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pharmaverse / admiral

ADaM in R Asset Library
https://pharmaverse.github.io/admiral
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Derived study day is not an integer #647

Closed thomas-neitmann closed 2 years ago

thomas-neitmann commented 2 years ago

START BY CONFIRMING THE ISSUE STILL EXISTS As reporter by one of our Roche internal testers when running the ADEX template script on BEE with R version 3.6.3 ASTDY and AENDY are not integers.

image

I cannot reproduce this with our {renv} setup. Here I get the correct result.

image

I suspect this has something to do with different package versions. Here's the session info from BEE:

─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Red Hat Enterprise Linux    
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2021-11-09                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────
 ! package     * version date       lib source                            
   admiral     * 0.3.0   2021-11-09 [1] Github (Roche-GSK/admiral@7422870)
   assertthat    0.2.1   2019-03-21 [2] CRAN (R 3.6.3)                    
   cli           2.0.2   2020-02-28 [2] CRAN (R 3.6.3)                    
   crayon        1.3.4   2017-09-16 [2] CRAN (R 3.6.3)                    
   dplyr       * 1.0.0   2020-05-29 [2] CRAN (R 3.6.3)                    
   ellipsis      0.3.0   2019-09-20 [2] CRAN (R 3.6.3)                    
   fansi         0.4.1   2020-01-08 [2] CRAN (R 3.6.3)                    
   generics      0.0.2   2018-11-29 [2] CRAN (R 3.6.3)                    
   glue          1.4.0   2020-04-03 [2] CRAN (R 3.6.3)                    
   lifecycle     0.2.0   2020-03-06 [2] CRAN (R 3.6.3)                    
 R lubridate   * 1.7.8   <NA>       [2] <NA>                              
   magrittr      1.5     2014-11-22 [2] CRAN (R 3.6.3)                    
   pillar        1.4.3   2019-12-20 [2] CRAN (R 3.6.3)                    
   pkgconfig     2.0.3   2019-09-22 [2] CRAN (R 3.6.3)                    
   purrr         0.3.4   2020-04-17 [2] CRAN (R 3.6.3)                    
   R6            2.4.1   2019-11-12 [2] CRAN (R 3.6.3)                    
   Rcpp          1.0.4.6 2020-04-09 [2] CRAN (R 3.6.3)                    
 R rlang         0.4.6   <NA>       [2] <NA>                              
   rstudioapi    0.11    2020-02-07 [2] CRAN (R 3.6.3)                    
   sessioninfo   1.1.1   2018-11-05 [2] CRAN (R 3.6.3)                    
   stringi       1.4.6   2020-02-17 [2] CRAN (R 3.6.3)                    
   stringr     * 1.4.0   2019-02-10 [2] CRAN (R 3.6.3)                    
   tibble        3.0.1   2020-04-20 [2] CRAN (R 3.6.3)                    
   tidyr         1.0.2   2020-01-24 [2] CRAN (R 3.6.3)                    
   tidyselect    1.1.0   2020-05-11 [2] CRAN (R 3.6.3)                    
 R vctrs         0.3.1   <NA>       [2] <NA>                              
   withr         2.2.0   2020-04-20 [2] CRAN (R 3.6.3)                    
   yaml          2.2.1   2020-02-01 [2] CRAN (R 3.6.3)                    

[1] /home/bceuser/neitmant/R/x86_64-pc-linux-gnu-library/3.6.3
[2] /opt/bee_tools/R/3.6.3/lib64/R/library_sec
[3] /opt/bee_tools/R/3.6.3/lib64/R/library

 R ── Package was removed from disk.

And here's the one from our admiral environment:

─ Session info ──────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Red Hat Enterprise Linux    
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2021-11-09                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────
 ! package     * version date       lib source                            
   admiral     * 0.3.0   2021-11-09 [1] Github (Roche-GSK/admiral@7422870)
 P assertthat    0.2.1   2019-03-21 [?] CRAN (R 3.6.3)                    
 P backports     1.1.5   2019-10-02 [?] CRAN (R 3.6.3)                    
 P callr         3.7.0   2021-04-20 [?] CRAN (R 3.6.3)                    
 P cli           2.0.2   2020-02-28 [?] CRAN (R 3.6.3)                    
 P crayon        1.3.4   2017-09-16 [?] CRAN (R 3.6.3)                    
 P curl          4.3     2019-12-02 [?] CRAN (R 3.6.3)                    
 P dplyr       * 0.8.5   2020-03-07 [?] CRAN (R 3.6.3)                    
 P fansi         0.4.1   2020-01-08 [?] CRAN (R 3.6.3)                    
 P glue          1.3.1   2019-03-12 [?] CRAN (R 3.6.3)                    
 P lubridate   * 1.7.4   2018-04-11 [?] CRAN (R 3.6.3)                    
 P magrittr      1.5     2014-11-22 [?] CRAN (R 3.6.3)                    
 P pillar        1.4.3   2019-12-20 [?] CRAN (R 3.6.3)                    
 P pkgbuild      1.0.6   2019-10-09 [?] CRAN (R 3.6.3)                    
 P pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 3.6.3)                    
 P prettyunits   1.1.1   2020-01-24 [?] CRAN (R 3.6.3)                    
 P processx      3.5.2   2021-04-30 [?] CRAN (R 3.6.3)                    
 P ps            1.6.0   2021-02-28 [?] CRAN (R 3.6.3)                    
 P purrr         0.3.3   2019-10-18 [?] CRAN (R 3.6.3)                    
 P R6            2.4.1   2019-11-12 [?] CRAN (R 3.6.3)                    
 P Rcpp          1.0.3   2019-11-08 [?] CRAN (R 3.6.3)                    
 P remotes       2.1.1   2020-02-15 [?] CRAN (R 3.6.3)                    
 P renv          0.13.0  2021-02-24 [?] CRAN (R 3.6.3)                    
 P rlang         0.4.10  2020-12-30 [?] CRAN (R 3.5.3)                    
 P rprojroot     1.3-2   2018-01-03 [?] CRAN (R 3.6.3)                    
 P rstudioapi    0.11    2020-02-07 [?] CRAN (R 3.6.3)                    
 P sessioninfo   1.1.1   2018-11-05 [?] CRAN (R 3.6.3)                    
 P stringi       1.4.6   2020-02-17 [?] CRAN (R 3.6.3)                    
 P stringr     * 1.4.0   2019-02-10 [?] CRAN (R 3.6.3)                    
 P tibble        2.1.3   2019-06-06 [?] CRAN (R 3.6.3)                    
 P tidyr         0.8.3   2019-03-01 [?] CRAN (R 3.6.3)                    
 P tidyselect    1.0.0   2020-01-27 [?] CRAN (R 3.6.3)                    
 P vctrs         0.3.8   2021-04-29 [?] CRAN (R 3.6.3)                    
 P withr         2.1.2   2018-03-15 [?] CRAN (R 3.6.3)                    

[1] /home/bceuser/neitmant/admiral/renv/library/R-3.6/x86_64-pc-linux-gnu
[2] /tmp/RtmpQhNO4b/renv-system-library

 P ── Loaded and on-disk path mismatch.
thomas-neitmann commented 2 years ago

fyi @Roche-GSK/admiral-devs

bms63 commented 2 years ago

Please investigate if this is still happening in the latest version. If so, then bring back to leads for more discussion

amsmith214 commented 2 years ago

Does not seem to me that this issue persists. I used devtools::load_all() from current devel and then ran: 

sl1 <- admiral::adsl %>% 
  select(STUDYID, USUBJID, matches('^TRT'))

ex1 <- admiral::adex %>%
  select(STUDYID, USUBJID, EXSTDTC, EXENDTC) %>%
  left_join(sl1, by=c("STUDYID", "USUBJID")) %>%
  derive_vars_dtm(dtc = EXSTDTC, date_imputation = "first", new_vars_prefix="AST") %>%
  derive_vars_dtm(dtc = EXENDTC, date_imputation = "last", new_vars_prefix="AEN") %>%
  derive_var_astdy(date = ASTDTM) %>%
  derive_var_aendy(date = AENDTM)

to receive

image

thomas-neitmann commented 2 years ago

Thanks @amsmith214! Could you add your sessionInfo() here?

amsmith214 commented 2 years ago 
- Session info -------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/New_York            
 date     2022-02-22                  

- Packages -----------------------------------------------------------------------------------------------------------
 ! package      * version date       lib source                                   
 R admiral      * 0.6.3   <NA>       [?] <NA>                                     
   admiral.test   0.1.0   2022-02-21 [1] Github (pharmaverse/admiral.test@bdae26a)
   assertthat     0.2.1   2019-03-21 [1] CRAN (R 3.6.3)                           
   backports      1.1.5   2019-10-02 [1] CRAN (R 3.6.3)                           
   callr          3.7.0   2021-04-20 [1] CRAN (R 3.6.3)                           
   cli            3.1.1   2022-01-20 [1] CRAN (R 3.6.3)                           
   crayon         1.3.4   2017-09-16 [1] CRAN (R 3.6.3)                           
   desc           1.4.0   2021-09-28 [1] CRAN (R 3.6.3)                           
   devtools       2.2.2   2020-02-17 [1] CRAN (R 3.6.3)                           
   digest         0.6.25  2020-02-23 [1] CRAN (R 3.6.3)                           
   dplyr        * 0.8.5   2020-03-07 [1] CRAN (R 3.6.3)                           
   ellipsis       0.3.0   2019-09-20 [1] CRAN (R 3.6.3)                           
   fs             1.3.2   2020-03-05 [1] CRAN (R 3.6.3)                           
   glue           1.3.1   2019-03-12 [1] CRAN (R 3.6.3)                           
   hms            0.5.3   2020-01-08 [1] CRAN (R 3.6.3)                           
   lifecycle      1.0.1   2021-09-24 [1] CRAN (R 3.6.3)                           
   lubridate      1.7.4   2018-04-11 [1] CRAN (R 3.6.3)                           
   magrittr       1.5     2014-11-22 [1] CRAN (R 3.6.3)                           
   memoise        1.1.0   2017-04-21 [1] CRAN (R 3.6.3)                           
   pillar         1.4.3   2019-12-20 [1] CRAN (R 3.6.3)                           
   pkgbuild       1.0.6   2019-10-09 [1] CRAN (R 3.6.3)                           
   pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 3.6.3)                           
   pkgload        1.0.2   2018-10-29 [1] CRAN (R 3.6.3)                           
   prettyunits    1.1.1   2020-01-24 [1] CRAN (R 3.6.3)                           
   processx       3.5.2   2021-04-30 [1] CRAN (R 3.6.3)                           
   ps             1.6.0   2021-02-28 [1] CRAN (R 3.6.3)                           
   purrr          0.3.3   2019-10-18 [1] CRAN (R 3.6.3)                           
   R6             2.4.1   2019-11-12 [1] CRAN (R 3.6.3)                           
   Rcpp           1.0.3   2019-11-08 [1] CRAN (R 3.6.3)                           
   remotes        2.1.1   2020-02-15 [1] CRAN (R 3.6.3)                           
   renv           0.13.0  2021-02-24 [1] CRAN (R 3.6.3)                           
   rlang          0.4.10  2020-12-30 [1] CRAN (R 3.6.3)                           
   rprojroot      1.3-2   2018-01-03 [1] CRAN (R 3.6.3)                           
   rstudioapi     0.11    2020-02-07 [1] CRAN (R 3.6.3)                           
   sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 3.6.3)                           
   stringi        1.4.6   2020-02-17 [1] CRAN (R 3.6.3)                           
   stringr        1.4.0   2019-02-10 [1] CRAN (R 3.6.3)                           
   testthat     * 3.0.0   2020-10-31 [1] CRAN (R 3.6.3)                           
   tibble         2.1.3   2019-06-06 [1] CRAN (R 3.6.3)                           
   tidyr          0.8.3   2019-03-01 [1] CRAN (R 3.6.3)                           
   tidyselect     1.0.0   2020-01-27 [1] CRAN (R 3.6.3)                           
   usethis        2.1.5   2021-12-09 [1] CRAN (R 3.6.3)                           
   vctrs          0.3.8   2021-04-29 [1] CRAN (R 3.6.3)                           
   withr          2.4.3   2021-11-30 [1] CRAN (R 3.6.3)                           

[1] C:/Users/ams86037/OneDrive - GSK/Documents/admiral/renv/library/R-3.6/x86_64-w64-mingw32
[2] C:/Users/ams86037/AppData/Local/Temp/Rtmpc1M8GR/renv-system-library

 R -- Package was removed from disk.