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Cannot install R package rstan on Peregrine #2

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richelbilderbeek opened this issue Jun 17, 2016 · 2 comments
Closed

Cannot install R package rstan on Peregrine #2

richelbilderbeek opened this issue Jun 17, 2016 · 2 comments

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@richelbilderbeek
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trying URL 'http://cran.xl-mirror.nl/src/contrib/rstan_2.9.0-3.tar.gz'
Content type 'application/x-gzip' length 1099610 bytes (1.0 Mb)
opened URL
==================================================
downloaded 1.0 Mb

* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -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
g++ -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
g++ -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
g++ -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
In file included from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/resolve.hpp:26,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/push.hpp:24,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/stream_buffer.hpp:22,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/iostreams/stream.hpp:21,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi/stream.hpp:15,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/home/qi.hpp:30,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/BH/include/boost/spirit/include/qi.hpp:16,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_def.hpp:4,
                 from /home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/StanHeaders/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp:1,
                 from lang__grammars__bare_type_grammar_inst.cpp:18:
/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
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")

[...]                                                                               ^
                                                                                    ^
g++: internal compiler error: Killed (program cc1plus)
0x409a70 execute
    ../../gcc/gcc.c:2823
0x409da4 do_spec_1
    ../../gcc/gcc.c:4615
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
0x40acc7 do_spec_1
    ../../gcc/gcc.c:5269
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
0x40acc7 do_spec_1
    ../../gcc/gcc.c:5269
0x40a9bf do_spec_1
    ../../gcc/gcc.c:5374
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
0x40acc7 do_spec_1
    ../../gcc/gcc.c:5269
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
0x40acc7 do_spec_1
    ../../gcc/gcc.c:5269
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
0x40acc7 do_spec_1
    ../../gcc/gcc.c:5269
0x40c725 process_brace_body
    ../../gcc/gcc.c:5872
0x40c725 handle_braces
    ../../gcc/gcc.c:5786
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <http://gcc.gnu.org/bugs.html> for instructions.
make: *** [lang__grammars__statement_grammar_inst.o] Error 4
ERROR: compilation failed for package ‘rstan’
* removing ‘/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/rstan’
* restoring previous ‘/home/p230198/R/x86_64-unknown-linux-gnu-library/3.1/rstan’

The downloaded source packages are in
    ‘/tmp/RtmpxeZByE/downloaded_packages’
Warning message:
In install.packages("rstan") :
  installation of package ‘rstan’ had non-zero exit status
@richelbilderbeek
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The errors indicate that there is not enough memory. Perhaps a batch script will work?

@richelbilderbeek
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Uploaded bash script in install_rstan. See README.md there

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