stan-dev / stan-dev/rstanarm

Missing dependencies for 2.17.4

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Description

Summary:

It seems rstanarm lacks some dependencies needed at run-time.

Description:

In RStudio rstanarm is installed successfully.
However, when the package is loaded, it reports that some packages are still missing (later, nloptr).

Reproducible Steps:
> install.packages('rstanarm')
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rstanarm_2.17.4.zip'
Content type 'application/zip' length 9670934 bytes (9.2 MB)
downloaded 9.2 MB

package ‘rstanarm’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Lorenzo\AppData\Local\Temp\RtmpWq9dLt\downloaded_packages
> library(rstanarm)
Loading required package: Rcpp
Error: package or namespace load failed for ‘rstanarm’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘later’
> install.packages('later')
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/later_0.7.5.zip'
Content type 'application/zip' length 617798 bytes (603 KB)
downloaded 603 KB

package ‘later’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Lorenzo\AppData\Local\Temp\RtmpWq9dLt\downloaded_packages
> library(rstanarm)
Error: package or namespace load failed for ‘rstanarm’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘nloptr’
> install.packages('nloptr')
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/nloptr_1.2.1.zip'
Content type 'application/zip' length 1071323 bytes (1.0 MB)
downloaded 1.0 MB

package ‘nloptr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Lorenzo\AppData\Local\Temp\RtmpWq9dLt\downloaded_packages
> library(rstanarm)
rstanarm (Version 2.17.4, packaged: 2018-04-13 01:51:52 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().
RStanARM Version:

2.17.4

R Version:

3.5.1

Output of sessionInfo:
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252    LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                  
[5] LC_TIME=Italian_Italy.1252    

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

other attached packages:
[1] rstanarm_2.17.4 later_0.7.5     Rcpp_0.12.18   

loaded via a namespace (and not attached):
 [1] lattice_0.20-35    zoo_1.8-4          gtools_3.8.1       assertthat_0.2.0   digest_0.6.17      packrat_0.4.9-3    mime_0.5          
 [8] R6_2.2.2           plyr_1.8.4         ggridges_0.5.0     stats4_3.5.1       ggplot2_3.0.0      colourpicker_1.0   pillar_1.3.0      
[15] rlang_0.2.2        lazyeval_0.2.1     minqa_1.2.4        rstudioapi_0.7     miniUI_0.1.1.1     nloptr_1.2.1       Matrix_1.2-14     
[22] DT_0.4             shinythemes_1.1.1  splines_3.5.1      shinyjs_1.0        lme4_1.1-18-1      stringr_1.3.1      loo_2.0.0         
[29] htmlwidgets_1.2    igraph_1.2.2       munsell_0.5.0      shiny_1.1.0        compiler_3.5.1     httpuv_1.4.5       rstan_2.17.3      
[36] pkgconfig_2.0.2    base64enc_0.1-3    rstantools_1.5.1   htmltools_0.3.6    tidyselect_0.2.4   tibble_1.4.2       gridExtra_2.3     
[43] codetools_0.2-15   matrixStats_0.54.0 threejs_0.3.1      crayon_1.3.4       dplyr_0.7.6        MASS_7.3-50        grid_3.5.1        
[50] nlme_3.1-137       xtable_1.8-3       gtable_0.2.0       magrittr_1.5       StanHeaders_2.17.2 scales_1.0.0       stringi_1.2.4     
[57] reshape2_1.4.3     promises_1.0.1     bindrcpp_0.2.2     dygraphs_1.1.1.6   xts_0.11-1         tools_3.5.1        glue_1.3.0        
[64] shinystan_2.5.0    markdown_0.8       purrr_0.2.5        crosstalk_1.0.0    survival_2.42-6    parallel_3.5.1     rsconnect_0.8.9   
[71] inline_0.3.15      colorspace_1.3-2   bayesplot_1.6.0    bindr_0.1.1

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First steps

  1. Read the whole issue, then the project's contributing guide.
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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the reported installation and loading sequence for rstanarm 2.17.4 on R 3.5.1, checking the package's declared runtime dependencies against the missing later and nloptr packages. The issue is done when a fresh installation can load rstanarm without requiring those packages to be installed manually.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
tooling
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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