trouble installing rstan 2.14.1 on Yosemite

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Blaine Mooers

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Mar 8, 2017, 9:21:38 PM3/8/17

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Last fall in succeded in installing rstan from R run from the command line on MacOS Yosemite.

I cannot upgrade to versoin 2.14.1 from 2.12.1.

I have followed the install instructions on the rstan github site.

I currently have the R packages saved my local Library folder.

more .R/Makevars

# created by rstan at Sat May 2 15:36:03 2015

CFLAGS=-g -O -mtune=native

FFLAGS=-g -O -mtune=native

FCFLAGS=-g -O -mtune=native

CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function

CXXFLAGS+=-flto -Wno-unused-local-typedefs

CC=clang

CXX=clang++ -arch x86_64 -ftemplate-depth-256

I have uninstalled gcc48 and R.

I switched to gcc49.

I have reinstalled R (3.3.2).

I still get the same final error messages.

I am stumped.

I have not found similar posts.

> install.packages("rstan", lib="/Users/blaine-mooers/Library/R/3.3/library/rstan/libs", dependencies=TRUE)

trying URL 'https://cran.rstudio.com/src/contrib/rstan_2.14.1.tar.gz'

Content type 'application/x-gzip' length 743652 bytes (726 KB)

==================================================

downloaded 726 KB

* installing *source* package ‘rstan’ ...

** package ‘rstan’ successfully unpacked and MD5 sums checked

** libs

clang++ -arch x86_64 -ftemplate-depth-256 -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/opt/local/Library/Frameworks/R.framework/Resources/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/opt/local/include -I"/Users/blaine-mooers/Library/R/3.3/library/Rcpp/include" -I"/Users/blaine-mooers/Library/R/3.3/library/RcppEigen/include" -I"/Users/blaine-mooers/Library/R/3.3/library/BH/include" -I"/Users/blaine-mooers/Library/R/3.3/library/StanHeaders/include" -fPIC -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -Wno-unused-local-typedefs -c chains.cpp -o chains.o

In file included from chains.cpp:26:

In file included from /opt/local/include/boost/accumulators/statistics/stats.hpp:14:

In file included from /opt/local/include/boost/accumulators/statistics_fwd.hpp:12:

/opt/local/include/boost/mpl/print.hpp:50:19: warning: in-class initialization of non-static data member is a C++11 extension [-Wc++11-extensions]

const int m_x = 1 / (sizeof(T) - sizeof(T));

1 warning generated.

clang++ -arch x86_64 -ftemplate-depth-256 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -o rstan.so chains.o init.o lang__ast_def.o lang__grammars__bare_type_grammar_inst.o lang__grammars__expression07_grammar_inst.o lang__grammars__expression_grammar_inst.o lang__grammars__functions_grammar_inst.o lang__grammars__indexes_grammar_inst.o lang__grammars__program_grammar_inst.o lang__grammars__semantic_actions.o lang__grammars__statement_2_grammar_inst.o lang__grammars__statement_grammar_inst.o lang__grammars__term_grammar_inst.o lang__grammars__var_deccls_grammar_inst.o lang__grammars__whitespace_grammar_inst.o misc.o sparse_extractors.o stanc.o -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

installing to /Users/blaine-mooers/Library/R/3.3/library/rstan/libs/rstan/libs

** R

** inst

** preparing package for lazy loading

Error in setMethod("traceplot", signature = "stanfit", function(object, :

no existing definition for function ‘traceplot’

Error : unable to load R code in package ‘rstan’

ERROR: lazy loading failed for package ‘rstan’

* removing ‘/Users/blaine-mooers/Library/R/3.3/library/rstan/libs/rstan’

Warning in install.packages :

installation of package ‘rstan’ had non-zero exit status

The downloaded source packages are in

‘/private/var/folders/v0/1cx4cd192j51cs1qs_v3hbjm0000gn/T/RtmpmSXhaJ/downloaded_packages’

Ben Goodrich

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Mar 8, 2017, 9:49:08 PM3/8/17

to Stan users mailing list

On Wednesday, March 8, 2017 at 9:21:38 PM UTC-5, Blaine Mooers wrote:

** preparing package for lazy loading
Error in setMethod("traceplot", signature = "stanfit", function(object, :
no existing definition for function ‘traceplot’
Error : unable to load R code in package ‘rstan’
ERROR: lazy loading failed for package ‘rstan’
* removing ‘/Users/blaine-mooers/Library/R/3.3/library/rstan/libs/rstan’
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status

My guess is that you have some other package loaded that exports a traceplot() function. In

https://github.com/stan-dev/rstan/blob/develop/rstan/rstan/R/stanfit-class.R#L592

it tests whether there is a S4 generic function called traceplot before creating one.

If you start R with the --vanilla option, installation of rstan may work (although you should be able to install the binary version from CRAN rather than building from source).

Ben

Blaine Mooers

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Mar 9, 2017, 12:13:39 AM3/9/17

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Thank you Ben for the suggestions!

I deleted everything in .Rprofile. I get the same error message in Rstudio when I try to install rstan from cran.

When I use R --vanilla on the command line, the installation quits much sooner and delivers a new message:

> install.packages('rstan')

Installing package into ‘/Users/blaine-mooers/Library/R/3.3/library’

(as ‘lib’ is unspecified)

--- Please select a CRAN mirror for use in this session ---

HTTPS CRAN mirror

1: 0-Cloud [https] 2: Algeria [https]

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Selection: 54

trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/rstan_2.14.1.tar.gz'

Content type 'application/x-gzip' length 743652 bytes (726 KB)

==================================================

downloaded 726 KB

* installing *source* package ‘rstan’ ...

** package ‘rstan’ successfully unpacked and MD5 sums checked

** libs

Rscript execution error: No such file or directory

In file included from chains.cpp:26:

In file included from /opt/local/include/boost/accumulators/statistics/stats.hpp:14:

In file included from /opt/local/include/boost/accumulators/statistics_fwd.hpp:12:

/opt/local/include/boost/mpl/print.hpp:50:19: warning: in-class initialization of non-static data member is a C++11 extension

[-Wc++11-extensions]

const int m_x = 1 / (sizeof(T) - sizeof(T));

1 warning generated.

Rscript execution error: No such file or directory

lang__ast_def.cpp:18:10: fatal error: 'stan/lang/ast_def.cpp' file not found

#include <stan/lang/ast_def.cpp>

1 error generated.

make: *** [lang__ast_def.o] Error 1

ERROR: compilation failed for package ‘rstan’

* removing ‘/Users/blaine-mooers/Library/R/3.3/library/rstan’

* restoring previous ‘/Users/blaine-mooers/Library/R/3.3/library/rstan’

The downloaded source packages are in

‘/private/var/folders/v0/1cx4cd192j51cs1qs_v3hbjm0000gn/T/Rtmpr70mag/downloaded_packages’

Warning message:

In install.packages("rstan") :

installation of package ‘rstan’ had non-zero exit status

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********************************************************
Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Letter address:                    Shipping address:
P.O. Box 26901, BRC 466      975 NE 10th Street, BRC 466
Oklahoma City, OK 73190     Oklahoma City, OK 73104-5419

office: (405) 271-8300   lab: (405) 271-8313 fax: (405) 271-3910
e-mail: blaine...@ouhsc.edu

(or bmoo...@gmail.com)
http://www.oumedicine.com/body.cfm?id=3877&oTopID=3877

Blaine Mooers

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Mar 10, 2017, 8:41:26 PM3/10/17

to Stan users mailing list

I deleted the \url{./Library/R/3.3} and forced install of rstan and its dependences into the macports library while using sudo
\url{/opt/local/Library/Frameworks/R.framework/Versions/3.3/Resources/library}. Perhaps the presence of two libraries was causing trouble.

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