stan-dev / stan-dev/rstan

unable install rstan and shinystan

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Description

> install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)
Installing package into ‘/home/cdsw/R’
(as ‘lib’ is unspecified)
also installing the dependency ‘shinystan’

trying URL 'https://cloud.r-project.org/src/contrib/shinystan_2.5.0.tar.gz'
Content type 'application/x-gzip' length 2400413 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/rstan_2.19.3.tar.gz'
Content type 'application/x-gzip' length 922337 bytes (900 KB)
==================================================
downloaded 900 KB

g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"." -I"/home/cdsw/R/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/cdsw/R/Rcpp/include" -I"/home/cdsw/R/RcppEigen/include" -I"/home/cdsw/R/BH/include" -I"/home/cdsw/R/StanHeaders/include" -I/usr/local/include   -fpic  -g -O2 -c chains.cpp -o chains.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"." -I"/home/cdsw/R/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/cdsw/R/Rcpp/include" -I"/home/cdsw/R/RcppEigen/include" -I"/home/cdsw/R/BH/include" -I"/home/cdsw/R/StanHeaders/include" -I/usr/local/include   -fpic  -g -O2 -c pointer-tools.cpp -o pointer-tools.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"." -I"/home/cdsw/R/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/cdsw/R/Rcpp/include" -I"/home/cdsw/R/RcppEigen/include" -I"/home/cdsw/R/BH/include" -I"/home/cdsw/R/StanHeaders/include" -I/usr/local/include   -fpic  -g -O2 -c init.cpp -o init.o
g++ -std=gnu++14 -I"/usr/local/lib/R/include" -DNDEBUG -I"../inst/include" -I"." -I"/home/cdsw/R/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -I"/home/cdsw/R/Rcpp/include" -I"/home/cdsw/R/RcppEigen/include" -I"/home/cdsw/R/BH/include" -I"/home/cdsw/R/StanHeaders/include" -I/usr/local/include   -fpic  -g -O2 -c stanc.cpp -o stanc.o
/usr/local/lib/R/etc/Makeconf:168: recipe for target 'stanc.o' failed
Warning in install.packages :
  installation of package ‘rstan’ had non-zero exit status
Warning in install.packages :
  installation of package ‘shinystan’ had non-zero exit status
> sessionInfo()
R version 3.5.1 (--)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bayesplot_1.7.1   EnvStats_2.3.1    gdata_2.18.0      lubridate_1.7.4   data.table_1.12.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        git2r_0.26.1      pillar_1.4.2      compiler_3.5.1    plyr_1.8.4        remotes_2.1.0    
 [7] prettyunits_1.0.2 tools_3.5.1       packrat_0.5.0     pkgload_1.0.2     digest_0.6.19     pkgbuild_1.0.3   
[13] memoise_1.1.0     tibble_2.1.3      gtable_0.3.0      pkgconfig_2.0.2   rlang_0.4.0       cli_1.1.0        
[19] rstudioapi_0.10   curl_3.3          parallel_3.5.1    withr_2.1.2       dplyr_0.8.2       stringr_1.4.0    
[25] fs_1.3.1          desc_1.2.0        gtools_3.8.2      devtools_2.0.2    rprojroot_1.3-2   grid_3.5.1       
[31] tidyselect_0.2.5  glue_1.3.1        R6_2.4.0          processx_3.3.1    sessioninfo_1.1.1 ggplot2_3.2.0    
[37] purrr_0.3.2       callr_3.2.0       magrittr_1.5      usethis_1.5.0     backports_1.1.4   ps_1.3.0         
[43] scales_1.0.0      ggridges_0.5.2    assertthat_0.2.1  colorspace_1.4-1  stringi_1.4.3     lazyeval_0.2.2   
[49] munsell_0.5.0     crayon_1.3.4     

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE) command and review the compiler output alongside sessionInfo(). The issue provides no source file, test, or complete compiler error; done would mean that both rstan and shinystan install successfully in the reported R 3.5.1 and Ubuntu 16.04 environment.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp, r
Domain
build-system
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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