From c356ee93a3db8e50b9e4de3a0a827149c7695e17 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kellysovacool@gmail.com>
Date: Sun, 20 Aug 2023 18:59:08 -0400
Subject: [PATCH] Fix roxygen package doc syntax

See https://github.com/r-lib/roxygen2/issues/1491
---
 DESCRIPTION             |  2 +-
 NEWS.md                 |  3 ++-
 R/schtools.R            |  5 ++---
 cran-comments.md        |  2 +-
 man/schtools-package.Rd | 46 +++++++++++++++++++++++++++++++++++++++++
 man/schtools.Rd         | 14 -------------
 6 files changed, 52 insertions(+), 20 deletions(-)
 create mode 100644 man/schtools-package.Rd
 delete mode 100644 man/schtools.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index a7161a5..c4a31c9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: schtools
 Title: Schloss Lab Tools for Reproducible Microbiome Research
-Version: 0.4.0.9001
+Version: 0.4.1
 Date: 2023-01-15
 Authors@R: 
     c(person(given = "Kelly",
diff --git a/NEWS.md b/NEWS.md
index 0a3284d..d58a826 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
-# schtools development version
+# schtools 0.4.1
 
 - Minor bug fix in `get_wildcards_tbl()` (#48, @kelly-sovacool).
+- Fix roxygen package doc syntax (https://github.com/r-lib/roxygen2/issues/1491, @kelly-sovacool).
 
 # schtools 0.4.0
 
diff --git a/R/schtools.R b/R/schtools.R
index 9207b8a..6567b01 100644
--- a/R/schtools.R
+++ b/R/schtools.R
@@ -7,6 +7,5 @@
 #' [website](http://www.schlosslab.org/schtools/) for more information,
 #' documentation, and examples.
 #'
-#' @docType package
-#' @name schtools
-NULL
+#' @keywords internal
+"_PACKAGE"
diff --git a/cran-comments.md b/cran-comments.md
index 35800dc..56b12f7 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,6 +1,6 @@
 ## Test environments
 
-- local macOS install; R 4.2.2
+- local macOS install; R 4.2.3
 - win-builder; R release
 - github-actions macOS-latest; R release
 - github-actions ubuntu-latest; R release, devel, and oldrel
diff --git a/man/schtools-package.Rd b/man/schtools-package.Rd
new file mode 100644
index 0000000..617fd78
--- /dev/null
+++ b/man/schtools-package.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/schtools.R
+\docType{package}
+\name{schtools-package}
+\alias{schtools}
+\alias{schtools-package}
+\title{schtools: Schloss Lab Tools for Reproducible Microbiome Research}
+\description{
+A collection of useful functions and example code created and used by the
+Schloss Lab for reproducible microbiome research. Perform common tasks like
+read files created by \href{https://mothur.org/}{mothur}, tidy up your microbiome
+data, and format rmarkdown documents for publication. See the
+\href{http://www.schlosslab.org/schtools/}{website} for more information,
+documentation, and examples.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{http://www.schlosslab.org/schtools/}
+  \item \url{https://github.com/SchlossLab/schtools}
+  \item Report bugs at \url{https://github.com/SchlossLab/schtools/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Kelly Sovacool \email{sovacool@umich.edu} (\href{https://orcid.org/0000-0003-3283-829X}{ORCID})
+
+Authors:
+\itemize{
+  \item Nicholas Lesniak \email{nlesniak@umich.edu} (\href{https://orcid.org/0000-0001-9359-5194}{ORCID})
+  \item Sarah Lucas (\href{https://orcid.org/0000-0003-1676-5801}{ORCID})
+  \item Courtney Armour (\href{https://orcid.org/0000-0002-5250-1224}{ORCID})
+  \item Patrick Schloss \email{pschloss@umich.edu}
+}
+
+Other contributors:
+\itemize{
+  \item Jacqueline Moltzau (\href{https://orcid.org/0000-0003-1398-5980}{ORCID}) [contributor]
+  \item Andrew Hannah [contributor]
+  \item Nielson Baxter [contributor]
+  \item Alyxandria Schubert [contributor]
+  \item Kathryn Iverson [contributor]
+}
+
+}
+\keyword{internal}
diff --git a/man/schtools.Rd b/man/schtools.Rd
deleted file mode 100644
index 001f48f..0000000
--- a/man/schtools.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/schtools.R
-\docType{package}
-\name{schtools}
-\alias{schtools}
-\title{schtools: Schloss Lab Tools for Reproducible Microbiome Research}
-\description{
-A collection of useful functions and example code created and used by the
-Schloss Lab for reproducible microbiome research. Perform common tasks like
-read files created by \href{https://mothur.org/}{mothur}, tidy up your microbiome
-data, and format rmarkdown documents for publication. See the
-\href{http://www.schlosslab.org/schtools/}{website} for more information,
-documentation, and examples.
-}