usr/lib64/R/library/qsâ

The downloaded source packages are in
        â/tmp/RtmpL0cL3G/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("qs") :
  installation of package âqsâ had non-zero exit status

from qs.

leungi commented on May 30, 2024

Update: qs install successful after reinstall of gcc and g++ compiler in RHEL machine.

Weird thing is gcc and g++ are of different versions, and yet it works; previously, I had forced gcc and g++ to be 4.9.3 via ~/Makevars.

[leungi@ohylpyt1-d bin]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc493/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.3/configure --prefix=/usr/local/gcc493 --program-suffix=49 --enable-languages=c,c++ --disable-libstdcxx-pch --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)

[leungi@ohylpyt1-d bin]$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC)

There are some warnings, but tested qsave() and qread() with not issue.

* installing *source* package âqsâ ...
** package âqsâ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /bin/pkg-config
zstd dynamic library not detected -- compiling from source
lz4 dynamic library not detected -- compiling from source
-L. -lQSZSTD -lQSLZ4
-IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4
LIBZSTD = ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o LIBLZ4 = LZ4/lz4.o LZ4/lz4hc.o $(SHLIB): libQSZSTD.a libQSLZ4.a libQSZSTD.a: $(LIBZSTD) $(AR) rcs libQSZSTD.a $(LIBZSTD) libQSLZ4.a: $(LIBLZ4) $(AR) rcs libQSLZ4.a $(LIBLZ4) clean: rm -f $(SHLIB) $(OBJECTS) $(LIBZSTD) libQSZSTD.a $(LIBLZ4) libQSLZ4.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c RcppExports.cpp -o RcppExports.o
In file included from /usr/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:61:0,
                 from /usr/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /usr/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from ../inst/include/qs_RcppExports.h:7,
                 from ../inst/include/qs.h:7,
                 from RcppExports.cpp:4:
RcppExports.cpp: In function âSEXPREC* _qs_is_big_endian_try()â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:14:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:14:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qsave_try(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:46:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:46:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qsave_fd_try(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:86:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:86:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qsave_handle_try(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:125:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:125:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qserialize_try(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:164:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:164:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qread_try(SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:202:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:202:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qread_fd_try(SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:238:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:238:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qread_handle_try(SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:273:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:273:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qread_ptr_try(SEXP, SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:308:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:308:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qdeserialize_try(SEXP, SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:344:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:344:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_c_qdump_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:379:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:379:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_randomStrings_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:412:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:412:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_zstd_compress_bound_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:447:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:447:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_lz4_compress_bound_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:480:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:480:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_zstd_compress_raw_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:513:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:513:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_zstd_decompress_raw_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:547:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:547:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_lz4_compress_raw_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:580:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:580:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_lz4_decompress_raw_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:614:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:614:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_blosc_shuffle_raw_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:647:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:647:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_blosc_unshuffle_raw_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:681:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:681:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_xxhash_raw_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:715:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:715:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_convertToAlt_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:748:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:748:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_openFd_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:781:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:781:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_readFdDirect_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:815:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:815:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_closeFd_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:849:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:849:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_openMmap_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:882:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:882:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_closeMmap_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:916:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:916:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_openHandle_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:950:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:950:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_closeHandle_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:984:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:984:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_openWinFileMapping_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:1017:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:1017:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_openWinMapView_try(SEXP, SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:1051:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:1051:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
RcppExports.cpp: In function âSEXPREC* _qs_closeWinMapView_try(SEXP)â:
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable ânprotâ [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:1085:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
/usr/lib64/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable âstop_symâ [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:1085:1: note: in expansion of macro âBEGIN_RCPPâ
 BEGIN_RCPP
 ^
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c qs_functions.cpp -o qs_functions.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/debug.c -o ZSTD/common/debug.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/entropy_common.c -o ZSTD/common/entropy_common.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/error_private.c -o ZSTD/common/error_private.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/fse_decompress.c -o ZSTD/common/fse_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/pool.c -o ZSTD/common/pool.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/threading.c -o ZSTD/common/threading.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/xxhash.c -o ZSTD/common/xxhash.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/common/zstd_common.c -o ZSTD/common/zstd_common.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/fse_compress.c -o ZSTD/compress/fse_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/hist.c -o ZSTD/compress/hist.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/huf_compress.c -o ZSTD/compress/huf_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_compress.c -o ZSTD/compress/zstd_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_double_fast.c -o ZSTD/compress/zstd_double_fast.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_fast.c -o ZSTD/compress/zstd_fast.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_lazy.c -o ZSTD/compress/zstd_lazy.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_ldm.c -o ZSTD/compress/zstd_ldm.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstdmt_compress.c -o ZSTD/compress/zstdmt_compress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/compress/zstd_opt.c -o ZSTD/compress/zstd_opt.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/huf_decompress.c -o ZSTD/decompress/huf_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_ddict.c -o ZSTD/decompress/zstd_ddict.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_decompress_block.c -o ZSTD/decompress/zstd_decompress_block.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/decompress/zstd_decompress.c -o ZSTD/decompress/zstd_decompress.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/cover.c -o ZSTD/dictBuilder/cover.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/divsufsort.c -o ZSTD/dictBuilder/divsufsort.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/fastcover.c -o ZSTD/dictBuilder/fastcover.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ZSTD/dictBuilder/zdict.c -o ZSTD/dictBuilder/zdict.o
ar rcs libQSZSTD.a ZSTD/common/debug.o ZSTD/common/entropy_common.o ZSTD/common/error_private.o ZSTD/common/fse_decompress.o ZSTD/common/pool.o ZSTD/common/threading.o ZSTD/common/xxhash.o ZSTD/common/zstd_common.o ZSTD/compress/fse_compress.o ZSTD/compress/hist.o ZSTD/compress/huf_compress.o ZSTD/compress/zstd_compress.o ZSTD/compress/zstd_double_fast.o ZSTD/compress/zstd_fast.o ZSTD/compress/zstd_lazy.o ZSTD/compress/zstd_ldm.o ZSTD/compress/zstdmt_compress.o ZSTD/compress/zstd_opt.o ZSTD/decompress/huf_decompress.o ZSTD/decompress/zstd_ddict.o ZSTD/decompress/zstd_decompress_block.o ZSTD/decompress/zstd_decompress.o ZSTD/dictBuilder/cover.o ZSTD/dictBuilder/divsufsort.o ZSTD/dictBuilder/fastcover.o ZSTD/dictBuilder/zdict.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c LZ4/lz4.c -o LZ4/lz4.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DRCPP_USE_UNWIND_PROTECT -I. -IZSTD -IZSTD/common -IZSTD/decompress -IZSTD/compress -ILZ4 -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RApiSerialize/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
ar rcs libQSLZ4.a LZ4/lz4.o LZ4/lz4hc.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o qs.so RcppExports.o qs_functions.o -lpthread -L. -lQSZSTD -lQSLZ4 -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/00LOCK-qs/00new/qs/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package âqsâ
    finding HTML links ... done
    blosc_shuffle_raw                       html
    blosc_unshuffle_raw                     html
    convertToAlt                            html
    is_big_endian                           html
    lz4_compress_bound                      html
    lz4_compress_raw                        html
    lz4_decompress_raw                      html
    qdeserialize                            html
    qdump                                   html
    qread                                   html
    qread_fd                                html
    qread_handle                            html
    qread_ptr                               html
    qsave                                   html
    qsave_fd                                html
    qsave_handle                            html
    qserialize                              html
    randomStrings                           html
    starnames                               html
    zstd_compress_bound                     html
    zstd_compress_raw                       html
    zstd_decompress_raw                     html
** 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 (qs)
Making 'packages.html' ... done

The downloaded source packages are in
        â/tmp/RtmpQucHjk/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

from qs.

install.packages() error in RHEL about qs HOT 9 CLOSED

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