search

stan-dev / rstan

RStan, the R interface to Stan
https://mc-stan.org
1.04k stars 267 forks source link

unable install rstan and shinystan #754

Open jkylearmstrong opened 4 years ago

jkylearmstrong commented 4 years ago 
> 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
SimonShamusRiley commented 4 years ago

I was facing the exact same issue; thought it was related to a "Transition Period" and tried rolling-back to various archived versions of StanHeaders before finally solving it simply by removing r-cran-stan and r-cran-stanheaders in the terminal and then following these instructions exactly: