From 1a669c704998164938608fce43719b02fbf71cd1 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Tue, 16 Jun 2026 11:28:39 +0200 Subject: [PATCH] Fix typos --- build-check-bioccheck.Rmd | 2 +- docs/package-review-checklist.md | 6 +++--- documentation.Rmd | 4 ++-- index.Rmd | 2 +- unit-tests.Rmd | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/build-check-bioccheck.Rmd b/build-check-bioccheck.Rmd index 300ddb2..34bfec5 100644 --- a/build-check-bioccheck.Rmd +++ b/build-check-bioccheck.Rmd @@ -7,7 +7,7 @@ version. The package should `R CMD build`, `R CMD check`, and `BiocCheck` without ERROR. -See useful tools like [devools][] and [BiocCheck][] for more information. +See useful tools like [devtools][] and [BiocCheck][] for more information. As Bioconductor moves towards integration with diff --git a/docs/package-review-checklist.md b/docs/package-review-checklist.md index c415ebf..de0719b 100644 --- a/docs/package-review-checklist.md +++ b/docs/package-review-checklist.md @@ -44,7 +44,7 @@ Example: Seurat and data.frames are not Bioconductor classes. Packages certainly may keep this interoperability and generality but they should also be able to work _directly_ with the equivalent Bioconductor class in this case likely a SummarizedExperiment or SingleCellExperiment (maybe with a designed wrapper function, e.g). The majority -of documentation and runnable code should emphasize/demonstarte the interaction +of documentation and runnable code should emphasize/demonstrate the interaction with Bioconductor objects (it may be in addition to the others capabilities). @@ -73,7 +73,7 @@ Refer to the [DESCRIPTION](https://contributions.bioconductor.org/description.ht - [ ] `URL` field. - [ ] `Video` field. Optional. - [ ] `Collate` field. Optional. -- [ ] `BiocType` field. (one of: Softare, ExperimentData, Annotation, Workflow, Book) +- [ ] `BiocType` field. (one of: Software, ExperimentData, Annotation, Workflow, Book) - [ ] `Config/Bioconductor/UnsupportedPlatforms`. Optional. If package designed NOT to work on a specific OS - [ ] Use of Remotes is NOT allowed. All packages must be on CRAN/Bioconductor @@ -92,7 +92,7 @@ strongly encouraged. Using both Authors@R and Maintainer/Author is not allowed! - [ ] Selective imports using `importFrom` instead of *import all* with `import`. Except where appropriate (like class structures and extensions or heavily utilized packages) - [ ] Individual functions/methods are exported instead of regular expression matching all. - [ ] NAMESPACE and DESCRIPTION Depends/Imports/Suggests/Enhances consistency. -- [ ] Avoid names of packages, functions, and classes that already exist in Bioconductor infrastrure or could be easily confused +- [ ] Avoid names of packages, functions, and classes that already exist in Bioconductor infrastructure or could be easily confused ## The NEWS file diff --git a/documentation.Rmd b/documentation.Rmd index 0aafb98..31b1997 100644 --- a/documentation.Rmd +++ b/documentation.Rmd @@ -82,7 +82,7 @@ the order that they are displayed on the package homepage and when the `browseVignettes()` function is called. Vignettes will show up in alphabetical order, which may not be a logical ordering without further specification. One approach to controlling the order of the -vignettes is to use a number in the `VignettteIndexEntry` setting, +vignettes is to use a number in the `VignetteIndexEntry` setting, e.g. using numbers `1-9`, if you have a single digit number of vignettes, or `01-99` if you have ten or more vignettes. For example, the first vignette could specify in the header: @@ -129,7 +129,7 @@ objective, models, unique functions, key points, etc that distinguish the package from other packages in the same area. This is a requirement of Bioconductor package vignettes. It should include a short motivation for the package in general as well as motivation for inclusion of the package in -Biconductor. When relevant, a brief review and comparison of packages with +Bioconductor. When relevant, a brief review and comparison of packages with similar functionality or scope should be provided either in the Introduction or in a separate dedicated vignette section. diff --git a/index.Rmd b/index.Rmd index 80edc9e..5127e03 100644 --- a/index.Rmd +++ b/index.Rmd @@ -184,6 +184,6 @@ knitr::write_bib(c( [Valgrind]: http://valgrind.org/ [Xcode]: https://developer.apple.com/xcode/ -[devools]: https://devtools.r-lib.org/reference/check.html +[devtools]: https://devtools.r-lib.org/reference/check.html [BiocCheck]: https://www.bioconductor.org/packages/BiocCheck/ [R-Universe]: https://r-universe.dev/search diff --git a/unit-tests.Rmd b/unit-tests.Rmd index 122836c..745ef7c 100644 --- a/unit-tests.Rmd +++ b/unit-tests.Rmd @@ -215,7 +215,7 @@ Writing unit tests is easy, though your Bioconductor package must be set up properly so that `R CMD check MyPackage` finds and run your tests. We take some pains to describe exactly how things should be set up, and what is going on behind the scenes. (See the [next -section](#r-unit-during-develoment) for the simple technique to use when you +section](#r-unit-during-development) for the simple technique to use when you want to test only a small part of your code). The standard command `R CMD check MyPackage` sources and runs all R @@ -251,7 +251,7 @@ There are two steps: `MyPackage/inst/unitTests/test_homeBrewArithmetic.R` -### Using Tests During Development {#r-unit-during-develoment} +### Using Tests During Development {#r-unit-during-development} R CMD check MyPackage