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cmdstanr backend with save_warmup = TRUE: shinystan error #1257

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fweber144 opened this issue Oct 31, 2021 · 4 comments
Closed

cmdstanr backend with save_warmup = TRUE: shinystan error #1257

fweber144 opened this issue Oct 31, 2021 · 4 comments
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bug
Milestone
brms 2.17.0

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@fweber144
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fweber144 commented Oct 31, 2021 •
edited

After fitting a model with the cmdstanr backend and save_warmup = TRUE, launching the shinystan app raises an error. I'm not sure if this is really related to brms, but that was my first guess.

Reprex:

data(bacteria, package = "MASS")
bfit <- brms::brm(
  formula = y ~ 1 + week * trt + (1 | ID),
  data = bacteria,
  family = brms::bernoulli(),
  chains = 2,
  iter = 500,
  backend = "cmdstanr",
  save_warmup = TRUE,
  seed = 1234
)
library(shinystan)
launch_shinystan(bfit)

with the last line throwing the error

Error in .validate_sampler_params(sampler_params, n_chain = ncol(X), n_iter = nrow(X),  : 
  Each matrix in 'sampler_params' must have number of rows equal to number of iterations in 'X'.

Session info:

> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.1 (2021-08-10)
 os       Ubuntu 20.04.3 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2021-10-31                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package        * version    date       lib source        
 abind            1.4-5      2016-07-21 [1] CRAN (R 4.0.4)
 assertthat       0.2.1      2019-03-21 [1] CRAN (R 4.0.4)
 backports        1.3.0      2021-10-27 [1] CRAN (R 4.1.1)
 base64enc        0.1-3      2015-07-28 [1] CRAN (R 4.0.4)
 bayesplot        1.8.1      2021-06-14 [1] CRAN (R 4.1.0)
 boot             1.3-28     2021-05-03 [4] CRAN (R 4.0.5)
 bridgesampling   1.1-2      2021-04-16 [1] CRAN (R 4.0.5)
 brms             2.16.1     2021-08-23 [1] CRAN (R 4.1.1)
 Brobdingnag      1.2-6      2018-08-13 [1] CRAN (R 4.0.4)
 callr            3.7.0      2021-04-20 [1] CRAN (R 4.0.5)
 checkmate        2.0.0      2020-02-06 [1] CRAN (R 4.0.4)
 cli              3.1.0      2021-10-27 [1] CRAN (R 4.1.1)
 cmdstanr         0.4.0      2021-04-16 [1] local         
 coda             0.19-4     2020-09-30 [1] CRAN (R 4.0.4)
 codetools        0.2-18     2020-11-04 [4] CRAN (R 4.0.3)
 colorspace       2.0-2      2021-06-24 [1] CRAN (R 4.1.0)
 colourpicker     1.1.1      2021-10-04 [1] CRAN (R 4.1.1)
 crayon           1.4.1      2021-02-08 [1] CRAN (R 4.0.4)
 crosstalk        1.1.1      2021-01-12 [1] CRAN (R 4.0.4)
 curl             4.3.2      2021-06-23 [1] CRAN (R 4.1.0)
 data.table       1.14.2     2021-09-27 [1] CRAN (R 4.1.1)
 DBI              1.1.1      2021-01-15 [1] CRAN (R 4.0.4)
 digest           0.6.28     2021-09-23 [1] CRAN (R 4.1.1)
 distributional   0.2.2      2021-02-02 [1] CRAN (R 4.0.4)
 dplyr            1.0.7      2021-06-18 [1] CRAN (R 4.1.0)
 DT               0.19       2021-09-02 [1] CRAN (R 4.1.1)
 dygraphs         1.1.1.6    2018-07-11 [1] CRAN (R 4.0.4)
 ellipsis         0.3.2      2021-04-29 [1] CRAN (R 4.0.5)
 emmeans          1.7.0      2021-09-29 [1] CRAN (R 4.1.1)
 estimability     1.3        2018-02-11 [1] CRAN (R 4.0.4)
 fansi            0.5.0      2021-05-25 [1] CRAN (R 4.1.0)
 farver           2.1.0      2021-02-28 [1] CRAN (R 4.0.4)
 fastmap          1.1.0      2021-01-25 [1] CRAN (R 4.0.4)
 gamm4            0.2-6      2020-04-03 [1] CRAN (R 4.0.4)
 generics         0.1.1      2021-10-25 [1] CRAN (R 4.1.1)
 ggplot2          3.3.5      2021-06-25 [1] CRAN (R 4.1.0)
 ggridges         0.5.3      2021-01-08 [1] CRAN (R 4.0.4)
 glue             1.4.2      2020-08-27 [1] CRAN (R 4.0.4)
 gridExtra        2.3        2017-09-09 [1] CRAN (R 4.0.4)
 gtable           0.3.0      2019-03-25 [1] CRAN (R 4.0.4)
 gtools           3.9.2      2021-06-06 [1] CRAN (R 4.1.0)
 htmltools        0.5.2      2021-08-25 [1] CRAN (R 4.1.1)
 htmlwidgets      1.5.4      2021-09-08 [1] CRAN (R 4.1.1)
 httpuv           1.6.3      2021-09-09 [1] CRAN (R 4.1.1)
 igraph           1.2.7      2021-10-15 [1] CRAN (R 4.1.1)
 inline           0.3.19     2021-05-31 [1] CRAN (R 4.1.0)
 jsonlite         1.7.2      2020-12-09 [1] CRAN (R 4.0.4)
 knitr            1.36       2021-09-29 [1] CRAN (R 4.1.1)
 later            1.3.0      2021-08-18 [1] CRAN (R 4.1.1)
 lattice          0.20-45    2021-09-22 [4] CRAN (R 4.1.1)
 lifecycle        1.0.1      2021-09-24 [1] CRAN (R 4.1.1)
 lme4             1.1-27.1   2021-06-22 [1] CRAN (R 4.1.0)
 loo              2.4.1      2020-12-09 [1] CRAN (R 4.1.1)
 magrittr         2.0.1      2020-11-17 [1] CRAN (R 4.0.4)
 markdown         1.1        2019-08-07 [1] CRAN (R 4.0.4)
 MASS             7.3-54     2021-05-03 [4] CRAN (R 4.0.5)
 Matrix           1.3-4      2021-06-01 [4] CRAN (R 4.1.0)
 matrixStats      0.61.0     2021-09-17 [1] CRAN (R 4.1.1)
 mgcv             1.8-38     2021-10-06 [4] CRAN (R 4.1.1)
 mime             0.12       2021-09-28 [1] CRAN (R 4.1.1)
 miniUI           0.1.1.1    2018-05-18 [1] CRAN (R 4.0.4)
 minqa            1.2.4      2014-10-09 [1] CRAN (R 4.0.4)
 multcomp         1.4-17     2021-04-29 [1] CRAN (R 4.1.0)
 munsell          0.5.0      2018-06-12 [1] CRAN (R 4.0.4)
 mvtnorm          1.1-3      2021-10-08 [1] CRAN (R 4.1.1)
 nlme             3.1-152    2021-02-04 [4] CRAN (R 4.0.3)
 nloptr           1.2.2.2    2020-07-02 [1] CRAN (R 4.0.4)
 pillar           1.6.4      2021-10-18 [1] CRAN (R 4.1.1)
 pkgbuild         1.2.0      2020-12-15 [1] CRAN (R 4.0.4)
 pkgconfig        2.0.3      2019-09-22 [1] CRAN (R 4.0.4)
 plyr             1.8.6      2020-03-03 [1] CRAN (R 4.0.4)
 posterior        1.1.0      2021-09-09 [1] CRAN (R 4.1.1)
 prettyunits      1.1.1      2020-01-24 [1] CRAN (R 4.0.4)
 processx         3.5.2      2021-04-30 [1] CRAN (R 4.0.5)
 projpred         2.0.5.9000 2021-10-22 [1] local         
 promises         1.2.0.1    2021-02-11 [1] CRAN (R 4.0.4)
 ps               1.6.0      2021-02-28 [1] CRAN (R 4.0.4)
 purrr            0.3.4      2020-04-17 [1] CRAN (R 4.0.4)
 R6               2.5.1      2021-08-19 [1] CRAN (R 4.1.1)
 Rcpp             1.0.7      2021-07-07 [1] CRAN (R 4.1.0)
 RcppParallel     5.1.4      2021-05-04 [1] CRAN (R 4.0.5)
 reshape2         1.4.4      2020-04-09 [1] CRAN (R 4.0.4)
 rlang            0.4.12     2021-10-18 [1] CRAN (R 4.1.1)
 rsconnect        0.8.24     2021-08-05 [1] CRAN (R 4.1.0)
 rstan            2.26.3     2021-08-09 [1] local         
 rstantools       2.1.1      2020-07-06 [1] CRAN (R 4.0.4)
 sandwich         3.0-1      2021-05-18 [1] CRAN (R 4.1.0)
 scales           1.1.1      2020-05-11 [1] CRAN (R 4.0.4)
 sessioninfo      1.1.1      2018-11-05 [1] CRAN (R 4.0.5)
 shiny          * 1.7.1      2021-10-02 [1] CRAN (R 4.1.1)
 shinyjs          2.0.0      2020-09-09 [1] CRAN (R 4.0.4)
 shinystan      * 2.5.0      2018-05-01 [1] CRAN (R 4.0.4)
 shinythemes      1.2.0      2021-01-25 [1] CRAN (R 4.0.4)
 StanHeaders      2.26.3     2021-08-09 [1] local         
 stringi          1.7.5      2021-10-04 [1] CRAN (R 4.1.1)
 stringr          1.4.0      2019-02-10 [1] CRAN (R 4.0.4)
 survival         3.2-13     2021-08-24 [4] CRAN (R 4.1.1)
 tensorA          0.36.2     2020-11-19 [1] CRAN (R 4.0.4)
 TH.data          1.1-0      2021-09-27 [1] CRAN (R 4.1.1)
 threejs          0.3.3      2020-01-21 [1] CRAN (R 4.0.4)
 tibble           3.1.5      2021-09-30 [1] CRAN (R 4.1.1)
 tidyselect       1.1.1      2021-04-30 [1] CRAN (R 4.0.5)
 utf8             1.2.2      2021-07-24 [1] CRAN (R 4.1.0)
 V8               3.4.2      2021-05-01 [1] CRAN (R 4.0.5)
 vctrs            0.3.8      2021-04-29 [1] CRAN (R 4.0.5)
 withr            2.4.2      2021-04-18 [1] CRAN (R 4.0.5)
 xfun             0.27       2021-10-18 [1] CRAN (R 4.1.1)
 xtable           1.8-4      2019-04-21 [1] CRAN (R 4.0.4)
 xts              0.12.1     2020-09-09 [1] CRAN (R 4.0.4)
 zoo              1.8-9      2021-03-09 [1] CRAN (R 4.0.4)

CmdStan version:

> cmdstanr::cmdstan_version()
[1] "2.28.1"

EDIT: Added CmdStan version and fixed syntax highlighting.
@fweber144 fweber144 changed the title **cmdstanr** backend with save_warmup = TRUE: **shinystan** error cmdstanr backend with save_warmup = TRUE: shinystan error Oct 31, 2021
@paul-buerkner
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I don't know what is going on there. Does the same thing happen with a manual cmdstanr fit?

@fweber144
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You mean something like the following? That works for me.

library(cmdstanr)
options(mc.cores = parallel::detectCores())
sdat <- list(N = 10, y = c(0, 1, 0, 0, 0, 0, 0, 0, 0, 1))
smod <- cmdstan_model(
  stan_file = file.path(cmdstan_path(),
                        "examples",
                        "bernoulli",
                        "bernoulli.stan")
)
sfit <- smod$sample(
  data = sdat,
  refresh = 0,
  save_warmup = TRUE,
  seed = 15337L
)
# Create object of class `stanfit`:
sfit <- rstan::read_stan_csv(sfit$output_files())
library(shinystan)
launch_shinystan(sfit)

@paul-buerkner paul-buerkner added this to the brms 2.16.0++ milestone Dec 16, 2021
paul-buerkner added a commit that referenced this issue Dec 16, 2021
@paul-buerkner
fix issue #1257
094052f
@paul-buerkner
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Should now be fixed.

@fweber144
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Unfortunately, when running the reprex from my initial comment, I still get the same error. Does it work for you?

@fweber144 fweber144 mentioned this issue Apr 4, 2022
Closed
paul-buerkner added a commit that referenced this issue Apr 7, 2022
@paul-buerkner
fix issue #1257 and #1329
ad033a5
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