{"action":"closed","issue":{"url":"https://api.github.com/repos/richelbilderbeek/Peregrine/issues/2","repository_url":"https://api.github.com/repos/richelbilderbeek/Peregrine","labels_url":"https://api.github.com/repos/richelbilderbeek/Peregrine/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/richelbilderbeek/Peregrine/issues/2/comments","events_url":"https://api.github.com/repos/richelbilderbeek/Peregrine/issues/2/events","html_url":"https://github.com/richelbilderbeek/Peregrine/issues/2","id":160856676,"number":2,"title":"Cannot install R package rstan on Peregrine","user":{"login":"richelbilderbeek","id":2098230,"avatar_url":"https://avatars.githubusercontent.com/u/2098230?v=3","gravatar_id":"","url":"https://api.github.com/users/richelbilderbeek","html_url":"https://github.com/richelbilderbeek","followers_url":"https://api.github.com/users/richelbilderbeek/followers","following_url":"https://api.github.com/users/richelbilderbeek/following{/other_user}","gists_url":"https://api.github.com/users/richelbilderbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/richelbilderbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richelbilderbeek/subscriptions","organizations_url":"https://api.github.com/users/richelbilderbeek/orgs","repos_url":"https://api.github.com/users/richelbilderbeek/repos","events_url":"https://api.github.com/users/richelbilderbeek/events{/privacy}","received_events_url":"https://api.github.com/users/richelbilderbeek/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-06-17T10:17:41Z","updated_at":"2016-06-17T10:18:44Z","closed_at":"2016-06-17T10:18:44Z","body":"```\r\ntrying URL 'http://cran.xl-mirror.nl/src/contrib/rstan_2.9.0-3.tar.gz'\r\nContent type 'application/x-gzip' length 1099610 bytes (1.0 Mb)\r\nopened URL\r\n==================================================\r\ndownloaded 1.0 Mb\r\n\r\n* installing *source* package ‘rstan’ ...\r\n** package ‘rstan’ successfully unpacked and MD5 sums checked\r\n** libs\r\ng++ -I/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/include -DNDEBUG -I\"../inst/include\" -I\"../inst/include/boost_not_in_BH\" -I\"`\"/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/bin/Rscript\" --vanilla -e \"cat(system.file('include', 'src', package = 'StanHeaders'))\"`\" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/software/software/OpenBLAS/0.2.13-gompic-2.7.11-LAPACK-3.5.0/include -I/software/software/ScaLAPACK/2.0.2-gompic-2.7.11-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/software/software/FFTW/3.3.4-gompic-2.7.11/include -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/RcppEigen/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include\"   -fpic  -O2 -march=native  -c chains.cpp -o chains.o\r\ng++ -I/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/include -DNDEBUG -I\"../inst/include\" -I\"../inst/include/boost_not_in_BH\" -I\"`\"/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/bin/Rscript\" --vanilla -e \"cat(system.file('include', 'src', package = 'StanHeaders'))\"`\" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/software/software/OpenBLAS/0.2.13-gompic-2.7.11-LAPACK-3.5.0/include -I/software/software/ScaLAPACK/2.0.2-gompic-2.7.11-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/software/software/FFTW/3.3.4-gompic-2.7.11/include -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/RcppEigen/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include\"   -fpic  -O2 -march=native  -c init.cpp -o init.o\r\ng++ -I/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/include -DNDEBUG -I\"../inst/include\" -I\"../inst/include/boost_not_in_BH\" -I\"`\"/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/bin/Rscript\" --vanilla -e \"cat(system.file('include', 'src', package = 'StanHeaders'))\"`\" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/software/software/OpenBLAS/0.2.13-gompic-2.7.11-LAPACK-3.5.0/include -I/software/software/ScaLAPACK/2.0.2-gompic-2.7.11-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/software/software/FFTW/3.3.4-gompic-2.7.11/include -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/RcppEigen/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include\"   -fpic  -O2 -march=native  -c lang__ast_def.cpp -o lang__ast_def.o\r\ng++ -I/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/include -DNDEBUG -I\"../inst/include\" -I\"../inst/include/boost_not_in_BH\" -I\"`\"/software/software/R/3.1.2-goolfc-2.7.11-default/lib64/R/bin/Rscript\" --vanilla -e \"cat(system.file('include', 'src', package = 'StanHeaders'))\"`\" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -I/software/software/OpenBLAS/0.2.13-gompic-2.7.11-LAPACK-3.5.0/include -I/software/software/ScaLAPACK/2.0.2-gompic-2.7.11-OpenBLAS-0.2.13-LAPACK-3.5.0/include -I/software/software/FFTW/3.3.4-gompic-2.7.11/include -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/Rcpp/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/RcppEigen/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include\" -I\"/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include\"   -fpic  -O2 -march=native  -c lang__grammars__bare_type_grammar_inst.cpp -o lang__grammars__bare_type_grammar_inst.o\r\nIn file included from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/resolve.hpp:26,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/push.hpp:24,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/stream_buffer.hpp:22,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/stream.hpp:21,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream.hpp:15,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi.hpp:30,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/include/qi.hpp:16,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,\r\n                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,\r\n                 from lang__grammars__bare_type_grammar_inst.cpp:18:\r\n/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/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\r\n # pragma message(\"NOTE: Use of this header (bool_trait_def.hpp) is deprecated\")\r\n\r\n[...]                                                                               ^\r\n                                                                                    ^\r\ng++: internal compiler error: Killed (program cc1plus)\r\n0x409a70 execute\r\n\t../../gcc/gcc.c:2823\r\n0x409da4 do_spec_1\r\n\t../../gcc/gcc.c:4615\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\n0x40acc7 do_spec_1\r\n\t../../gcc/gcc.c:5269\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\n0x40acc7 do_spec_1\r\n\t../../gcc/gcc.c:5269\r\n0x40a9bf do_spec_1\r\n\t../../gcc/gcc.c:5374\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\n0x40acc7 do_spec_1\r\n\t../../gcc/gcc.c:5269\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\n0x40acc7 do_spec_1\r\n\t../../gcc/gcc.c:5269\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\n0x40acc7 do_spec_1\r\n\t../../gcc/gcc.c:5269\r\n0x40c725 process_brace_body\r\n\t../../gcc/gcc.c:5872\r\n0x40c725 handle_braces\r\n\t../../gcc/gcc.c:5786\r\nPlease submit a full bug report,\r\nwith preprocessed source if appropriate.\r\nPlease include the complete backtrace with any bug report.\r\nSee <http://gcc.gnu.org/bugs.html> for instructions.\r\nmake: *** [lang__grammars__statement_grammar_inst.o] Error 4\r\nERROR: compilation failed for package ‘rstan’\r\n* removing ‘/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/rstan’\r\n* restoring previous ‘/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/rstan’\r\n\r\nThe downloaded source packages are in\r\n\t‘/tmp/RtmpxeZByE/downloaded_packages’\r\nWarning message:\r\nIn install.packages(\"rstan\") :\r\n  installation of package ‘rstan’ had non-zero exit status\r\n```"}}
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