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stan-dev / shinystan

shinystan R package and ShinyStan GUI
https://mc-stan.org/shinystan
GNU General Public License v3.0
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segmentation fault #149

Closed tjmahr closed 4 years ago

tjmahr commented 7 years ago

I run the following from the command line:

Rscript -e "library(shinystan);devtools::session_info();launch_shinystan_demo()" --vanilla &> test.txt

I click on diagnostics. Window goes dim because of a shiny disconnect, and the command line session prints Segmentation fault and stops.

This is what gets printed to the text file.

Loading required package: shiny
Loading required package: methods

This is shinystan version 2.3.0

Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.0 (2017-04-21)
 system   x86_64, mingw32             
 ui       RTerm                       
 language (EN)                        
 collate  English_United States.1252  
 tz       America/Chicago             
 date     2017-05-22                  

Packages ----------------------------------------------------------------------
 package      * version  date       source        
 assertthat     0.2.0    2017-04-11 CRAN (R 3.3.3)
 base         * 3.4.0    2017-04-21 local         
 base64enc      0.1-3    2015-07-28 CRAN (R 3.2.3)
 bayesplot      1.2.0    2017-04-12 CRAN (R 3.3.3)
 colorspace     1.3-2    2016-12-14 CRAN (R 3.3.2)
 colourpicker   0.3      2016-12-05 CRAN (R 3.3.2)
 compiler       3.4.0    2017-04-21 local         
 datasets     * 3.4.0    2017-04-21 local         
 DBI            0.6-1    2017-04-01 CRAN (R 3.3.3)
 devtools       1.13.1   2017-05-13 CRAN (R 3.4.0)
 digest         0.6.12   2017-01-27 CRAN (R 3.3.2)
 dplyr          0.5.0    2016-06-24 CRAN (R 3.3.2)
 DT             0.2      2016-08-09 CRAN (R 3.2.5)
 dygraphs       1.1.1.4  2017-01-04 CRAN (R 3.3.2)
 ggplot2        2.2.1    2016-12-30 CRAN (R 3.4.0)
 graphics     * 3.4.0    2017-04-21 local         
 grDevices    * 3.4.0    2017-04-21 local         
 grid           3.4.0    2017-04-21 local         
 gridExtra      2.2.1    2016-02-29 CRAN (R 3.2.3)
 gtable         0.2.0    2016-02-26 CRAN (R 3.2.3)
 gtools         3.5.0    2015-05-29 CRAN (R 3.2.2)
 htmltools      0.3.6    2017-04-28 CRAN (R 3.4.0)
 htmlwidgets    0.8      2016-11-09 CRAN (R 3.3.2)
 httpuv         1.3.3    2015-08-04 CRAN (R 3.2.3)
 inline         0.3.14   2015-04-13 CRAN (R 3.2.3)
 jsonlite       1.4      2017-04-08 CRAN (R 3.3.3)
 lattice        0.20-35  2017-03-25 CRAN (R 3.4.0)
 lazyeval       0.2.0    2016-06-12 CRAN (R 3.2.5)
 magrittr       1.5      2014-11-22 CRAN (R 3.2.2)
 markdown       0.8      2017-04-20 CRAN (R 3.4.0)
 Matrix         1.2-10   2017-04-28 CRAN (R 3.4.0)
 memoise        1.1.0    2017-04-21 CRAN (R 3.4.0)
 methods      * 3.4.0    2017-04-21 local         
 mime           0.5      2016-07-07 CRAN (R 3.2.5)
 miniUI         0.1.1    2016-01-15 CRAN (R 3.2.4)
 munsell        0.4.3    2016-02-13 CRAN (R 3.2.3)
 plyr           1.8.4    2016-06-08 CRAN (R 3.2.5)
 R6             2.2.1    2017-05-10 CRAN (R 3.4.0)
 Rcpp           0.12.10  2017-03-19 CRAN (R 3.4.0)
 reshape2       1.4.2    2016-10-22 CRAN (R 3.3.1)
 rlang          0.1.1    2017-05-18 CRAN (R 3.4.0)
 rsconnect      0.8      2017-05-08 CRAN (R 3.4.0)
 rstan          2.15.1   2017-04-19 CRAN (R 3.4.0)
 scales         0.4.1    2016-11-09 CRAN (R 3.3.2)
 shiny        * 1.0.3    2017-04-26 CRAN (R 3.4.0)
 shinyjs        0.9      2016-12-26 CRAN (R 3.3.2)
 shinystan    * 2.3.0    2017-02-01 CRAN (R 3.3.2)
 shinythemes    1.1.1    2016-10-12 CRAN (R 3.3.1)
 StanHeaders    2.15.0-1 2017-04-19 CRAN (R 3.4.0)
 stats        * 3.4.0    2017-04-21 local         
 stats4         3.4.0    2017-04-21 local         
 stringi        1.1.5    2017-04-07 CRAN (R 3.3.3)
 stringr        1.2.0    2017-02-18 CRAN (R 3.3.3)
 threejs        0.2.2    2016-04-01 CRAN (R 3.2.4)
 tibble         1.3.1    2017-05-17 CRAN (R 3.4.0)
 tools          3.4.0    2017-04-21 local         
 utils        * 3.4.0    2017-04-21 local         
 withr          1.0.2    2016-06-20 CRAN (R 3.2.5)
 xtable         1.8-2    2016-02-05 CRAN (R 3.2.3)
 xts            0.9-7    2014-01-02 CRAN (R 3.2.3)
 zoo            1.8-0    2017-04-12 CRAN (R 3.4.0)

Listening on http://127.0.0.1:5081

Edit: Updated so that command uses --vanilla flag for maximum reproducibility.

jgabry commented 7 years ago

Thanks for reporting this. I can't replicate this segfault on my Mac, so I wonder if this is platform specific (looks like you're on Windows). Does this only happen for you when you run it through the command line?

tjmahr commented 7 years ago

Yup, Windows 10.

I first got the problem in RStudio, but in that case, I would see RStudio session-crash window with the bomb, so I decided to test it on the command line to rule out RStudio.

I also tried again after reinstalling rstan, rstanarm, rstantools, and shinystan (edit: and bayesplot) from CRAN (just in case I had accidentally compiled the binaries myself during the last update). Still no luck.

jgabry commented 7 years ago

Ok hmm, gonna need to get one of the devs with Windows to see if they can reproduce this.

@bgoodri when you have a sec can you see if you can reproduce this on your Windows machine?

On Mon, May 22, 2017 at 12:05 PM TJ Mahr notifications@github.com wrote:

Yup, Windows 10.

I first got the problem in RStudio, but in that case, I would see RStudio session-crash window with the bomb, so I decided to test it on the command line to rule out RStudio.

I also tried again after reinstalling rstan, rstanarm, rstantools, and shinystan from CRAN (just in case I had accidentally compiled the binaries myself during the last update). Still no luck.

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tjmahr commented 7 years ago

It works fine on my Windows 7 machine (of course :confused:). I'll have to try it on my other Windows 10 machine. later.

``` devtools::session_info() Session info -------------------------------------------------------------------------------------------------------------------- setting value version R version 3.4.0 (2017-04-21) system x86_64, mingw32 ui RStudio (1.0.143) language (EN) collate English_United States.1252 tz America/Chicago date 2017-05-22 Packages ------------------------------------------------------------------------------------------------------------------------ package * version date source assertthat 0.2.0 2017-04-11 CRAN (R 3.3.2) base * 3.4.0 2017-04-21 local base64enc 0.1-3 2015-07-28 CRAN (R 3.2.3) bayesplot 1.2.0 2017-04-12 CRAN (R 3.3.3) colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2) colourpicker 0.3 2016-12-05 CRAN (R 3.3.2) compiler 3.4.0 2017-04-21 local datasets * 3.4.0 2017-04-21 local DBI 0.6-1 2017-04-01 CRAN (R 3.3.3) devtools 1.13.1 2017-05-13 CRAN (R 3.4.0) digest 0.6.12 2017-01-27 CRAN (R 3.3.2) dplyr 0.5.0 2016-06-24 CRAN (R 3.3.1) DT 0.2 2016-08-09 CRAN (R 3.3.1) dygraphs 1.1.1.4 2017-01-04 CRAN (R 3.3.2) ggplot2 2.2.1 2016-12-30 CRAN (R 3.3.2) graphics * 3.4.0 2017-04-21 local grDevices * 3.4.0 2017-04-21 local grid 3.4.0 2017-04-21 local gridExtra 2.2.1 2016-02-29 CRAN (R 3.2.3) gtable 0.2.0 2016-02-26 CRAN (R 3.2.3) gtools 3.5.0 2015-05-29 CRAN (R 3.2.0) htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0) htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.2) httpuv 1.3.3 2015-08-04 CRAN (R 3.2.2) inline 0.3.14 2015-04-13 CRAN (R 3.2.1) jsonlite 1.4 2017-04-08 CRAN (R 3.3.3) labeling 0.3 2014-08-23 CRAN (R 3.1.1) lattice 0.20-35 2017-03-25 CRAN (R 3.3.3) lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0) magrittr 1.5 2014-11-22 CRAN (R 3.1.2) markdown 0.8 2017-04-20 CRAN (R 3.4.0) Matrix 1.2-9 2017-03-14 CRAN (R 3.4.0) memoise 1.1.0 2017-04-21 CRAN (R 3.3.2) methods * 3.4.0 2017-04-21 local mime 0.5 2016-07-07 CRAN (R 3.3.1) miniUI 0.1.1 2016-01-15 CRAN (R 3.2.3) munsell 0.4.3 2016-02-13 CRAN (R 3.2.3) plyr 1.8.4 2016-06-08 CRAN (R 3.3.0) R6 2.2.1 2017-05-10 CRAN (R 3.4.0) Rcpp 0.12.10 2017-03-19 CRAN (R 3.4.0) reshape2 1.4.2 2016-10-22 CRAN (R 3.3.1) rlang 0.1.1 2017-05-18 CRAN (R 3.4.0) rsconnect 0.8 2017-05-08 CRAN (R 3.4.0) rstan 2.15.1 2017-04-19 CRAN (R 3.4.0) scales 0.4.1 2016-11-09 CRAN (R 3.3.2) shiny * 1.0.3 2017-04-26 CRAN (R 3.4.0) shinyjs 0.9 2016-12-26 CRAN (R 3.3.2) shinystan 2.3.0 2017-02-01 CRAN (R 3.3.2) shinythemes 1.1.1 2016-10-12 CRAN (R 3.3.1) StanHeaders 2.15.0-1 2017-04-19 CRAN (R 3.4.0) stats * 3.4.0 2017-04-21 local stats4 3.4.0 2017-04-21 local stringi 1.1.5 2017-04-07 CRAN (R 3.3.3) stringr 1.2.0 2017-02-18 CRAN (R 3.3.2) threejs 0.2.2 2016-04-01 CRAN (R 3.2.4) tibble 1.3.1 2017-05-17 CRAN (R 3.4.0) tools 3.4.0 2017-04-21 local utils * 3.4.0 2017-04-21 local withr 1.0.2 2016-06-20 CRAN (R 3.3.1) xtable 1.8-2 2016-02-05 CRAN (R 3.2.3) xts 0.9-7 2014-01-02 CRAN (R 3.2.3) yaml 2.1.14 2016-11-12 CRAN (R 3.3.2) zoo 1.8-0 2017-04-12 CRAN (R 3.3.3) ```
VeenDuco commented 4 years ago

We are currently working on version 3.0 and hopefully this error will not occur anymore. Because of the new version we are currently closing old issues as a clean-up for version 3.0 such that we have a new overview of current open issues. If the issue persist is the new version please do let us know.

Best, Duco