Check and Install rstan

XiangyunHuang commented 6 years ago

R CMD INSTALL rstan_2.18.1.tar.gz

* installing *source* package ‘rstan’ ...
** 成功将‘rstan’程序包解包并MD5和检查
** libs
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c chains.cpp -o chains.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c init.cpp -o init.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__ast_def.cpp -o lang__ast_def.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__bare_type_grammar_inst.cpp -o lang__grammars__bare_type_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__expression07_grammar_inst.cpp -o lang__grammars__expression07_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__expression_grammar_inst.cpp -o lang__grammars__expression_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__functions_grammar_inst.cpp -o lang__grammars__functions_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__indexes_grammar_inst.cpp -o lang__grammars__indexes_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__program_grammar_inst.cpp -o lang__grammars__program_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__semantic_actions.cpp -o lang__grammars__semantic_actions.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__statement_2_grammar_inst.cpp -o lang__grammars__statement_2_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__statement_grammar_inst.cpp -o lang__grammars__statement_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__term_grammar_inst.cpp -o lang__grammars__term_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__var_deccls_grammar_inst.cpp -o lang__grammars__var_deccls_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c lang__grammars__whitespace_grammar_inst.cpp -o lang__grammars__whitespace_grammar_inst.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c misc.cpp -o misc.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c pointer-tools.cpp -o pointer-tools.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c sparse_extractors.cpp -o sparse_extractors.o
g++  -I"/usr/local/lib64/R/include" -DNDEBUG -I"../inst/include" -I"`"/usr/local/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/usr/local/lib64/R/site-library/Rcpp/include" -I"/usr/local/lib64/R/site-library/RcppEigen/include" -I"/usr/local/lib64/R/site-library/BH/include" -I"/usr/local/lib64/R/site-library/StanHeaders/include" -I/usr/local/include     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations -c stanc.cpp -o stanc.o
g++ -shared -L/usr/local/lib64/R/lib -L/usr/local/lib64 -o rstan.so chains.o init.o lang__ast_def.o lang__grammars__bare_type_grammar_inst.o lang__grammars__expression07_grammar_inst.o lang__grammars__expression_grammar_inst.o lang__grammars__functions_grammar_inst.o lang__grammars__indexes_grammar_inst.o lang__grammars__program_grammar_inst.o lang__grammars__semantic_actions.o lang__grammars__statement_2_grammar_inst.o lang__grammars__statement_grammar_inst.o lang__grammars__term_grammar_inst.o lang__grammars__var_deccls_grammar_inst.o lang__grammars__whitespace_grammar_inst.o misc.o pointer-tools.o sparse_extractors.o stanc.o -L/usr/local/lib64/R/lib -lR
installing to /usr/local/lib64/R/site-library/rstan/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rstan)

gcc -v

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-4/root/usr/libexec/gcc/x86_64-redhat-linux/5.3.1/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-4/root/usr --mandir=/opt/rh/devtoolset-4/root/usr/share/man --infodir=/opt/rh/devtoolset-4/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --enable-plugin --with-linker-hash-style=gnu --enable-initfini-array --disable-libgcj --with-default-libstdcxx-abi=gcc4-compatible --with-isl=/builddir/build/BUILD/gcc-5.3.1-20160406/obj-x86_64-redhat-linux/isl-install --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 5.3.1 20160406 (Red Hat 5.3.1-6) (GCC)

cat .R/Makevars

MAKEFLAGS = -j4
CXX14 = g++
CXX14FLAGS = -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC
CXX14FLAGS += -flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations

devtools::session_info('rstan')

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R Under development (unstable) (2018-10-07 r75409)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  zh_CN.UTF-8
 ctype    zh_CN.UTF-8
 tz       Asia/Shanghai
 date     2018-10-26

─ Packages ───────────────────────────────────────────────────────────────────
 package      * version    date       lib source
 assertthat     0.2.0      2017-04-11 [1] CRAN (R 3.6.0)
 backports      1.1.2      2017-12-13 [1] CRAN (R 3.6.0)
 base64enc      0.1-3      2015-07-28 [1] CRAN (R 3.6.0)
 BH             1.66.0-1   2018-02-13 [1] CRAN (R 3.6.0)
 callr          3.0.0.9001 2018-10-09 [1] Github (r-lib/callr@d0ea2b6)
 cli            1.0.1.9000 2018-10-09 [1] Github (r-lib/cli@56538e3)
 colorspace     1.4-0      2018-09-19 [1] R-Forge (R 3.6.0)
 crayon         1.3.4      2017-09-16 [1] CRAN (R 3.6.0)
 desc           1.2.0      2018-10-09 [1] Github (r-lib/desc@7c12d36)
 digest         0.6.18     2018-10-10 [1] CRAN (R 3.6.0)
 fansi          0.4.0      2018-10-05 [1] CRAN (R 3.6.0)
 ggplot2        3.1.0      2018-10-25 [1] CRAN (R 3.6.0)
 glue           1.3.0      2018-07-17 [1] CRAN (R 3.6.0)
 gridExtra      2.3        2017-09-09 [1] CRAN (R 3.6.0)
 gtable         0.2.0      2016-02-26 [1] CRAN (R 3.6.0)
 inline         0.3.15     2018-05-18 [1] CRAN (R 3.6.0)
 labeling       0.3        2014-08-23 [1] CRAN (R 3.6.0)
 lattice        0.20-35    2017-03-25 [2] CRAN (R 3.6.0)
 lazyeval       0.2.1      2017-10-29 [1] CRAN (R 3.6.0)
 loo            2.0.0      2018-04-11 [1] CRAN (R 3.6.0)
 magrittr       1.5        2014-11-22 [1] CRAN (R 3.6.0)
 MASS           7.3-51     2018-10-16 [2] CRAN (R 3.6.0)
 Matrix         1.2-14     2018-04-13 [2] CRAN (R 3.6.0)
 matrixStats    0.54.0     2018-07-23 [1] CRAN (R 3.6.0)
 mgcv           1.8-24     2018-06-23 [2] CRAN (R 3.6.0)
 munsell        0.5.0      2018-06-12 [1] CRAN (R 3.6.0)
 nlme           3.1-137    2018-04-07 [2] CRAN (R 3.6.0)
 pillar         1.3.0      2018-07-14 [1] CRAN (R 3.6.0)
 pkgbuild       1.0.2      2018-10-16 [1] CRAN (R 3.6.0)
 plyr           1.8.4      2016-06-08 [1] CRAN (R 3.6.0)
 prettyunits    1.0.2      2015-07-13 [1] CRAN (R 3.6.0)
 processx       3.2.0.9000 2018-10-09 [1] Github (r-lib/processx@8374340)
 ps             1.2.0      2018-10-16 [1] CRAN (R 3.6.0)
 R6             2.3.0      2018-10-04 [1] CRAN (R 3.6.0)
 RColorBrewer   1.1-2      2014-12-07 [1] CRAN (R 3.6.0)
 Rcpp           0.12.19    2018-10-01 [1] CRAN (R 3.6.0)
 RcppEigen      0.3.3.4.0  2018-02-07 [1] CRAN (R 3.6.0)
 reshape2       1.4.3      2017-12-11 [1] CRAN (R 3.6.0)
 rlang          0.3.0.1    2018-10-25 [1] CRAN (R 3.6.0)
 rprojroot      1.3-2      2018-01-03 [1] CRAN (R 3.6.0)
 rstan          2.18.1     2018-10-16 [1] CRAN (R 3.6.0)
 scales         1.0.0      2018-08-09 [1] CRAN (R 3.6.0)
 StanHeaders    2.18.0     2018-10-07 [1] CRAN (R 3.6.0)
 stringi        1.2.4      2018-07-20 [1] CRAN (R 3.6.0)
 stringr        1.3.1      2018-05-10 [1] CRAN (R 3.6.0)
 tibble         1.4.2      2018-01-22 [1] CRAN (R 3.6.0)
 utf8           1.1.4      2018-05-24 [1] CRAN (R 3.6.0)
 viridisLite    0.3.0      2018-02-01 [1] CRAN (R 3.6.0)
 withr          2.1.2      2018-03-15 [1] CRAN (R 3.6.0)

[1] /usr/local/lib64/R/site-library
[2] /usr/local/lib64/R/library

XiangyunHuang commented 6 years ago

RUNIT TEST PROTOCOL--Tue Oct 2 22:36:35 2018

Number of test functions: 31 Number of errors: 0 Number of failures: 0

Details:

Test Suite: rstantest Test function regexp: ^test_+ Test file regexp: ^runit.+.R Involved directory: /home/xiangyun/rstan.Rcheck/rstan/unitTests

Test file: runit.test.chains.R
- test_essnrhat: (4 checks) ... OK (0.06 seconds)
- test_seq_perm: (4 checks) ... OK (0 seconds)
Test file: runit.test.extract_sparse_parts.R
- test_extract_sparse_parts: (9 checks) ... OK (0.8 seconds)
Test file: runit.test.misc.R
- test_config_argss: (13 checks) ... OK (0 seconds)
- test_data_list2array: (9 checks) ... OK (0 seconds)
- test_data_preprocess: (5 checks) ... OK (0 seconds)
- test_data_preprocess2: (6 checks) ... OK (0 seconds)
- test_dotfnames_fromto_sqrfnames: (1 checks) ... OK (0 seconds)
- test_flatnames: (2 checks) ... OK (0 seconds)
- test_get_dims_from_fnames: (1 checks) ... OK (0 seconds)
- test_get_model_strcode: (11 checks) ... OK (0 seconds)
- test_idx_col2rowm: (3 checks) ... OK (0 seconds)
- test_idx_row2colm: (3 checks) ... OK (0 seconds)
- test_is_named_list: (4 checks) ... OK (0 seconds)
- test_is_valid_stan_name: (5 checks) ... OK (0 seconds)
- test_mklist: (5 checks) ... OK (0 seconds)
- test_multi_idx_row2colm: (3 checks) ... OK (0 seconds)
- test_par_vector2list: (5 checks) ... OK (0 seconds)
- test_pars_total_indexes: (6 checks) ... OK (0 seconds)
- test_read_comments: (4 checks) ... OK (0 seconds)
- test_read_csv_header: (2 checks) ... OK (0 seconds)
- test_read_rdump: (3 checks) ... OK (0 seconds)
- test_remove_empty_pars: (4 checks) ... OK (0 seconds)
- test_seq_array_ind: (4 checks) ... OK (0 seconds)
- test_stan_rdump: (8 checks) ... OK (0 seconds)
Test file: runit.test.options.R
- test_options1: (2 checks) ... OK (0 seconds)
- test_options2: (7 checks) ... OK (0 seconds)
- test_plot_rhat_breaks: (2 checks) ... OK (0 seconds)
- test_rstan_options: (0 checks) ... OK (0 seconds)
Test file: runit.test.stan_csv.R
- test_paridx_fun: (3 checks) ... OK (0 seconds)
- test_parse_stancsv_comments3: (6 checks) ... OK (0 seconds)

Name	Value
platform	x86_64-pc-linux-gnu
arch	x86_64
os	linux-gnu
system	x86_64, linux-gnu
status	Under development (unstable)
major	3
minor	6.0
year	2018
month	09
day	18
svn rev	75325
language	R
version.string	R Under development (unstable) (2018-09-18 r75325)
nickname	Unsuffered Consequences
host	xiangyun
compiler	g++ -std=gnu++11

XiangyunHuang commented 6 years ago

安装编译器

# https://gcc.gnu.org/projects/cxx-status.html#cxx14
# 安装 Scientific Linux distribution 发行版的安装源
# https://www.softwarecollections.org/en/docs/
sudo yum install centos-release-scl-rh centos-release-scl
# 更新源
sudo yum update

# 安装新版 gcc 5.3.1 完全支持 C++ 14 特性
sudo yum install \
  devtoolset-4-gcc \
  devtoolset-4-gcc-c++ \
  devtoolset-4-gcc-gfortran

# 设置 gcc/g++/gfortran 环境变量
source /opt/rh/devtoolset-4/enable

编辑 `~/.bashrc` 添加上一行

sudo yum install \
  devtoolset-6-gcc \
  devtoolset-6-gcc-c++ \
  devtoolset-6-gcc-gfortran

sudo yum install \
  devtoolset-7-gcc \
  devtoolset-7-gcc-c++ \
  devtoolset-7-gcc-gfortran

# gcc 4.9
sudo yum install \
  devtoolset-3-gcc \
  devtoolset-3-gcc-c++ \
  devtoolset-3-gcc-gfortran

# https://discourse.mc-stan.org/t/do-not-install-rstan-2-17-4-from-cran/5822

XiangyunHuang / Thesis-Template-Bookdown

Check and Install rstan #1

RUNIT TEST PROTOCOL--Tue Oct 2 22:36:35 2018