What's OpenCPU? And why is it sending email to mc.stanislaw@gmail.com?
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Daniel Lee
Sep 6, 2016, 1:45:36 PM9/6/16
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From: OpenCPU CI <nor...@opencpu.org>
Date: Tue, Sep 6, 2016 at 1:39 PM
Subject: Build failed: stan-dev/rstanarm
To: stan-dev <mc.sta...@gmail.com>
Build a12e6c9cb0 of stan-dev/rstanarm failed. Either an error occured during package installation, or the package name does not match the name of the Github repository.
NEW COMMITS:
[a12e6c9cb0]
Time: 2016-09-06 13:34:54
Author: jgabry
Message: "update gitignore
[ci skip]"
URL: https://github.com/stan-dev/rstanarm/commit/a12e6c9cb06559ea757513f04b0020f9947efe25
BUILD LOG:
Downloading GitHub repo stan-dev/rstanarm@master
from URL https://api.github.com/repos/stan-dev/rstanarm/zipball/master
Installing rstanarm
trying URL 'http://cran.rstudio.com/src/contrib/shinystan_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2374842 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
Installing shinystan
trying URL 'http://cran.rstudio.com/src/contrib/colourpicker_0.1.tar.gz'
Content type 'application/x-gzip' length 798156 bytes (779 KB)
==================================================
downloaded 779 KB
Installing colourpicker
trying URL 'http://cran.rstudio.com/src/contrib/shinyjs_0.7.tar.gz'
Content type 'application/x-gzip' length 961166 bytes (938 KB)
==================================================
downloaded 938 KB
Installing shinyjs
trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.10.tar.gz'
Content type 'application/x-gzip' length 118336 bytes (115 KB)
==================================================
downloaded 115 KB
Installing digest
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11822b5537a/digest' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/digest/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (digest)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools1182470ca1ec/shinyjs' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘shinyjs’ ...
** package ‘shinyjs’ successfully unpacked and MD5 sums checked
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (shinyjs)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools118255f59d3a/colourpicker' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘colourpicker’ ...
** package ‘colourpicker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (colourpicker)
trying URL 'http://cran.rstudio.com/src/contrib/rsconnect_0.4.3.tar.gz'
Content type 'application/x-gzip' length 206258 bytes (201 KB)
==================================================
downloaded 201 KB
Installing rsconnect
trying URL 'http://cran.rstudio.com/src/contrib/PKI_0.1-3.tar.gz'
Content type 'application/x-gzip' length 31058 bytes (30 KB)
==================================================
downloaded 30 KB
Installing PKI
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11821ad06e76/PKI' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘PKI’ ...
** package ‘PKI’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c asn1.c -o asn1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pki-x509.c -o pki-x509.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tools.c -o tools.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PKI.so asn1.o init.o pki-x509.o tools.o -lssl -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/PKI/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (PKI)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools1182725edccd/rsconnect' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘rsconnect’ ...
** package ‘rsconnect’ successfully unpacked and MD5 sums checked
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rsconnect)
trying URL 'http://cran.rstudio.com/src/contrib/rstan_2.11.1.tar.gz'
Content type 'application/x-gzip' length 688973 bytes (672 KB)
==================================================
downloaded 672 KB
Installing rstan
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.7.tar.gz'
Content type 'application/x-gzip' length 2421965 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
Installing Rcpp
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11827760a229/Rcpp' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/Rcpp/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11824cafcb25/rstan' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chains.cpp -o chains.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__ast_def.cpp -o lang__ast_def.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__bare_type_grammar_inst.cpp -o lang__grammars__bare_type_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__expression07_grammar_inst.cpp -o lang__grammars__expression07_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__expression_grammar_inst.cpp -o lang__grammars__expression_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__functions_grammar_inst.cpp -o lang__grammars__functions_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
virtual memory exhausted: Cannot allocate memory
/usr/lib/R/etc/Makeconf:141: recipe for target 'lang__grammars__functions_grammar_inst.o' failed
make: *** [lang__grammars__functions_grammar_inst.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/tmp/ocpu-temp/githubdir11804f470226/rstan’
Error: Command failed (1)
Execution halted
SESSION INFO
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] opencpu_1.6.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.6 lattice_0.20-33 plyr_1.8.4 grid_3.3.1 [5] jsonlite_1.0 gtable_0.2.0 magrittr_1.5 RAppArmor_2.0.2 [9] evaluate_0.9 scales_0.4.0 ggplot2_2.1.0 stringi_1.1.1 [13] unixtools_0.1-1 tools_3.3.1 stringr_1.0.0 munsell_0.4.3 [17] parallel_3.3.1 sendmailR_1.2-1 colorspace_1.2-6 base64enc_0.1-3 [21] openssl_0.9.4
From: OpenCPU CI <nor...@opencpu.org>
Date: Tue, Sep 6, 2016 at 1:39 PM
Subject: Build failed: stan-dev/rstanarm
To: stan-dev <mc.sta...@gmail.com>
Build a12e6c9cb0 of stan-dev/rstanarm failed. Either an error occured during package installation, or the package name does not match the name of the Github repository.
NEW COMMITS:
[a12e6c9cb0]
Time: 2016-09-06 13:34:54
Author: jgabry
Message: "update gitignore
[ci skip]"
URL: https://github.com/stan-dev/rstanarm/commit/a12e6c9cb06559ea757513f04b0020f9947efe25
BUILD LOG:
Downloading GitHub repo stan-dev/rstanarm@master
from URL https://api.github.com/repos/stan-dev/rstanarm/zipball/master
Installing rstanarm
trying URL 'http://cran.rstudio.com/src/contrib/shinystan_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2374842 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
Installing shinystan
trying URL 'http://cran.rstudio.com/src/contrib/colourpicker_0.1.tar.gz'
Content type 'application/x-gzip' length 798156 bytes (779 KB)
==================================================
downloaded 779 KB
Installing colourpicker
trying URL 'http://cran.rstudio.com/src/contrib/shinyjs_0.7.tar.gz'
Content type 'application/x-gzip' length 961166 bytes (938 KB)
==================================================
downloaded 938 KB
Installing shinyjs
trying URL 'http://cran.rstudio.com/src/contrib/digest_0.6.10.tar.gz'
Content type 'application/x-gzip' length 118336 bytes (115 KB)
==================================================
downloaded 115 KB
Installing digest
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11822b5537a/digest' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/digest/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (digest)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools1182470ca1ec/shinyjs' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘shinyjs’ ...
** package ‘shinyjs’ successfully unpacked and MD5 sums checked
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (shinyjs)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools118255f59d3a/colourpicker' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘colourpicker’ ...
** package ‘colourpicker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (colourpicker)
trying URL 'http://cran.rstudio.com/src/contrib/rsconnect_0.4.3.tar.gz'
Content type 'application/x-gzip' length 206258 bytes (201 KB)
==================================================
downloaded 201 KB
Installing rsconnect
trying URL 'http://cran.rstudio.com/src/contrib/PKI_0.1-3.tar.gz'
Content type 'application/x-gzip' length 31058 bytes (30 KB)
==================================================
downloaded 30 KB
Installing PKI
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11821ad06e76/PKI' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘PKI’ ...
** package ‘PKI’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c asn1.c -o asn1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pki-x509.c -o pki-x509.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tools.c -o tools.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o PKI.so asn1.o init.o pki-x509.o tools.o -lssl -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/PKI/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (PKI)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools1182725edccd/rsconnect' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘rsconnect’ ...
** package ‘rsconnect’ successfully unpacked and MD5 sums checked
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rsconnect)
trying URL 'http://cran.rstudio.com/src/contrib/rstan_2.11.1.tar.gz'
Content type 'application/x-gzip' length 688973 bytes (672 KB)
==================================================
downloaded 672 KB
Installing rstan
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.7.tar.gz'
Content type 'application/x-gzip' length 2421965 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
Installing Rcpp
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11827760a229/Rcpp' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR
installing to /tmp/ocpu-temp/githubdir11804f470226/Rcpp/libs
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \
CMD INSTALL '/tmp/ocpu-temp/Rtmpwtp9hU/devtools11824cafcb25/rstan' \
--library='/tmp/ocpu-temp/githubdir11804f470226' --install-tests
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chains.cpp -o chains.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__ast_def.cpp -o lang__ast_def.o
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__bare_type_grammar_inst.cpp -o lang__grammars__bare_type_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
from lang__grammars__bare_type_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__expression07_grammar_inst.cpp -o lang__grammars__expression07_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_def.hpp:6,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar_inst.cpp:1,
from lang__grammars__expression07_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__expression_grammar_inst.cpp -o lang__grammars__expression_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression07_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_def.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/expression_grammar_inst.cpp:1,
from lang__grammars__expression_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
g++ -I/usr/share/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/usr/lib/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I"/tmp/ocpu-temp/githubdir11804f470226/Rcpp/include" -I"/usr/lib/R/site-library/RcppEigen/include" -I"/usr/lib/R/site-library/BH/include" -I"/usr/lib/R/site-library/StanHeaders/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lang__grammars__functions_grammar_inst.cpp -o lang__grammars__functions_grammar_inst.o
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
# pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
In file included from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/push.hpp:24,
from /usr/lib/R/site-library/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /usr/lib/R/site-library/BH/include/boost/iostreams/stream.hpp:21,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /usr/lib/R/site-library/BH/include/boost/spirit/home/qi.hpp:30,
from /usr/lib/R/site-library/BH/include/boost/spirit/include/qi.hpp:16,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar.hpp:4,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_def.hpp:5,
from /usr/lib/R/site-library/StanHeaders/include/src/stan/lang/grammars/functions_grammar_inst.cpp:1,
from lang__grammars__functions_grammar_inst.cpp:18:
/usr/lib/R/site-library/BH/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
# pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
^
virtual memory exhausted: Cannot allocate memory
/usr/lib/R/etc/Makeconf:141: recipe for target 'lang__grammars__functions_grammar_inst.o' failed
make: *** [lang__grammars__functions_grammar_inst.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/tmp/ocpu-temp/githubdir11804f470226/rstan’
Error: Command failed (1)
Execution halted
SESSION INFO
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] opencpu_1.6.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.6 lattice_0.20-33 plyr_1.8.4 grid_3.3.1 [5] jsonlite_1.0 gtable_0.2.0 magrittr_1.5 RAppArmor_2.0.2 [9] evaluate_0.9 scales_0.4.0 ggplot2_2.1.0 stringi_1.1.1 [13] unixtools_0.1-1 tools_3.3.1 stringr_1.0.0 munsell_0.4.3 [17] parallel_3.3.1 sendmailR_1.2-1 colorspace_1.2-6 base64enc_0.1-3 [21] openssl_0.9.4
Ben Goodrich
Sep 6, 2016, 5:52:09 PM9/6/16
to stan development mailing list
It is a webservice along the lines of what K.S. and Allen have been talking about using protocol buffers and stuff with. It claims to be able to install R packages from GitHub but seems to be running out of memory when it tries to install rstan. I'll see what I can do about it.
Ben
Ben
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