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EmilMiP / LTFHPlus

Implementation of LTFH++
https://emilmip.github.io/LTFHPlus/
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LTFHPlusxample.Rmd vignette not running #20

Closed mariosaare closed 2 years ago

mariosaare commented 2 years ago

Hi, I am trying to run the LTFHPlusxample.Rmd vignette. Unfortunately, it does not work on my computer. Specifically, the script stops at the generating phenotypes with the following error message: image

I am not able to debug it. Please see my settings below.

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22 ucrt)
 os       Windows 10 x64 (build 19044)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  English_United Kingdom.utf8
 ctype    English_United Kingdom.utf8
 tz       Europe/Helsinki
 date     2022-08-26
 rstudio  2022.07.1+554 Spotted Wakerobin (desktop)
 pandoc   2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
 brio           1.1.3   2021-11-30 [1] CRAN (R 4.2.0)
 cachem         1.0.6   2021-08-19 [1] CRAN (R 4.2.0)
 callr          3.7.0   2021-04-20 [1] CRAN (R 4.2.0)
 cli            3.3.0   2022-04-25 [1] CRAN (R 4.2.0)
 codetools      0.2-18  2020-11-04 [2] CRAN (R 4.2.0)
 crayon         1.5.1   2022-03-26 [1] CRAN (R 4.2.0)
 DBI            1.1.2   2021-12-20 [1] CRAN (R 4.2.0)
 desc           1.4.1   2022-03-06 [1] CRAN (R 4.2.0)
 devtools       2.4.3   2021-11-30 [1] CRAN (R 4.2.0)
 digest         0.6.29  2021-12-01 [1] CRAN (R 4.2.0)
 dplyr        * 1.0.9   2022-04-28 [1] CRAN (R 4.2.0)
 ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
 evaluate       0.15    2022-02-18 [1] CRAN (R 4.2.0)
 fansi          1.0.3   2022-03-24 [1] CRAN (R 4.2.0)
 fastmap        1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
 fs             1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
 future       * 1.27.0  2022-07-22 [1] CRAN (R 4.2.1)
 future.apply * 1.9.0   2022-04-25 [1] CRAN (R 4.2.1)
 generics       0.1.3   2022-07-05 [1] CRAN (R 4.2.1)
 globals        0.16.0  2022-08-05 [1] CRAN (R 4.2.1)
 glue           1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
 gmm            1.7     2022-08-12 [1] CRAN (R 4.2.1)
 htmltools      0.5.2   2021-08-25 [1] CRAN (R 4.2.0)
 knitr          1.39    2022-04-26 [1] CRAN (R 4.2.0)
 lattice        0.20-45 2021-09-22 [2] CRAN (R 4.2.0)
 lifecycle      1.0.1   2021-09-24 [1] CRAN (R 4.2.0)
 listenv        0.8.0   2019-12-05 [1] CRAN (R 4.2.1)
 LTFHPlus     * 2.0.3   2022-08-25 [1] Github (EmilMiP/LTFHPlus@1b9b3bf)
 magrittr       2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
 MASS         * 7.3-56  2022-03-23 [2] CRAN (R 4.2.0)
 Matrix         1.4-1   2022-03-23 [2] CRAN (R 4.2.0)
 memoise        2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
 mvtnorm        1.1-3   2021-10-08 [1] CRAN (R 4.2.0)
 parallelly     1.32.1  2022-07-21 [1] CRAN (R 4.2.1)
 pillar         1.8.0   2022-07-18 [1] CRAN (R 4.2.1)
 pkgbuild       1.3.1   2021-12-20 [1] CRAN (R 4.2.0)
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
 pkgload        1.2.4   2021-11-30 [1] CRAN (R 4.2.0)
 prettyunits    1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
 processx       3.5.3   2022-03-25 [1] CRAN (R 4.2.0)
 ps             1.7.0   2022-04-23 [1] CRAN (R 4.2.0)
 purrr          0.3.4   2020-04-17 [1] CRAN (R 4.2.0)
 R6             2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
 Rcpp           1.0.9   2022-07-08 [1] CRAN (R 4.2.1)
 remotes        2.4.2   2021-11-30 [1] CRAN (R 4.2.0)
 rlang          1.0.4   2022-07-12 [1] CRAN (R 4.2.1)
 rmarkdown      2.14    2022-04-25 [1] CRAN (R 4.2.0)
 rprojroot      2.0.3   2022-04-02 [1] CRAN (R 4.2.0)
 rstudioapi     0.13    2020-11-12 [1] CRAN (R 4.2.0)
 sandwich       3.0-2   2022-06-15 [1] CRAN (R 4.2.1)
 sessioninfo    1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
 stringi        1.7.8   2022-07-11 [1] CRAN (R 4.2.1)
 stringr        1.4.0   2019-02-10 [1] CRAN (R 4.2.0)
 testthat       3.1.4   2022-04-26 [1] CRAN (R 4.2.0)
 tibble         3.1.8   2022-07-22 [1] CRAN (R 4.2.1)
 tidyr        * 1.2.0   2022-02-01 [1] CRAN (R 4.2.0)
 tidyselect     1.1.2   2022-02-21 [1] CRAN (R 4.2.0)
 tmvtnorm       1.5     2022-03-22 [1] CRAN (R 4.2.1)
 usethis        2.1.6   2022-05-25 [1] CRAN (R 4.2.0)
 utf8           1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
 vctrs          0.4.1   2022-04-13 [1] CRAN (R 4.2.0)
 withr          2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
 xfun           0.31    2022-05-10 [1] CRAN (R 4.2.0)
 yaml           2.3.5   2022-02-21 [1] CRAN (R 4.2.0)
 zoo            1.8-10  2022-04-15 [1] CRAN (R 4.2.0)

 [1] C:/Users/mario_s/AppData/Local/R/win-library/4.2
 [2] C:/Program Files/R/R-4.2.0/library

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Best regards, Mario

EmilMiP commented 2 years ago

Unfortunately, I have been rather busy the last few days.

However, I have not had the time to go over the vignettes until now. We have made some changes internally to the package, which were not properly reflected in the vignettes you referenced.

I hope the changes to the examples will make sense, if not, feel free to create a new issue.

Best, Emil