Hi,
I’ve recently upgraded my MacOS, and consequently some other software too - such as the xtools command line compiler stuff.
I am now having problems with RStan (I have previously had a functioning installation), although since I am not currently a daily user of RStan I cannot state that the problem followed the OS upgrades.
I have tried uninstalling RStan and reinstalling as per the github getting started page, having read about similar issues on this forum. And simplified my .R/Makevars file.
But when I run stan.mod <- stan_model('p1_p2_o.stan'), I am getting:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from filef6bf407f62b.cpp:8:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
In file included from /Users/lfslbx/Library/R/3.5/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:8:
In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86:
/usr/local/clang4/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found
#include_next <stdlib.h>
^~~~~~~~~~
1 error generated.
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB filef6bf407f62b.cpp 2> filef6bf407f62b.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection
Any suggestions welcomed.
The standard information follows…
Operating system: MacOS 10.14.1 (Mojave)
RStan version: 2.18.2
Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
# The following statements are required to use the clang4 binary
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX1X=/usr/local/clang4/bin/clang++
CXX98=/usr/local/clang4/bin/clang++
CXX11=/usr/local/clang4/bin/clang++
CXX14=/usr/local/clang4/bin/clang++
CXX17=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
# End clang4 inclusion statements
# The following statement changes the Fortran linking path
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0
# End Fortran linking path statement
Output of devtools::session_info("rstan")
Session info ------------------------------------------------------------------
setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_GB.UTF-8
tz Europe/London
date 2018-11-27
Packages ----------------------------------------------------------------------
package * version date source
assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
backports 1.1.2 2017-12-13 CRAN (R 3.5.0)
BH 1.66.0-1 2018-02-13 CRAN (R 3.5.0)
callr 2.0.4 2018-05-15 CRAN (R 3.5.0)
cli 1.0.0 2017-11-05 CRAN (R 3.5.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
compiler 3.5.1 2018-07-05 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
desc 1.2.0 2018-05-01 CRAN (R 3.5.0)
dichromat 2.0-0 2013-01-24 CRAN (R 3.5.0)
digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
ggplot2 * 3.0.0 2018-07-03 CRAN (R 3.5.0)
glue 1.2.0 2017-10-29 CRAN (R 3.5.0)
graphics * 3.5.1 2018-07-05 local
grDevices * 3.5.1 2018-07-05 local
grid 3.5.1 2018-07-05 local
gridExtra 2.3 2017-09-09 CRAN (R 3.5.0)
gtable 0.2.0 2016-02-26 CRAN (R 3.5.0)
inline 0.3.15 2018-05-18 CRAN (R 3.5.0)
labeling 0.3 2014-08-23 CRAN (R 3.5.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.5.1)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.5.0)
loo 2.0.0 2018-04-11 CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
MASS 7.3-50 2018-04-30 CRAN (R 3.5.1)
Matrix 1.2-14 2018-04-13 CRAN (R 3.5.1)
matrixStats 0.53.1 2018-02-11 CRAN (R 3.5.0)
methods * 3.5.1 2018-07-05 local
mgcv 1.8-24 2018-06-23 CRAN (R 3.5.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.5.0)
nlme 3.1-137 2018-04-07 CRAN (R 3.5.1)
parallel 3.5.1 2018-07-05 local
pillar 1.2.2 2018-04-26 CRAN (R 3.5.0)
pkgbuild 1.0.2 2018-10-16 CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
praise 1.0.0 2015-08-11 CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.5.0)
processx 3.1.0 2018-05-15 CRAN (R 3.5.0)
R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.5.0)
Rcpp 0.12.17 2018-05-18 CRAN (R 3.5.0)
RcppEigen 0.3.3.4.0 2018-02-07 CRAN (R 3.5.0)
reshape2 1.4.3 2017-12-11 CRAN (R 3.5.0)
rlang 0.2.0 2018-02-20 CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
rstan * 2.18.2 2018-11-07 CRAN (R 3.5.0)
scales 0.5.0 2017-08-24 CRAN (R 3.5.0)
StanHeaders * 2.18.0 2018-10-07 CRAN (R 3.5.0)
stats * 3.5.1 2018-07-05 local
stats4 3.5.1 2018-07-05 local
stringi 1.2.2 2018-05-02 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
testthat 2.0.0 2017-12-13 CRAN (R 3.5.0)
tibble 1.4.2 2018-01-22 CRAN (R 3.5.0)
tools 3.5.1 2018-07-05 local
utf8 1.1.3 2018-01-03 CRAN (R 3.5.0)
utils * 3.5.1 2018-07-05 local
viridisLite 0.3.0 2018-02-01 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)