Missing dependencies for 2.17.4
Open
Nobody has claimed this yet.
- Dominant language
- R
- Stars
- 401
- Forks
- 136
- PR merge metrics
- No merged PRs in 30d
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
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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