ADTTE xportr_write() Call Error

[DeclanHodges]

After upgrading the renv.lock file to use xportr v0.2.0, the ADTTE code is now erroring from the call to xportr_write() at line 125:

[robertdevine]

Thank you @DeclanHodges. Working on this issue in my Posit Cloud sandbox.

[robertdevine]

Future reference from checkout point:

renv::restore()
The following package(s) will be updated:

CRAN ===============================

• BH [1.78.0-0 -> 1.81.0-1]
• MASS [7.3-58.1 -> 7.3-58.3]
• Matrix [1.5-1 -> 1.5-3]
• R.utils [2.12.1 -> 2.12.2]
• Rcpp [1.0.9 -> 1.0.10]
• Tplyr [1.0.1 -> 1.1.0]
• admiral [0.9.0 -> 0.10.1]
• admiraldev [0.2.0 -> 0.3.0]
• bit [4.0.4 -> 4.0.5]
• broom [1.0.1 -> 1.0.4]
• bslib [0.4.0 -> 0.4.2]
• cachem [1.0.6 -> 1.0.7]
• callr [3.7.2 -> 3.7.3]
• cli [3.4.1 -> 3.6.0]
• codetools [0.2-18 -> 0.2-19]
• colorspace [2.0-3 -> 2.1-0]
• curl [4.3.3 -> 5.0.0]
• digest [0.6.30 -> 0.6.31]
• dplyr [1.0.10 -> 1.1.0]
• emmeans [1.8.2 -> 1.8.5]
• evaluate [0.17 -> 0.20]
• fansi [1.0.3 -> 1.0.4]
• fastmap [1.1.0 -> 1.1.1]
• fontawesome [0.4.0 -> 0.5.0]
• forcats [0.5.2 -> 1.0.0]
• formatters [0.3.2 -> 0.4.0]
• fs [1.5.2 -> 1.6.1]
• gert [1.9.1 -> 1.9.2]
• ggplot2 [3.3.6 -> 3.4.1]
• gh [1.3.1 -> 1.4.0]
• haven [2.5.1 -> 2.5.2]
• highr [0.9 -> 0.10]
• htmltools [0.5.3 -> 0.5.4]
• httpuv [1.6.6 -> 1.6.9]
• httr [1.4.4 -> 1.4.5]
• huxtable [5.5.0 -> 5.5.2]
• isoband [0.2.6 -> 0.2.7]
• janitor [2.1.0 -> 2.2.0]
• jsonlite [1.8.3 -> 1.8.4]
• knitr [1.40 -> 1.42]
• lubridate [1.9.0 -> 1.9.2]
• metatools [0.1.3 -> 0.1.5]
• mgcv [1.8-41 -> 1.8-42]
• nlme [3.1-160 -> 3.1-162]
• openssl [2.0.4 -> 2.0.6]
• pkgbuild [1.3.1 -> 1.4.0]
• pkgdown [2.0.6 -> 2.0.7]
• pkgload [1.3.1 -> 1.3.2]
• purrr [0.3.5 -> 1.0.1]
• r2rtf [0.3.5 -> 1.0.1]
• ragg [1.2.4 -> 1.2.5]
• readr [2.1.3 -> 2.1.4]
• readxl [1.4.1 -> 1.4.2]
• rlang [1.0.6 -> 1.1.0]
• rmarkdown [2.17 -> 2.20]
• roxygen2 [7.2.1 -> 7.2.3]
• rtables [0.5.1 -> 0.6.0]
• sass [0.4.2 -> 0.4.5]
• shiny [1.7.3 -> 1.7.4]
• sourcetools [0.1.7 -> 0.1.7-1]
• stringi [1.7.8 -> 1.7.12]
• styler [1.8.0 -> 1.9.1]
• survival [3.4-0 -> 3.5-5]
• svglite [2.1.0 -> 2.1.1]
• testthat [3.1.5 -> 3.1.7]
• tidyr [1.2.1 -> 1.3.0]
• timechange [0.1.1 -> 0.2.0]
• tinytex [0.42 -> 0.44]
• tm [0.7-9 -> 0.7-11]
• utf8 [1.2.2 -> 1.2.3]
• vroom [1.6.0 -> 1.6.1]
• whisker [0.4 -> 0.4.1]
• xfun [0.34 -> 0.37]
• yaml [2.3.6 -> 2.3.7]
• checkmate [* -> 2.1.0]
• httr2 [* -> 0.2.2]

GitHub =============================

• envsetup [pharmaverse/envsetup@main: 539514d8 -> 9ae5f214]
• xportr [atorus-research/xportr@main: e5987358 -> cd4da91e]

RSPM ===============================

• htmlwidgets [repo: CRAN -> RSPM; ver: 1.5.4 -> 1.6.1]
• metacore [atorus-research/metacore@main -> 0.1.2]
• renv [0.16.0 -> 0.17.0]
• tibble [repo: CRAN -> RSPM; ver: 3.1.8 -> 3.2.0]
• vctrs [repo: CRAN -> RSPM; ver: 0.5.1 -> 0.5.2]

[robertdevine]

@DeclanHodges, please see the link below:
atorus-research/xportr#78

Should we wait on the xportr::xportr_write() 2.0.x.patch or rollback renv lock to latest stable production app for pilot3?

Please advise. Thank you.
@thomas-neitmann , @laxamanaj, @bms63

[robertdevine]

Error in xportr_write():
! The following validation failed:
• Formats 'TRTDUR', 'EVNTDESC', 'SRCDOM', and 'SRCVAR' must have a valid format.

Backtrace:
▆

1. ├─... %>% ...
2. └─xportr::xportr_write(., "submission/datasets/adtte.xpt", label = "AE Time To 1st Derm. Event Analysis")
3. └─rlang::abort(c("The following validation failed:", checks))

[bms63]

This was a workaround from the hackathon to deal with this issue I believe. Will need to update for your purposes

xportr_format(adas_spec$var_spec %>% mutate_at(c("format"), ~replace_na(.,'')), domain = "ADADAS")

[robertdevine]

Thank you, @bms63

@DeclanHodges, in summary, xportr_format implementation in the .R script should address the validation check issue
involving the four variables {'TRTDUR', ''EVNTDESC', 'SRCDOM', 'SRCVAR' }. [In my posit Cloud sandbox with merge
from today's @laxamanaj update to main only these four ADTTE variables failed validation, a subset of the 18 variables in
the Issue #89 description. Should have this resolved next week.] Wrapping up for the week. Thanks again.

[robertdevine]

@DeclanHodges, this issue is corrected in my posit Cloud sandbox. Worth noting, the xportr_format in adtte.R (main) is necessary (and sufficient) to format {'TRTSDT', 'TRTEDT', and 'STARTDT'} DATE9 type, for consistency with the {'TRTDUR', 'EVNTDESC','SRCDOM' , 'SRCVAR'} variables the issue is best addressed in the spec itself. Thanks again.

[DeclanHodges]

Hi @robertdevine, it sounds like you've found a solution. Thanks for looking into this! Are you okay to update the specs?

[robertdevine]

Thanks, @DeclanHodges, yes, I will update the specs today and issue PR adding you as 'Reviewer'. We can also move the issue from 'In Progress' to 'In Review' on the Project Board. We should be able to close the issue this week.