From 1e04d747ce96dde22665f9dcf5e3e7755c654175 Mon Sep 17 00:00:00 2001 From: Cameron Nugent Date: Wed, 3 Sep 2025 10:26:12 -0300 Subject: [PATCH] docs(Testing-as-cran-build): minor changes to remove warnings and errors when building as cran should allow for submission to CRAN when time comes --- .DS_Store | Bin 0 -> 6148 bytes .Rbuildignore | 16 ++++++++++++++++ .gitignore | 2 ++ DESCRIPTION | 9 ++++++--- vignettes/KinformR-penetrance_and_ibd.Rmd | 3 ++- vignettes/KinformR-variant_scoring.Rmd | 2 +- 6 files changed, 27 insertions(+), 5 deletions(-) create mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..0002c62e06e3ff263d0594388d9749b802b4e413 GIT binary patch literal 6148 zcmeHK%SyvQ6rE|SO({Ya3SADkE!Y=gaT8+w0VBFlsfj5XjG5A;W>E@R>ks)QevkLg zOu%B+BKBUGIrlk}IgoiU#<;r-`;6I)F$)?ZN2Nm0T^XvGWJHc*r1Kz_0azcw+{FGm z;J4RV$Rv9R^6%dtM`_mUeeznpv9sH>npWGo^PXhxWq!6yU4L8ME0;-_s#;G6td`Z9+MU&^e=_ch;b^e#iq&|~>x$9v zc)e~}2Zu+e7t`nXC6RBMP7Z7<*)v$eJ1Ax~uihewW%3A~GP}$oBnF59Vt^RfZU)S` zV70fK23kEaKnzqcfct}hhUge9G^(uwI=nt(yn%=UI=&?kg+a$)p%Ee=T$cjsQf{6Y zT$h7im^{Z|p;4DJu4aaD%*^HEg{#@YFH}0?jz;Q<0b*d2fx0$rJpa$(m#KW@ZEWzNHq1q@#j5E>MR&$6%omM?t?T Q2c(ODB7{0(;1?M90!1E4WB>pF literal 0 HcmV?d00001 diff --git a/.Rbuildignore b/.Rbuildignore index e13c405..a8eff32 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,19 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ +^doc$ +^Meta$ +^\.git$ +^./.git/*$ +CHANGELOG.md +KinformR.Rproj +^.Rproj.user/*$ +.Rhistory +.flake8 +.gitignore +.ignore_spelling.txt +.lintr +.pre-commit-config.yaml +.Rproj.user +.git +.github \ No newline at end of file diff --git a/.gitignore b/.gitignore index 16b31c3..7a43b82 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ .ignore_spelling.txt .flake8 .lintr +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 9e59962..e3523cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,11 @@ Package: KinformR -Title: Relationship-informed pedigree and variant scoring +Title: Relationship-Informed Pedigree and Variant Scoring Version: 0.1.0 Authors@R: - person("Cameron", "Nugent", , "cam.nugent@sequencebio.com", role = c("aut", "cre"), + person("Cameron M.", "Nugent", , "cam.nugent@sequencebio.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1135-2605")) +Author: Cameron M. Nugent +Maintainer: Cameron M. Nugent Description: The KinformR R package is meant to aid in comparative evaluation of families and candidate variants in rare-variant association studies. The package can be used for @@ -20,4 +22,5 @@ VignetteBuilder: knitr Suggests: devtools, testthat, - knitr + knitr, + rmarkdown diff --git a/vignettes/KinformR-penetrance_and_ibd.Rmd b/vignettes/KinformR-penetrance_and_ibd.Rmd index 87ae310..869165a 100644 --- a/vignettes/KinformR-penetrance_and_ibd.Rmd +++ b/vignettes/KinformR-penetrance_and_ibd.Rmd @@ -3,7 +3,7 @@ title: "KinformR - penetrance and idb informed scoring of families" author: "Cameron M. Nugent" date: "`r format(Sys.time(), '%d %B, %Y')`" data: "`r Sys.Date()`" -output: pdf_document #rmarkdown::html_vignette # +output: rmarkdown::pdf_document # rmarkdown::html_vignette # pdf_document: df_print: kable vignette: > @@ -96,6 +96,7 @@ show(penetrance.df) ``` The output includes seven columns that with the following information: + |Output Column|Description| |---|---| |family|The family id.| diff --git a/vignettes/KinformR-variant_scoring.Rmd b/vignettes/KinformR-variant_scoring.Rmd index 1042fee..ae66954 100644 --- a/vignettes/KinformR-variant_scoring.Rmd +++ b/vignettes/KinformR-variant_scoring.Rmd @@ -3,7 +3,7 @@ title: "KinformR - pedigree-informed rare variant association scoring" author: "Cameron M. Nugent" date: "`r format(Sys.time(), '%d %B, %Y')`" data: "`r Sys.Date()`" -output: pdf_document #rmarkdown::html_vignette # +output: rmarkdown::pdf_document #rmarkdown::html_vignette # pdf_document: df_print: kable vignette: >