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Failed when install packages rstan #304

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sproblvem opened this issue Jun 24, 2016 · 3 comments
Closed

Failed when install packages rstan #304

sproblvem opened this issue Jun 24, 2016 · 3 comments

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@sproblvem
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sproblvem commented Jun 24, 2016 •
edited

Summary:

Try to install rstan on Kubuntu 16.04 but failed, following the official guide step by step.

Description:

I follow this guide try to install rstan on my Kubuntu 16.04.
install R

sudo apt-get install r-base

configure
my g++ version is -

g++ (Ubuntu 5.3.1-14ubuntu2.1) 5.3.1 20160413
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

so I use the following configuration

cat("\nCXXFLAGS+=-flto -ffat-lto-objects -Wno-unused-local-typedefs",
file = M, sep = "\n", append = TRUE)

install package

First I tryied

install.packages('rstan', repos = 'https://cloud.r-project.org/', dependencies = TRUE)

It failed, but not because of https
then I try

install.packages("rstan", type = "source")

It also failed

Current Output:

In file included from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/push.hpp:24,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/stream.hpp:21,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi.hpp:30,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/include/qi.hpp:16,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar.hpp:4,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar_def.hpp:4,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar_inst.cpp:1,
from lang__grammars__whitespace_grammar_inst.cpp:19:
/home/yama/R/x86_64-pc-linux-gnu-library/3.2/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 /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/resolve.hpp:26,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/push.hpp:24,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/detail/streambuf/indirect_streambuf.hpp:31,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/stream_buffer.hpp:22,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/iostreams/stream.hpp:21,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream/detail/iterator_source.hpp:14,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream/stream.hpp:16,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi/stream.hpp:15,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/home/qi.hpp:30,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/BH/include/boost/spirit/include/qi.hpp:16,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar.hpp:4,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar_def.hpp:4,
from /home/yama/R/x86_64-pc-linux-gnu-library/3.2/StanHeaders/include/src/stan/lang/grammars/whitespace_grammar_inst.cpp:1,
from lang__grammars__whitespace_grammar_inst.cpp:19:
/home/yama/R/x86_64-pc-linux-gnu-library/3.2/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")

                                                                                ^

/usr/lib/R/etc/Makeconf:143: recipe for target 'lang__grammars__term_grammar_inst.o' failed
make: *** [lang__grammars__term_grammar_inst.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘rstan’

  • removing ‘/home/yama/R/x86_64-pc-linux-gnu-library/3.2/rstan’

The downloaded source packages are in
‘/tmp/Rtmp8IyAj8/downloaded_packages’
Warning message:
In install.packages("rstan", type = "source") :
installation of package ‘rstan’ had non-zero exit status

R Version:

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

Operating System:

Linux nuc 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
@bgoodri
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bgoodri commented Jun 24, 2016

This was most likely just a temporary thing due to StanHeaders being ahead of rstan on CRAN. You can install rstan now if you use a mirror that has version 2.10.1.

@sproblvem
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Hi bgoodri, thank you for your reply!
But I am a newbie of R and stan, I am not very understand your solution.
How to set the mirror which has version 2.10.1?
add a version option in "install.packages("rstan", type = "source")"？
Thank you!

@bgoodri
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bgoodri commented Jun 25, 2016

install.packages("rstan", repos = "https://cran.r-project.org",
dependencies = TRUE)

should do it.

Closes #304

On Sat, Jun 25, 2016 at 2:05 AM, sproblvem notifications@github.com wrote:

Hi bgoodri, thank you for your reply!
But I am a newbie of R and stan, I am not very understand your solution.
How to set the mirror which has version 2.10.1?
add a version option in "install.packages("rstan", type = "source")"？
Thank you!

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@bgoodri bgoodri closed this as completed Jun 27, 2016
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