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getting_started.Rmd won't build #59

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jonthegeek opened this issue Oct 9, 2019 · 5 comments · Fixed by #62 or #63
Closed

getting_started.Rmd won't build #59

jonthegeek opened this issue Oct 9, 2019 · 5 comments · Fixed by #62 or #63

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@jonthegeek
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The problem

getting_started.Rmd fails to build. It appears to be an issue in tune_Bayes, but I'm not yet able to understand what causes the issue.

Reproducible example

(run everything in the getting_started.Rmd before line 254)

ctrl <- Bayes_control(verbose = TRUE)
set.seed(8154)
knn_search <- tune_Bayes(knn_wflow, rs = cv_splits, initial = 5, iter = 20,
                         param_info = knn_param, control = ctrl)

❯  Generating a set of 5 initial parameter results
✓ Initialization complete

Error: All of the models failed.
In addition: Warning message:
All models failed in tune_grid(). 
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.1 (2019-07-05)
 os       CentOS Linux 7 (Core)       
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Chicago             
 date     2019-10-09                  

─ Packages ──────────────────────────────────────────────────────────────────────────
 package       * version    date       lib source                             
 AmesHousing   * 0.0.3      2017-12-17 [1] CRAN (R 3.6.1)                     
 assertthat      0.2.1      2019-03-21 [2] CRAN (R 3.5.2)                     
 backports       1.1.5      2019-10-02 [2] CRAN (R 3.6.1)                     
 base64enc       0.1-3      2015-07-28 [2] CRAN (R 3.5.1)                     
 bayesplot       1.7.0      2019-05-23 [2] CRAN (R 3.5.2)                     
 boot            1.3-22     2019-04-02 [2] CRAN (R 3.6.1)                     
 broom         * 0.5.2      2019-04-07 [2] CRAN (R 3.5.2)                     
 callr           3.3.1      2019-07-18 [2] CRAN (R 3.5.2)                     
 class           7.3-15     2019-01-01 [2] CRAN (R 3.6.1)                     
 cli             1.9.9.9000 2019-10-09 [1] Github (r-lib/cli@ad6410a)         
 clisymbols      1.2.0      2017-05-21 [2] CRAN (R 3.5.1)                     
 codetools       0.2-16     2018-12-24 [2] CRAN (R 3.6.1)                     
 colorspace      1.4-1      2019-03-18 [2] CRAN (R 3.5.2)                     
 colourpicker    1.0        2017-09-27 [2] CRAN (R 3.5.1)                     
 crayon          1.3.4      2017-09-16 [2] CRAN (R 3.5.1)                     
 crosstalk       1.0.0      2016-12-21 [2] CRAN (R 3.5.1)                     
 curl            4.2        2019-09-24 [2] CRAN (R 3.6.1)                     
 desc            1.2.0      2018-05-01 [2] CRAN (R 3.5.1)                     
 devtools        2.1.0      2019-07-06 [2] CRAN (R 3.5.2)                     
 dials         * 0.0.3      2019-10-01 [2] CRAN (R 3.6.1)                     
 DiceDesign      1.8-1      2019-07-31 [2] CRAN (R 3.6.1)                     
 digest          0.6.21     2019-09-20 [2] CRAN (R 3.6.1)                     
 dplyr         * 0.8.3      2019-07-04 [2] CRAN (R 3.5.2)                     
 DT              0.8        2019-08-07 [2] CRAN (R 3.5.2)                     
 dygraphs        1.1.1.6    2018-07-11 [2] CRAN (R 3.5.1)                     
 evaluate        0.14       2019-05-28 [2] CRAN (R 3.5.2)                     
 fansi           0.4.0      2018-10-05 [2] CRAN (R 3.5.1)                     
 foreach         1.4.7      2019-07-27 [2] CRAN (R 3.5.2)                     
 fs              1.3.1      2019-05-06 [2] CRAN (R 3.5.2)                     
 furrr           0.1.0      2018-05-16 [2] CRAN (R 3.5.1)                     
 future          1.14.0     2019-07-02 [2] CRAN (R 3.5.2)                     
 generics        0.0.2      2018-11-29 [2] CRAN (R 3.5.1)                     
 ggplot2       * 3.2.1      2019-08-10 [2] CRAN (R 3.5.2)                     
 ggridges        0.5.1      2018-09-27 [2] CRAN (R 3.5.1)                     
 git2r           0.26.1     2019-06-29 [2] CRAN (R 3.5.2)                     
 globals         0.12.4     2018-10-11 [2] CRAN (R 3.5.1)                     
 glue            1.3.1      2019-03-12 [2] CRAN (R 3.5.2)                     
 gower           0.2.1      2019-05-14 [2] CRAN (R 3.5.2)                     
 GPfit           1.0-8      2019-02-08 [1] CRAN (R 3.6.1)                     
 gridExtra       2.3        2017-09-09 [2] CRAN (R 3.5.1)                     
 gtable          0.3.0      2019-03-25 [2] CRAN (R 3.5.2)                     
 gtools          3.8.1      2018-06-26 [2] CRAN (R 3.5.1)                     
 hms             0.5.1      2019-08-23 [2] CRAN (R 3.5.2)                     
 htmltools       0.3.6      2017-04-28 [2] CRAN (R 3.5.1)                     
 htmlwidgets     1.3        2018-09-30 [2] CRAN (R 3.5.1)                     
 httpuv          1.5.1      2019-04-05 [2] CRAN (R 3.5.2)                     
 igraph          1.2.4.1    2019-04-22 [2] CRAN (R 3.5.2)                     
 infer         * 0.4.0.1    2019-04-22 [2] CRAN (R 3.5.2)                     
 inline          0.3.15     2018-05-18 [2] CRAN (R 3.5.1)                     
 ipred           0.9-9      2019-04-28 [2] CRAN (R 3.5.2)                     
 iterators       1.0.12     2019-07-26 [2] CRAN (R 3.5.2)                     
 janeaustenr     0.1.5      2017-06-10 [2] CRAN (R 3.5.1)                     
 knitr           1.24       2019-08-08 [2] CRAN (R 3.5.2)                     
 labeling        0.3        2014-08-23 [2] CRAN (R 3.5.1)                     
 later           0.8.0      2019-02-11 [2] CRAN (R 3.5.2)                     
 lattice         0.20-38    2018-11-04 [2] CRAN (R 3.6.1)                     
 lava            1.6.6      2019-08-01 [2] CRAN (R 3.5.2)                     
 lazyeval        0.2.2      2019-03-15 [2] CRAN (R 3.5.2)                     
 lhs             1.0.1      2019-02-03 [1] CRAN (R 3.6.1)                     
 lifecycle       0.1.0      2019-08-01 [2] CRAN (R 3.6.1)                     
 listenv         0.7.0      2018-01-21 [2] CRAN (R 3.5.1)                     
 lme4            1.1-21     2019-03-05 [2] CRAN (R 3.5.2)                     
 loo             2.1.0      2019-03-13 [2] CRAN (R 3.5.2)                     
 lubridate       1.7.4      2018-04-11 [2] CRAN (R 3.5.1)                     
 magrittr        1.5        2014-11-22 [2] CRAN (R 3.5.1)                     
 markdown        1.1        2019-08-07 [2] CRAN (R 3.5.2)                     
 MASS            7.3-51.4   2019-03-31 [2] CRAN (R 3.6.1)                     
 Matrix          1.2-17     2019-03-22 [2] CRAN (R 3.6.1)                     
 matrixStats     0.54.0     2018-07-23 [2] CRAN (R 3.5.1)                     
 memoise         1.1.0      2017-04-21 [2] CRAN (R 3.5.1)                     
 mgcv            1.8-28     2019-03-21 [2] CRAN (R 3.6.1)                     
 mime            0.7        2019-06-11 [2] CRAN (R 3.5.2)                     
 miniUI          0.1.1.1    2018-05-18 [2] CRAN (R 3.5.1)                     
 minqa           1.2.4      2014-10-09 [2] CRAN (R 3.5.1)                     
 munsell         0.5.0      2018-06-12 [2] CRAN (R 3.5.1)                     
 nlme            3.1-140    2019-05-12 [2] CRAN (R 3.6.1)                     
 nloptr          1.2.1      2018-10-03 [2] CRAN (R 3.5.1)                     
 nnet            7.3-12     2016-02-02 [2] CRAN (R 3.6.1)                     
 parsnip       * 0.0.3.9001 2019-10-09 [1] Github (tidymodels/parsnip@ae42617)
 pillar          1.4.2      2019-06-29 [2] CRAN (R 3.5.2)                     
 pkgbuild        1.0.4      2019-08-05 [2] CRAN (R 3.5.2)                     
 pkgconfig       2.0.3      2019-09-22 [2] CRAN (R 3.6.1)                     
 pkgload         1.0.2      2018-10-29 [2] CRAN (R 3.5.1)                     
 plyr            1.8.4      2016-06-08 [2] CRAN (R 3.5.1)                     
 prettyunits     1.0.2      2015-07-13 [2] CRAN (R 3.5.1)                     
 pROC            1.15.3     2019-07-21 [2] CRAN (R 3.5.2)                     
 processx        3.4.1      2019-07-18 [2] CRAN (R 3.5.2)                     
 prodlim         2018.04.18 2018-04-18 [2] CRAN (R 3.5.1)                     
 progress        1.2.2      2019-05-16 [2] CRAN (R 3.5.2)                     
 promises        1.0.1      2018-04-13 [2] CRAN (R 3.5.1)                     
 ps              1.3.0      2018-12-21 [2] CRAN (R 3.5.1)                     
 purrr         * 0.3.2      2019-03-15 [2] CRAN (R 3.5.2)                     
 R6              2.4.0      2019-02-14 [2] CRAN (R 3.5.2)                     
 Rcpp            1.0.2      2019-07-25 [2] CRAN (R 3.5.2)                     
 recipes       * 0.1.7      2019-09-15 [1] CRAN (R 3.6.1)                     
 remotes         2.1.0      2019-06-24 [2] CRAN (R 3.5.2)                     
 reshape2        1.4.3      2017-12-11 [2] CRAN (R 3.5.1)                     
 rlang           0.4.0      2019-06-25 [2] CRAN (R 3.6.1)                     
 rmarkdown       1.14       2019-07-12 [2] CRAN (R 3.5.2)                     
 rpart           4.1-15     2019-04-12 [2] CRAN (R 3.6.1)                     
 rprojroot       1.3-2      2018-01-03 [2] CRAN (R 3.5.1)                     
 rsample       * 0.0.5      2019-07-12 [2] CRAN (R 3.5.2)                     
 rsconnect       0.8.15     2019-07-22 [2] CRAN (R 3.5.2)                     
 rstan           2.19.2     2019-07-09 [2] CRAN (R 3.5.2)                     
 rstanarm        2.18.2     2018-11-10 [2] CRAN (R 3.5.1)                     
 rstantools      1.5.1      2018-08-22 [2] CRAN (R 3.5.1)                     
 rstudioapi      0.10       2019-03-19 [2] CRAN (R 3.5.2)                     
 scales        * 1.0.0      2018-08-09 [2] CRAN (R 3.5.1)                     
 sessioninfo     1.1.1      2018-11-05 [2] CRAN (R 3.5.1)                     
 shiny           1.3.2      2019-04-22 [2] CRAN (R 3.5.2)                     
 shinyjs         1.0        2018-01-08 [2] CRAN (R 3.5.1)                     
 shinystan       2.5.0      2018-05-01 [2] CRAN (R 3.5.1)                     
 shinythemes     1.1.2      2018-11-06 [2] CRAN (R 3.5.1)                     
 SnowballC       0.6.0      2019-01-15 [2] CRAN (R 3.5.1)                     
 StanHeaders     2.18.1-10  2019-06-14 [2] CRAN (R 3.5.2)                     
 stringi         1.4.3      2019-03-12 [2] CRAN (R 3.5.2)                     
 stringr         1.4.0      2019-02-10 [2] CRAN (R 3.5.2)                     
 survival        2.44-1.1   2019-04-01 [2] CRAN (R 3.6.1)                     
 testthat        2.2.1      2019-07-25 [2] CRAN (R 3.5.2)                     
 threejs         0.3.1      2017-08-13 [2] CRAN (R 3.5.1)                     
 tibble        * 2.1.3      2019-06-06 [2] CRAN (R 3.5.2)                     
 tidymodels    * 0.0.2      2018-11-27 [2] CRAN (R 3.6.1)                     
 tidyposterior   0.0.2      2018-11-15 [2] CRAN (R 3.5.1)                     
 tidypredict     0.4.2      2019-07-15 [2] CRAN (R 3.5.2)                     
 tidyr         * 1.0.0      2019-09-11 [1] CRAN (R 3.6.1)                     
 tidyselect      0.2.5      2018-10-11 [2] CRAN (R 3.5.1)                     
 tidytext        0.2.2      2019-07-29 [2] CRAN (R 3.5.2)                     
 timeDate        3043.102   2018-02-21 [2] CRAN (R 3.5.1)                     
 tokenizers      0.2.1      2018-03-29 [2] CRAN (R 3.5.1)                     
 tune          * 0.0.0.9001 2019-10-09 [1] local                              
 usethis         1.5.1      2019-07-04 [2] CRAN (R 3.5.2)                     
 utf8            1.1.4      2018-05-24 [2] CRAN (R 3.5.1)                     
 vctrs           0.2.0      2019-07-05 [2] CRAN (R 3.6.1)                     
 whisker         0.3-2      2013-04-28 [2] CRAN (R 3.5.1)                     
 withr           2.1.2      2018-03-15 [2] CRAN (R 3.5.1)                     
 xfun            0.8        2019-06-25 [2] CRAN (R 3.5.2)                     
 xtable          1.8-4      2019-04-21 [2] CRAN (R 3.5.2)                     
 xts             0.11-2     2018-11-05 [2] CRAN (R 3.5.1)                     
 yaml            2.2.0      2018-07-25 [2] CRAN (R 3.5.1)                     
 yardstick     * 0.0.4      2019-08-26 [1] CRAN (R 3.6.1)                     
 zeallot         0.1.0      2018-01-28 [2] CRAN (R 3.5.1)                     
 zoo             1.8-6      2019-05-28 [2] CRAN (R 3.5.2)
@Jim89 Jim89 mentioned this issue Oct 9, 2019
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@Jim89
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Jim89 commented Oct 9, 2019

Doing some investigation for a similar issue in #60 @jonthegeek

It may be that you're missing a package that is expected to be installed somewhere for your turning. For me it was kernlab, but not sure if it would be the same for you.

Either way, debug()-ing my way down to the function with the error got me to an error about a missing package which wasn't getting shown to me due to (I think?) how errors get returned in foreach.

Not sure if this will be the same issue, but it's the same error message, and probably relates to something going on that relates to #44 (i.e. how errors get returned from foreach()).

@jonthegeek
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With @Jim89's advice, I found it was kknn, which is in suggests of parsnip, which... kinda covers this? I'm not sure on protocol here.

This was referenced Oct 9, 2019
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@topepo
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topepo commented Oct 10, 2019

Did either of you run using parallel processing? parsnip usually alerts people when packages need installing. I can replicate that in tune but wanted to make sure I knew what the issue was.

@topepo topepo mentioned this issue Oct 10, 2019
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@jonthegeek
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Nope, no parallel.

topepo pushed a commit that referenced this issue Oct 10, 2019
@jonthegeek @topepo
Added an explicit note to the kknn example where kknn is needed. (#62)
caee11c 
* Added an explicit note to the kknn example where kknn is needed. Closes #59.

* Updated per suggestion.
@MxNl MxNl mentioned this issue Sep 3, 2020
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github-actions bot commented Mar 8, 2021

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

@github-actions github-actions bot locked and limited conversation to collaborators Mar 8, 2021
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@topepo @Jim89 @jonthegeek