From 104d457f99a220b1f2b7c567caa7102e42e4dd0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Wed, 15 Jan 2025 11:40:59 +0100 Subject: [PATCH 1/9] Add initial hook --- inst/report/pkg_template.qmd | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index 387c821..3495acc 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -30,6 +30,18 @@ knitr::opts_chunk$set( cache = FALSE ) library("tools") +# Adapted from https://stackoverflow.com/a/52327256 +library("knitr") +knit_hooks$set(showDetails = function(before, options, envir, summary) { + if (before) { + str <- "
\n" + paste0(str, "", summary,"\n") + return() + } else { + return("\n
") + } +}) + ``` # Context From dda85f7dcaee65f43e8726dfaea62e24a1f94d6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Mon, 27 Jan 2025 11:56:02 +0100 Subject: [PATCH 2/9] Improve hooks --- inst/report/pkg_template.qmd | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index 3495acc..aecf2af 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -32,14 +32,12 @@ knitr::opts_chunk$set( library("tools") # Adapted from https://stackoverflow.com/a/52327256 library("knitr") -knit_hooks$set(showDetails = function(before, options, envir, summary) { - if (before) { - str <- "
\n" - paste0(str, "", summary,"\n") - return() - } else { - return("\n
") - } +hook_old <- knitr::knit_hooks$get("output") +knit_hooks$set(output = function(x, options) { + if (!is.null(options$summary)){ + x <- paste0("

", options$summary,"
", hook_old(x, options), "
") + } + x }) ``` @@ -108,7 +106,7 @@ unlist(.Platform) R's capabilities: -```{r capabilities} +```{r capabilities, summary = "Capabilities details"} capabilities() ``` From fafe8e93dd0617fce21969d484f9cf62a8ed185f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 30 Jan 2025 14:36:04 +0100 Subject: [PATCH 3/9] Add typst to render pdfs --- inst/report/pkg_template.qmd | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index 6f727c3..b33d50e 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -14,13 +14,13 @@ format: embed-resources: true gfm: html-math-method: webtex - # typst: - # toc: true - # section-numbering: 1.1.1 - # df-print: default - # margin: - # x: 2cm - # y: 2cm + typst: + toc: true + section-numbering: 1.1.1 + df-print: default + margin: + x: 2cm + y: 2cm --- ```{r setup, include = FALSE} From a495f745f20804b728c32c73cc2c09781275bf3a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 6 Mar 2025 14:06:41 +0100 Subject: [PATCH 4/9] Add logo for pkgdown --- pkgdown/favicon/apple-touch-icon.png | Bin 0 -> 4881 bytes pkgdown/favicon/favicon-96x96.png | Bin 0 -> 2539 bytes pkgdown/favicon/favicon.ico | Bin 0 -> 15086 bytes pkgdown/favicon/favicon.svg | 3 +++ pkgdown/favicon/site.webmanifest | 21 +++++++++++++++++++ pkgdown/favicon/web-app-manifest-192x192.png | Bin 0 -> 5267 bytes pkgdown/favicon/web-app-manifest-512x512.png | Bin 0 -> 15449 bytes 7 files changed, 24 insertions(+) create mode 100644 pkgdown/favicon/apple-touch-icon.png create mode 100644 pkgdown/favicon/favicon-96x96.png create mode 100644 pkgdown/favicon/favicon.ico create mode 100644 pkgdown/favicon/favicon.svg create mode 100644 pkgdown/favicon/site.webmanifest create mode 100644 pkgdown/favicon/web-app-manifest-192x192.png create mode 100644 pkgdown/favicon/web-app-manifest-512x512.png 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zym@Gq_5~Jri^od>X}_C1zA@S1=D)F{hMspS>b(d&&o(Rc>5*RQ;*z|))zS5lU&=zs z4^imk4@chwgRr3IOAoz|GcQ{dB$^a-eGR>*oX>N50bmG!eV0`{s;7M$B_{_qv2S}M z17Q>U0oL+b-7-R(JL|KG77sPHk&dT&>h(yeD7R%JQ1Q>n&c+61#8Yw`E#e<{jlW2j0y1Lw!edHbmxEBH zq+T1U1GQy0`H`JM=RDc)vaQj!Ix(zS=Jo!QGC9Bn80P@=y}T2s?@7*E#9rOeBq^s5 zv{y`@QCXsWDpNp%?s$rNI(YVk8esU3m7i=fC@hevTVRJFD$8b0i0LZ6d&-G-z~G zPT)Kjs)Ko5JRZSiJE@2QEoKWHj(Sx?^5tU}Qg0@S-HME>jn@*mgAZ=281Tk?{SSh8 zUejBiFovf+>A9C1XY=*j$}2u?hrorTu;AH$4MEVGovJLzqHd8urLLs3xj!ppo0WU8 zsnxrQKtroHB(Cwst6!rACPVnttPbO!gZT068_%*c1)!=8I(J^qRJFJXe9@<51MQI3 zw{_YZh3X0?+MzS;TI&p_Z$Olw-j|#!Nc60#-e`yFh|Am0Y(MpGr2w9%s5_juM-2A} zi;B%?Q?P@l-RRtB{-PS?gBy5qv3uD|93Y$nn-L3$aSs13al+B(L2@8Q`QPJz8Th{p dWK Date: Thu, 6 Mar 2025 14:50:11 +0100 Subject: [PATCH 5/9] Add option to hide Reverse dependencies section --- inst/report/pkg_template.qmd | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index 5d9c6ae..d435505 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -7,6 +7,7 @@ params: package: NULL image: "rhub/ref-image" assessment_path: "assessments/dplyr.rds" + hide_reverse_deps: true format: html: toc: true @@ -110,6 +111,8 @@ row.names(deps) <- NULL knitr::kable(deps, row.names = TRUE) ``` +::: {.content-hidden unless-meta="hide_reverse_deps"} + ## Reverse dependencies Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse dependencies: @@ -118,6 +121,8 @@ Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse de cat(paste(d_riskmetric$reverse_dependencies, collapse = ", ")) ``` +::: + ## Namespace Overall the package has `r length(d_riskmetric$exported_namespace)` exported objects. From 9cc3721711be5c119e0f0c474f51c93bd7571afc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 6 Mar 2025 14:51:16 +0100 Subject: [PATCH 6/9] Set the right level for the titles --- inst/report/pkg_template.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index d435505..ecf54a3 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -132,15 +132,15 @@ Overall the package has `r length(d_riskmetric$exported_namespace)` exported obj d_riskmetric$export_help[sort(d_riskmetric$exported_namespace)] ``` -### Examples +## Examples There are `r if (!is_na["has_examples"]) sum(d_riskmetric$has_examples)` help pages with examples, from `r if (!is_na["has_examples"]) {length(d_riskmetric$has_examples)}` (`r if (!is_na["has_examples"]) {sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100)} else {"?"} ` %). -### NEWS +## NEWS The package has `r if ("has_news" %in% names(d_riskmetric) && !is.null(d_riskmetric$has_news)) print(d_riskmetric$has_news)` NEWS file and it is `r if (is.null(d_riskmetric$news_current) && !d_riskmetric$news_current) "not"` current. -### License +## License The package uses `r if ("license" %in% names(d_riskmetric) && !is.null(d_riskmetric$license)) print(d_riskmetric$license)`. From 8d03bbde39eb60048188a5f4edf24809a77434f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 6 Mar 2025 15:34:21 +0100 Subject: [PATCH 7/9] Update/check for website --- DESCRIPTION | 4 ++-- R/riskmetic.R | 39 ++++++++++++++++++++++++++++++++++++ inst/report/pkg_template.qmd | 4 ++-- man/riskreports-package.Rd | 2 +- man/summary_table.Rd | 17 ++++++++++++++++ 5 files changed, 61 insertions(+), 5 deletions(-) create mode 100644 man/summary_table.Rd diff --git a/DESCRIPTION b/DESCRIPTION index 35779bf..6c267f9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Package: riskreports Title: Package Validation Reports -Version: 0.0.0.9004 +Version: 0.0.0.9006 Authors@R: c( person("Lluís", "Revilla Sancho", , "lluis.revilla_sancho@roche.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9747-2570")), person("R Validation Hub", role = "cph", email = "r-val-hub-maintainers@lists.r-consortium.org") ) -Description: Documents package checks for validation in a pharmaceutic +Description: Documents package checks for validation in a pharmaceutic context. License: MIT + file LICENSE URL: https://github.com/pharmaR/riskreports, https://pharmar.github.io/riskreports/ diff --git a/R/riskmetic.R b/R/riskmetic.R index 92a4b9f..7028b96 100644 --- a/R/riskmetic.R +++ b/R/riskmetic.R @@ -52,3 +52,42 @@ risk_error <- function(output, y) { } y } + +is_logical <- function(x) { + if (x == 1 || isTRUE(x)) { + "Yes" + } else { + x + } +} + +simple_cap <- function(x) { + s <- toupper(substr(x, 1, 1)) + paste0(s, substring(x, 2)) +} + +#' Summary talbe +#' +#' @param risk The output of `assessment()`. +#' +#' @returns A data.frame with the two columns one for the fields and one for the values. +#' @export +summary_table <- function(risk) { + is_na <- sapply(x, function(x) { + is.na(x) || (is.character(x) && startsWith(x, "no applicable")) + }) + y <- risk[, !is_na] + y[] <- lapply(y, is_logical) + y$has_examples <- sprintf("%.2f%%", y$has_examples*100) + y$bugs_status <- sprintf("%.2f%%", y$bugs_status*100) + if (y$has_vignettes > 0) { + y$has_vignettes <- "Yes" + } + x <- t(y) + yx <- simple_cap(gsub("_", " ", rownames(x), fixed = TRUE)) + df <- as.data.frame(x) + df <- cbind(Section = yx, Values = df) + colnames(df) <- c("Section", "Values") + rownames(df) <- NULL + df +} diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index ecf54a3..d52e963 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -93,8 +93,8 @@ d_riskmetric <- readRDS(risk_path) # Assesment produces a data.frame with one row r_riskmetric <- riskreports::assessment(d_riskmetric) -is_na <- sapply(r_riskmetric, function(x){is.na(x) || (is.character(x) && startsWith(x, "no applicable"))}) -knitr::kable(t(r_riskmetric[, !is_na])) # Use this to have some summary text and report it. +x <- summary_table(r_riskmetric) +knitr::kable(x, row.names = FALSE align = "cc") # Use this to have some summary text and report it. # d_riskmetric ``` diff --git a/man/riskreports-package.Rd b/man/riskreports-package.Rd index 67d80e8..ddd19ae 100644 --- a/man/riskreports-package.Rd +++ b/man/riskreports-package.Rd @@ -22,7 +22,7 @@ Useful links: Other contributors: \itemize{ - \item F. Hoffmann-La Roche AG [copyright holder, funder] + \item R Validation Hub \email{r-val-hub-maintainers@lists.r-consortium.org} [copyright holder] } } diff --git a/man/summary_table.Rd b/man/summary_table.Rd new file mode 100644 index 0000000..9495e16 --- /dev/null +++ b/man/summary_table.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/riskmetic.R +\name{summary_table} +\alias{summary_table} +\title{Summary talbe} +\usage{ +summary_table(risk) +} +\arguments{ +\item{risk}{The output of \code{assessment()}.} +} +\value{ +A data.frame with the two columns one for the fields and one for the values. +} +\description{ +Summary talbe +} From 4101aca5e4f916b829ed4a5f5653b12c160cd7c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 6 Mar 2025 17:49:11 +0100 Subject: [PATCH 8/9] Add everything --- .Rbuildignore | 6 ++++-- NAMESPACE | 3 +++ R/riskmetic.R | 5 +---- inst/report/pkg_template.qmd | 5 ++++- 4 files changed, 12 insertions(+), 7 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 716a627..1f97ea3 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -10,5 +10,7 @@ inst/source/* inst/source/Library inst/source/*Rcheck inst/source/*tar.gz -inst/*.rds = = = = = -= +inst/*.rds +_pkgdown.yaml +pkgdown +.github diff --git a/NAMESPACE b/NAMESPACE index 5747cbb..a28e5be 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,7 +3,10 @@ export(assessment) export(check_reporter) export(environ_report) +export(license_url) +export(licensing_match) export(options_report) export(package_report) +export(summary_table) importFrom(methods,is) importFrom(tools,check_packages_in_dir_details) diff --git a/R/riskmetic.R b/R/riskmetic.R index 7028b96..89a0b51 100644 --- a/R/riskmetic.R +++ b/R/riskmetic.R @@ -73,10 +73,7 @@ simple_cap <- function(x) { #' @returns A data.frame with the two columns one for the fields and one for the values. #' @export summary_table <- function(risk) { - is_na <- sapply(x, function(x) { - is.na(x) || (is.character(x) && startsWith(x, "no applicable")) - }) - y <- risk[, !is_na] + y <- risk y[] <- lapply(y, is_logical) y$has_examples <- sprintf("%.2f%%", y$has_examples*100) y$bugs_status <- sprintf("%.2f%%", y$bugs_status*100) diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd index d52e963..2128716 100644 --- a/inst/report/pkg_template.qmd +++ b/inst/report/pkg_template.qmd @@ -93,7 +93,10 @@ d_riskmetric <- readRDS(risk_path) # Assesment produces a data.frame with one row r_riskmetric <- riskreports::assessment(d_riskmetric) -x <- summary_table(r_riskmetric) +is_na <- sapply(x, function(x) { + is.na(x) || (is.character(x) && startsWith(x, "no applicable")) + }) +x <- summary_table(r_riskmetric[, !is_na]) knitr::kable(x, row.names = FALSE align = "cc") # Use this to have some summary text and report it. # d_riskmetric ``` From b2b1c21065e5866a51ac10a5024e90d9b3227342 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 6 Mar 2025 18:00:15 +0100 Subject: [PATCH 9/9] Update to match what is on this branch --- NAMESPACE | 2 -- R/riskmetic.R | 2 +- man/summary_table.Rd | 4 ++-- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index a28e5be..a6f07f6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,8 +3,6 @@ export(assessment) export(check_reporter) export(environ_report) -export(license_url) -export(licensing_match) export(options_report) export(package_report) export(summary_table) diff --git a/R/riskmetic.R b/R/riskmetic.R index 89a0b51..6538747 100644 --- a/R/riskmetic.R +++ b/R/riskmetic.R @@ -66,7 +66,7 @@ simple_cap <- function(x) { paste0(s, substring(x, 2)) } -#' Summary talbe +#' Summary table #' #' @param risk The output of `assessment()`. #' diff --git a/man/summary_table.Rd b/man/summary_table.Rd index 9495e16..3a20272 100644 --- a/man/summary_table.Rd +++ b/man/summary_table.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/riskmetic.R \name{summary_table} \alias{summary_table} -\title{Summary talbe} +\title{Summary table} \usage{ summary_table(risk) } @@ -13,5 +13,5 @@ summary_table(risk) A data.frame with the two columns one for the fields and one for the values. } \description{ -Summary talbe +Summary table }