diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 00000000..6296c135 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 0.2.2 +Date: 2026-02-05 16:00:42 UTC +SHA: f493b90fe7801902326b70a8b312dfd204f3ceb0 diff --git a/cran-comments.md b/cran-comments.md index cda92671..f2ae4919 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -13,16 +13,14 @@ checking package dependencies ... NOTE use conditionally. ``` -To address the note: there have been no additional dependencies introduced to the package since the last CRAN release (`v0.2.0`). For reference, here was my justification for this note previously: +To address the note, here was my justification for this note in the previous release: > `tidyCDISC` is (nearly) a "one stop shop" application for clinical reporting in the pharmaceutical space. As such, it leverages many modules to perform many tasks. Many tasks require many packages. While preparing for CRAN submission, we've surgically paired down the dependency list to 37 packages that (I feel) are necessary. These are primarily "mainstream" packages, meaning they are maintained by reputable & well known authors & dev teams in the R community. ### Test Environments -* Github action performing linux check with old, current, and devel release of R -* Github action performing windows and macOS check with current R release +* RHub Github action performing linux, macOS, and Windows R CMD Check * Local windows `devtools::check()` -* RHub Check ## Downstream dependencies There are none. diff --git a/dev/02_dev.R b/dev/02_dev.R index c9136aa0..75774d99 100644 --- a/dev/02_dev.R +++ b/dev/02_dev.R @@ -274,11 +274,42 @@ urlchecker::url_update() # check on other distributions # _rhub -first_chk <- devtools::check_rhub() -cran_chk <- rhub::check_for_cran(check_args = c("--as-cran")) -rhub::check_on_windows(check_args = "--force-multiarch") -rhub::check_on_solaris() +# Deprecated: +# first_chk <- devtools::check_rhub() +# cran_chk <- rhub::check_for_cran(check_args = c("--as-cran")) +# rhub::check_on_windows(check_args = "--force-multiarch") +# rhub::check_on_solaris() + +# rhubv2! +# rhub::rhub_setup() +# rhub::rhub_doctor() +rhub::rhub_check() # select linux, macos, and windows + + +# reduce file size of images +utils::install.packages("imager") +library(imager) + +# Load the image +image_name <- "./vignettes/cran_figures/t_disp_red.PNG" +image_name <- "./vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.PNG" +image_name <- "./vignettes/cran_figures/t_disp.PNG" +image_name <- "./vignettes/cran_figures/line_plot_mean_over_time_breakdown.PNG" +image_name <- "./vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.PNG" +image_name <- "./vignettes/cran_figures/04-diabp_mean.jpeg" +image_name <- "./vignettes/cran_figures/03-age_mean.PNG" +image_name <- "./vignettes/cran_figures/drill_down_events.PNG" +image_name <- "./vignettes/cran_figures/drill_down_visits.PNG" + +my_img <- load.image(image_name) + +# Save as JPEG (specify quality for JPEG compression) +save.image(my_img, gsub("PNG", "jpeg", image_name), quality = 0.25) # Quality is a value between 0 and 1 + + + + # _win devel devtools::check_win_devel() diff --git a/vignettes/cran_figures/03-age_mean.PNG b/vignettes/cran_figures/03-age_mean.PNG deleted file mode 100644 index 8e19ec0d..00000000 Binary files a/vignettes/cran_figures/03-age_mean.PNG and /dev/null differ diff --git a/vignettes/cran_figures/03-age_mean.jpeg b/vignettes/cran_figures/03-age_mean.jpeg new file mode 100644 index 00000000..96d7fef9 Binary files /dev/null and b/vignettes/cran_figures/03-age_mean.jpeg differ diff --git a/vignettes/cran_figures/04-diabp_mean.PNG b/vignettes/cran_figures/04-diabp_mean.PNG deleted file mode 100644 index 045249e5..00000000 Binary files a/vignettes/cran_figures/04-diabp_mean.PNG and /dev/null differ diff --git a/vignettes/cran_figures/04-diabp_mean.jpeg b/vignettes/cran_figures/04-diabp_mean.jpeg new file mode 100644 index 00000000..147912b1 Binary files /dev/null and b/vignettes/cran_figures/04-diabp_mean.jpeg differ diff --git a/vignettes/cran_figures/drill_down_events.PNG b/vignettes/cran_figures/drill_down_events.PNG deleted file mode 100644 index d18f6dd1..00000000 Binary files a/vignettes/cran_figures/drill_down_events.PNG and /dev/null differ diff --git a/vignettes/cran_figures/drill_down_events.jpeg b/vignettes/cran_figures/drill_down_events.jpeg new file mode 100644 index 00000000..135ff979 Binary files /dev/null and b/vignettes/cran_figures/drill_down_events.jpeg differ diff --git a/vignettes/cran_figures/drill_down_visits.PNG b/vignettes/cran_figures/drill_down_visits.PNG deleted file mode 100644 index 94a1b42c..00000000 Binary files a/vignettes/cran_figures/drill_down_visits.PNG and /dev/null differ diff --git a/vignettes/cran_figures/drill_down_visits.jpeg b/vignettes/cran_figures/drill_down_visits.jpeg new file mode 100644 index 00000000..b34313a2 Binary files /dev/null and b/vignettes/cran_figures/drill_down_visits.jpeg differ diff --git a/vignettes/cran_figures/line_plot_mean_over_time_breakdown.PNG b/vignettes/cran_figures/line_plot_mean_over_time_breakdown.PNG deleted file mode 100644 index b19f8384..00000000 Binary files a/vignettes/cran_figures/line_plot_mean_over_time_breakdown.PNG and /dev/null differ diff --git a/vignettes/cran_figures/line_plot_mean_over_time_breakdown.jpeg b/vignettes/cran_figures/line_plot_mean_over_time_breakdown.jpeg new file mode 100644 index 00000000..906c2672 Binary files /dev/null and b/vignettes/cran_figures/line_plot_mean_over_time_breakdown.jpeg differ diff --git a/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.PNG b/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.PNG deleted file mode 100644 index 5ed23267..00000000 Binary files a/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.PNG and /dev/null differ diff --git a/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.jpeg b/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.jpeg new file mode 100644 index 00000000..af3a8c2f Binary files /dev/null and b/vignettes/cran_figures/line_plot_mean_over_time_tidyCDISC.jpeg differ diff --git a/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC.PNG b/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC.PNG deleted file mode 100644 index 36f71d84..00000000 Binary files a/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC.PNG and /dev/null differ diff --git a/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.PNG b/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.PNG deleted file mode 100644 index 84a1b7f2..00000000 Binary files a/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.PNG and /dev/null differ diff --git a/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.jpeg b/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.jpeg new file mode 100644 index 00000000..59c3d860 Binary files /dev/null and b/vignettes/cran_figures/quick_upload_then_tg_tidyCDISC_red.jpeg differ diff --git a/vignettes/cran_figures/t_disp.PNG b/vignettes/cran_figures/t_disp.PNG deleted file mode 100644 index ff6c0f76..00000000 Binary files a/vignettes/cran_figures/t_disp.PNG and /dev/null differ diff --git a/vignettes/cran_figures/t_disp_red.PNG b/vignettes/cran_figures/t_disp_red.PNG deleted file mode 100644 index a00822e9..00000000 Binary files a/vignettes/cran_figures/t_disp_red.PNG and /dev/null differ diff --git a/vignettes/cran_figures/t_disp_red.jpeg b/vignettes/cran_figures/t_disp_red.jpeg new file mode 100644 index 00000000..1f90404d Binary files /dev/null and b/vignettes/cran_figures/t_disp_red.jpeg differ diff --git a/vignettes/getting_started.Rmd b/vignettes/getting_started.Rmd index ed8d3872..a0891cfa 100644 --- a/vignettes/getting_started.Rmd +++ b/vignettes/getting_started.Rmd @@ -68,7 +68,7 @@ Our first stop will be the table generator!
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/quick_upload_then_tg_tidyCDISC_red.PNG") +knitr::include_graphics("cran_figures/quick_upload_then_tg_tidyCDISC_red.jpeg") ```
@@ -111,7 +111,7 @@ In order to build a table, we need only drag a variable block to the "Variable"
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/03-age_mean.PNG") +knitr::include_graphics("cran_figures/03-age_mean.jpeg") ```
@@ -121,7 +121,7 @@ Similarly, we can drag in `DIABP` from the `ADVS` and use the `MEAN` block to ca
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/04-diabp_mean.PNG") +knitr::include_graphics("cran_figures/04-diabp_mean.jpeg") ```
@@ -143,7 +143,7 @@ When one of these tables is selected, like disposition (Accounting of Subjects)^
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/t_disp_red.PNG") +knitr::include_graphics("cran_figures/t_disp_red.jpeg") ```
@@ -165,7 +165,7 @@ Let's assume a scenario where we want to check on our patients' vital signs thro
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/line_plot_mean_over_time_tidyCDISC.PNG") +knitr::include_graphics("cran_figures/line_plot_mean_over_time_tidyCDISC.jpeg") ```
@@ -175,7 +175,7 @@ Using the **"Separate plots by"** drop down list, we select `TRT01A` to investig
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/line_plot_mean_over_time_breakdown.PNG") +knitr::include_graphics("cran_figures/line_plot_mean_over_time_breakdown.jpeg") ```
@@ -211,7 +211,7 @@ After selecting a `USUBJID`, we scroll down the page to examine that patient's d
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/drill_down_events.PNG") +knitr::include_graphics("cran_figures/drill_down_events.jpeg") ```
@@ -223,7 +223,7 @@ Switching to the "Visits" tab, we can see that this patient did indeed have cons
```{r, echo=FALSE, out.width="95%", fig.align = 'center'} -knitr::include_graphics("cran_figures/drill_down_visits.PNG") +knitr::include_graphics("cran_figures/drill_down_visits.jpeg") ```