installation error for rstan 2.18.2 on centos cluster
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Description
Summary:
Installation fails with compilation error in rstan.
Description:
Please see Current Output below, and please let me know if you need more info, thanks.
Reproducible Steps:
$ cat ~/.R/Makevars
CXX14FLAGS = -O3 -march=native -mtune=native -fPIC -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION\
-I $(MKLROOT)/include -DEIGEN_USE_MKL_ALL
LDLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64
LDLIBS += -lmkl_core -lmkl_sequential -lpthread -lm
CXX14 = icc -std=c++1y
$ module list
Currently Loaded Modulefiles:
1) slurm/14.03.0 5) zlib/1.2.8 9) R/3.4.1-intel
2) idev 6) bzip2/1.0.6 10) gcc/4.9.4
3) bbcp/amd64_rhel60 7) xz/5.2.2
4) intel-psxe/2015-update1(default) 8) pcre/8.39
$ time Rscript -e 'install.packages("rstan", repos="https://cloud.r-project.org/", dependencies = TRUE)' 2>&1 | tee rstan-install-log
Current Output:
<snip>
* DONE (rstudioapi)
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
icc -std=c++1y -I/share/apps/R/3.4.1-intel/lib64/R/include -DNDEBUG -I"../inst/include" -I"`"/share/apps/R/3.4.1-intel/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/lustre/project/<user>/R/Library/3.4/Rcpp/include" -I"/lustre/project/<user>/R/Library/3.4/RcppEigen/include" -I"/lustre/project/<user>/R/Library/3.4/BH/include" -I"/lustre/project/<user>/R/Library/3.4/StanHeaders/include" -I/usr/local/include -O3 -march=native -mtune=native -fPIC -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I /share/apps/intel_parallel_studio_xe/2015_update1/composer_xe_2015.1.133/mkl/include -DEIGEN_USE_MKL_ALL -c chains.cpp -o chains.o
In file included from /lustre/project/<user>/R/Library/3.4/BH/include/boost/utility.hpp(22),
from /lustre/project/<user>/R/Library/3.4/BH/include/boost/range/size.hpp(25),
from /lustre/project/<user>/R/Library/3.4/BH/include/boost/range/functions.hpp(20),
from /lustre/project/<user>/R/Library/3.4/BH/include/boost/range/iterator_range_core.hpp(38),
from /lustre/project/<user>/R/Library/3.4/BH/include/boost/lexical_cast.hpp(30),
from chains.cpp(28):
/lustre/project/<user>/R/Library/3.4/BH/include/boost/core/noncopyable.hpp(42): error: defaulted default constructor cannot be constexpr because the corresponding implicitly declared default constructor would not be constexpr
BOOST_CONSTEXPR noncopyable() = default;
^
/lustre/project/<user>/R/Library/3.4/BH/include/boost/pending/integer_log2.hpp(7): note: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
compilation aborted for chains.cpp (code 2)
make: *** [chains.o] Error 2
ERROR: compilation failed for package ‘rstan’
<snip>
Expected Output:
No error.
RStan Version:
2.18.2
R Version:
(3.4.1 compiled with Intel MKL)
$ Rscript -e "R.version"
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 4.1
year 2017
month 06
day 30
svn rev 72865
language R
version.string R version 3.4.1 (2017-06-30)
nickname Single Candle
Operating System:
$ cat /etc/centos-release
CentOS release 6.5 (Final)
Best,
CB
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the ~/.R/Makevars settings, loaded module list, and the Rscript installation command, then inspect the reported Boost compiler error for rstan 2.18.2 on CentOS 6.5. Done means the package installs without the compilation failure in the shown environment.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- centos, r
- Domain
- build-system, operating-systems
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100