Compilation error with latest CRAN packages (and R 3.5.2)
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Description
Summary:
Compilation error with a test execution of rstan after successful package installation.
Description:
Initially discovered when installing prophet (see https://github.com/facebook/prophet/issues/1027) with a new host. Installations on previous versions of packages was successful, but the latest version fails.
Reproducible Steps:
With R 3.5.2-2 (Enterprise Linux 7 package) on CentOS 7
install.packages('rstan')
library('rstan')
model_code <- 'parameters {real y;} model {y ~ normal(0,1);}'
fit <- stan(model_code=model_code)
mean(extract(fit)$y)
Current Output:
> library('rstan')
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
> model_code <- 'parameters {real y;} model {y ~ normal(0,1);}'
> fit <- stan(model_code=model_code)
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /usr/lib64/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from /usr/lib64/R/library/BH/include/boost/random/detail/int_float_pair.hpp:26,
from /usr/lib64/R/library/BH/include/boost/random/exponential_distribution.hpp:27,
from /usr/lib64/R/library/BH/include/boost/random/gamma_distribution.hpp:25,
from /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5,
from /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat.hpp:292,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /usr/lib64/R/library/StanHeaders/include/stan/math.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file1316ae24e3.cpp:8:
/usr/lib64/R/library/BH/include/boost/
In addition: Warning message:
In system(cmd, intern = !verbose) :
running command '/usr/lib64/R/bin/R CMD SHLIB file1316ae24e3.cpp 2> file1316ae24e3.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection
>
Expected Output:
Proper calculation of mean value (should be close to 0)
RStan Version:
2.18.2
R Version:
3.5.2
Operating System:
CentOS 7
Extra info
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.18.2 StanHeaders_2.18.1-10 ggplot2_3.2.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 magrittr_1.5 munsell_0.5.0 colorspace_1.4-1
[5] R6_2.4.0 rlang_0.3.4 tools_3.5.2 parallel_3.5.2
[9] pkgbuild_1.0.3 grid_3.5.2 gtable_0.3.0 loo_2.1.0
[13] cli_1.1.0 withr_2.1.2 matrixStats_0.54.0 lazyeval_0.2.2
[17] assertthat_0.2.1 tibble_2.1.3 crayon_1.3.4 processx_3.3.1
[21] gridExtra_2.3 callr_3.2.0 ps_1.3.0 inline_0.3.15
[25] compiler_3.5.2 pillar_1.4.1 scales_1.0.0 prettyunits_1.0.2
[29] stats4_3.5.2 pkgconfig_2.0.2
>
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Research direction
Reproduce the reported sequence with R 3.5.2 on CentOS 7: install.packages('rstan'), load rstan, and call stan() with the supplied model code. Inspect the compileCode and R CMD SHLIB error output, then verify the fix by confirming that mean(extract(fit)$y) completes and is close to 0.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- build-system
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100