docs: fix some typos

general-package-development.Rmd

@@ -60,23 +60,23 @@ Experiment Data, Annotation, and Workflow packages are allowed additional space
 
 Due to hardware limitations on the Bioconductor Build System (BBS), it is
 recommended that the vignettes, man page examples, and unit tests do not require
-more than 8 GB of memory to run. 
+more than 8 GB of memory to run.
 
 ### Individual file size {#individual-file-size}
 
 For software packages, individual files must be <= 5MB.
 This restriction exists even after the package is accepted and added to the
 [_Bioconductor_][] repository. See [data section](#data) for
-advice on packages using large data files. 
+advice on packages using large data files.
 
 ### Undesirable files {#undesirable-files}
 
 The raw package directory should not contain unnecessary files, system files, or
 hidden files such as `.DS_Store`, `.project`, `.git`, cache files, log files,
-`*.Rproj`, `*.so`, etc. These files may be present in your local directory but should not be commited to
+`*.Rproj`, `*.so`, etc. These files may be present in your local directory but should not be committed to
 git (see [`.gitignore`]{#gitignore}). Any files or directories for other
 applications (Github Actions, devtool, etc) should ideally be in a different
-branch and not submitted to the _Bioconductor_ version of the package. 
+branch and not submitted to the _Bioconductor_ version of the package.
 
 ## R CMD check environment {#r-cmd-check-environment}
 

git-version-control.Rmd

@@ -51,7 +51,7 @@ repository.
 To make more extensive changes see [Fix bugs in devel and release][].
 
 Bug fixes can be ported to the current release branch. Use
-`cherry-pick` to identify the commmit(s) you would like to port. E.g.,
+`cherry-pick` to identify the commit(s) you would like to port. E.g.,
 for release 3.6, porting the most recent commit to devel
 
     BiocGenerics$ git checkout RELEASE_3_6
@@ -1085,7 +1085,7 @@ git clone --mirror git@git.bioconductor.org:packages/<PACKAGE>.git
 cd <PACKAGE>.git
 ```
 
-A mirror clone preserves all branches and refrences. 
+A mirror clone preserves all branches and references.
 
 2. Identify the offending file(s)
 

index.Rmd

@@ -1,4 +1,4 @@
---- 
+---
 title: "Bioconductor Packages: Development, Maintenance, and Peer Review"
 author:
   - Kevin Rue-Albrecht
@@ -27,7 +27,7 @@ knitr::include_graphics("https://raw.githubusercontent.com/Bioconductor/BiocStic
 
 The [_Bioconductor_][] project promotes high-quality, well documented, and interoperable software.
 These guidelines help to achieve this objective; they are not meant to put undue
-burden on package authors, and authors having difficultly satisfying guidelines
+burden on package authors, and authors having difficulty satisfying guidelines
 should seek advice on the [bioc-devel][bioc-devel-mail] mailing list.
 
 Package maintainers are urged to follow these guidelines as closely as possible

non-software-packages.Rmd

@@ -76,7 +76,7 @@ expected the majority of vignette code chunks are evaluated.
 
 * Workflows are git version controlled. Once the package is accepted it will be
   added to our git repository at git@git.bioconductor.org and instructions will
-  be sent for gaining access for maintainence.
+  be sent for gaining access for maintenance.
 
 
 ### Consistent formatting

r-code.Rmd

@@ -196,7 +196,7 @@ helper functions.
 * Nesting functions should be avoiding. It unnecessarily increases the main
   function length and makes the main function harder to read. Helper functions
   and internal functions should avoid being nested and include at the end of the
-  file or as a seperate file (e.g. internal.R, helpers.R, utils.R)
+  file or as a separate file (e.g. internal.R, helpers.R, utils.R)
 
 #### Function arguments {#function-arguments}
 
@@ -273,7 +273,7 @@ highly encouraged.
 * Do not leave in commented out code chunks that are not utilized
 * Commenting TODO's should be avoided in published package code
 
-#### Additonal style and formatting references
+#### Additional style and formatting references
 
 * [formatR][] a package that assists with formatting.
 

troubleshoot-build-report.Rmd

@@ -23,7 +23,7 @@ The schedule for software, data experiment, annotation, books, workflows can be
 found on the [check results page](http://bioconductor.org/checkResults/). In
 order for changes to be included in the report, changes should be committed to
 the Bioconductor git.bioconductor.org location the morning before the listed day
-with a valid version bump. 
+with a valid version bump.
 
 ## How do I reproduce the build system ERROR?
 
@@ -342,7 +342,7 @@ argument matching. Best described with the following example
 Notice the generic uses `breaks` while the setMethod uses `break`; This is an
 example of a partial argument match that will no longer be valid.
 
-Partial argument matching when envoking functions should also be avoided as
+Partial argument matching when invoking functions should also be avoided as
 part of best practices. For example
 
     mycoolfunction <- function( x, myargum, secondarg ) { code }
@@ -444,4 +444,3 @@ noted in Bioconductor 3.11
     Error:
     'calculateQCMetrics' is defunct.
     Use 'perCellQCMetrics' instead.
-

unit-tests.Rmd

@@ -58,7 +58,7 @@ Here is a `RUnit` test for `divideBy`:
         checkTrue(is.na(divideBy(4, 0)))
         checkEqualsNumeric(divideBy(4, 1.2345), 3.24, tolerance=1.0e-4)
     }
-    
+
 the equivalent test using `tinytest`:
 
     expect_equal(divideBy(4, 2), 2)
@@ -123,7 +123,7 @@ complete set of tests.
 RUnit, tinytest, and testthat are robust testing solutions that are great tools
 for package development, which you choose to use for your package largely comes
 down to personal preference. However here is a brief list of strengths and
-weaknesses of each. Bioconductor slighlty prefers testthat
+weaknesses of each. Bioconductor slightly prefers testthat
 
 ### RUnit Strengths ###
 
@@ -179,7 +179,7 @@ Three things are required:
    functions.
 2. Add a few small (and idiosyncratic) files in other directories.
 3. Make sure the *RUnit* and `r BiocStyle::Biocpkg("BiocGenerics")` packages are
-   available.   
+   available.
 
 Steps two and three are explained in [conventions for the build
 process](#conventions).
@@ -328,8 +328,8 @@ structure.
 1. Test files are placed in the `inst/tinytest` directory with names such as
 `test_FILE.R`.
 2. Remove `RUnit` function shells and extract the function bodies into a single
-script. 
-3. Include a `tinytest.R` file in the `tests` folder that runs: 
+script.
+3. Include a `tinytest.R` file in the `tests` folder that runs:
 ```
 if (requireNamespace("tinytest", quietly = TRUE))
     tinytest::test_package("PACKAGE")
@@ -344,7 +344,7 @@ that is tested by your unit tests. Packages with higher coverage
 have a lower chance of containing bugs.
 
 We highly recommend using the [covr package](https://cran.r-project.org/web/packages/covr/index.html) function
-`package_coverage()` for evaluation.  
+`package_coverage()` for evaluation.
 
 If tests are taking too long to achieve full test coverage, see [long tests][].
 Before implementing long tests we highly recommend reaching out to the
@@ -362,4 +362,3 @@ Some web resources worth reading:
 * [Agile software development][agile]
 * [Testing with testthat][]
 * [testthat: Get Started with Testing][]
-