Wrong message `All variables in specification file are in dataset`
ynsec37 opened this issue · comments
Dear developer,
When I change the input ADSL that contains only one variable STUDYID, the message All variables in specification file are in dataset still be output.
I am not sure I understand right for this message, it will mean that we have all necessary variables defined in the ADSL variable metadata specification and only be output when the input data frame have these variables
Reproducible Example
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(xportr)
data("adsl_xportr")
ADSL <- adsl_xportr
spec_path <- system.file(file.path("specs", "ADaM_spec.xlsx"), package = "xportr")
var_spec <- readxl::read_xlsx(spec_path, sheet = "Variables") %>%
dplyr::rename(type = "Data Type") %>%
dplyr::rename_with(tolower)
dataset_spec <- readxl::read_xlsx(spec_path, sheet = "Datasets") %>%
dplyr::rename(label = "Description") %>%
dplyr::rename_with(tolower)
ADSL %>% dplyr::select(STUDYID) %>%
xportr_metadata(var_spec, "ADSL") %>%
xportr_type(verbose = "warn") %>%
xportr_length(verbose = "warn") %>%
xportr_label(verbose = "warn") %>%
xportr_order(verbose = "warn") %>%
xportr_format() %>%
xportr_df_label(dataset_spec, "ADSL") %>%
xportr_write("adsl.xpt")
#>
#> ── All variables in specification file are in dataset ──
#>
#> ── All variables in dataset are ordered ──
#>
Session Information
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.3 (2023-03-15)
#> os Ubuntu 22.04.4 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2024-04-10
#> pandoc 2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] RSPM (R 4.2.0)
#> cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.2.0)
#> checkmate 2.1.0 2022-04-21 [1] RSPM
#> cli 3.6.2 2023-12-11 [1] RSPM (R 4.2.0)
#> digest 0.6.34 2024-01-11 [1] RSPM (R 4.2.0)
#> dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.2.0)
#> evaluate 0.20 2023-01-17 [1] RSPM (R 4.2.0)
#> fansi 1.0.4 2023-01-22 [1] RSPM
#> fastmap 1.1.1 2023-02-24 [1] RSPM
#> forcats 1.0.0 2023-01-29 [1] RSPM
#> fs 1.6.3 2023-07-20 [1] RSPM (R 4.2.0)
#> generics 0.1.3 2022-07-05 [1] RSPM
#> glue 1.7.0 2024-01-09 [1] RSPM (R 4.2.0)
#> haven 2.5.4 2023-11-30 [1] RSPM (R 4.2.0)
#> hms 1.1.3 2023-03-21 [1] RSPM (R 4.2.0)
#> htmltools 0.5.5 2023-03-23 [1] RSPM
#> knitr 1.42 2023-01-25 [1] RSPM (R 4.2.0)
#> lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.2.0)
#> pillar 1.9.0 2023-03-22 [1] RSPM (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.2.0)
#> purrr 1.0.2 2023-08-10 [1] RSPM (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [1] RSPM
#> R.methodsS3 1.8.2 2022-06-13 [1] RSPM
#> R.oo 1.25.0 2022-06-12 [1] RSPM
#> R.utils 2.12.2 2022-11-11 [1] RSPM
#> R6 2.5.1 2021-08-19 [1] RSPM (R 4.2.0)
#> readr 2.1.5 2024-01-10 [1] RSPM (R 4.2.0)
#> readxl 1.4.3 2023-07-06 [1] RSPM (R 4.2.0)
#> reprex 2.0.2 2022-08-17 [1] RSPM (R 4.2.0)
#> rlang 1.1.3 2024-01-10 [1] RSPM (R 4.2.0)
#> rmarkdown 2.21 2023-03-26 [1] RSPM (R 4.2.0)
#> rstudioapi 0.14 2022-08-22 [1] RSPM (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.2.0)
#> stringi 1.7.12 2023-01-11 [1] RSPM
#> stringr 1.5.1 2023-11-14 [1] RSPM (R 4.2.0)
#> styler 1.9.1 2023-03-04 [1] RSPM
#> tibble 3.2.1 2023-03-20 [1] RSPM (R 4.2.0)
#> tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.2.0)
#> tzdb 0.3.0 2022-03-28 [1] RSPM (R 4.2.0)
#> utf8 1.2.3 2023-01-31 [1] RSPM
#> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.2.0)
#> withr 3.0.0 2024-01-16 [1] RSPM (R 4.2.0)
#> xfun 0.38 2023-03-24 [1] RSPM (R 4.2.0)
#> xportr * 0.4.0 2024-04-10 [1] Github (atorus-research/xportr@1a612ed)
#> yaml 2.3.7 2023-01-23 [1] RSPM
#>
#> [1] /usr/local/lib/R/site-library
#> [2] /usr/local/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
ummm...that doesn't look right!! Thanks for flagging this @ynsec37!!
@atorus-research/xportr-development-team can anyone take a look at this please?
@bms63 I can take this up once I'm back from vacation
Thank you Eli!! I'm surprised we don't have a test for this.