Added required jackalope-package man file, updated docs

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: jackalope
 Type: Package
 Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
-Version: 1.1.3
-Authors@R: person(c("Lucas", "A."), "Nell", email = "lucas@lucasnell.com", 
+Version: 1.1.4
+Authors@R: person(c("Lucas", "A."), "Nell", email = "lucnell@gmail.com", 
                     role = c("cph", "aut", "cre"),
                     comment = c(ORCID = "0000-0003-3209-0517"))
 Description: Simply and efficiently
@@ -39,7 +39,7 @@ LinkingTo:
     Rhtslib,
     zlibbioc
 SystemRequirements: GNU make, C++11
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Suggests:
     coala,

NEWS.md

@@ -1,4 +1,9 @@
 
+# jackalope 1.1.4
+* Added required jackalope-package man file
+* Updated all docs with roxygen2 v7.2.3
+
+
 # jackalope 1.1.3
 * Remove one NULL_ENTRY to support STRICT_R_HEADERS
 

R/jackalope-package.R

@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom Rcpp evalCpp
+#' @import zlibbioc
+#' @useDynLib jackalope, .registration = TRUE
+## usethis namespace: end
+NULL

README.Rmd

@@ -21,7 +21,7 @@ set.seed(1) # for keeping the printing of `reference` below the same
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![R build status](https://github.com/lucasnell/jackalope/workflows/R-CMD-check/badge.svg)](https://github.com/lucasnell/jackalope/actions)
-[![codecov](https://codecov.io/gh/lucasnell/jackalope/branch/master/graph/badge.svg)](https://codecov.io/gh/lucasnell/jackalope)
+[![codecov](https://codecov.io/gh/lucasnell/jackalope/branch/master/graph/badge.svg)](https://app.codecov.io/gh/lucasnell/jackalope)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/jackalope)](https://cran.r-project.org/package=jackalope)
 
 

README.md

@@ -6,8 +6,8 @@ state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![R build
 status](https://github.com/lucasnell/jackalope/workflows/R-CMD-check/badge.svg)](https://github.com/lucasnell/jackalope/actions)
-[![codecov](https://codecov.io/gh/lucasnell/jackalope/branch/master/graph/badge.svg)](https://codecov.io/gh/lucasnell/jackalope)
-[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/jackalope)](https://cran.r-project.org/package=jackalope)
+[![codecov](https://codecov.io/gh/lucasnell/jackalope/branch/master/graph/badge.svg)](https://app.codecov.io/gh/lucasnell/jackalope)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/jackalope)](https://cran.r-project.org/package=jackalope)
 
 # jackalope <img src="man/figures/logo.png" align="right" alt="" width="120" />
 
@@ -90,7 +90,7 @@ install.packages("jackalope", type = "source")
 # remotes::install_github("lucasnell/jackalope")
 ```
 
-#### macOS, R version &gt;= 4.0.0
+#### macOS, R version \>= 4.0.0
 
 Follow the directions here to install R compiler tools:
 <https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/>.
@@ -130,7 +130,7 @@ withr::with_makevars(c(CPPFLAGS = "-Xclang -fopenmp", LDFLAGS = "-lomp"),
                      assignment = "+=")
 ```
 
-#### macOS, R version &gt;= 3.4\* and &lt; 4.0.0
+#### macOS, R version \>= 3.4\* and \< 4.0.0
 
 Add the following to the `.R/Makevars` file inside the home directory:
 

cran-comments.md

@@ -2,17 +2,18 @@
 
 This is a resubmission. In this version, I have done the following:
 
-- Remove one NULL_ENTRY to support STRICT_R_HEADERS
+- Added required jackalope-package man file
+- Updated all docs with roxygen2 v7.2.3
+- In CITATION, now using bibentry and for authors, using `c()` on person objects
 
 
 ## Test environments
 
-* macOS 11.4 (local), R 4.1.0
-* ubuntu 20.04.2 (GitHub Actions), R-devel, R 4.1.0, R 4.0.5
-* macOS 10.15.7 (GitHub Actions), R-devel, R 4.1.0, R 4.0.5
-* Windows (win-builder), R-devel, R 4.1.0, R 4.0.5
+* macOS 13.4.1 (local), R 4.3.1
+* ubuntu 20.04.2 (GitHub Actions), R-devel, R 4.3.1, R 4.2.3
+* macOS 10.15.7 (GitHub Actions), R-devel, R 4.3.1, R 4.2.3
+* Windows (win-builder), R-devel, R 4.3.1, R 4.2.3
 * Rhub
-    - Oracle Solaris 10, R-release, 32-bit
     - Fedora Linux, R-devel, clang (with valgrind)
 
 
@@ -26,13 +27,10 @@ There were no ERRORs or WARNINGs.
 There were 2 NOTEs:
 
 ```
-installed size is 21.3Mb
-  sub-directories of 1Mb or more:
-    art_profiles   1.5Mb
-    libs          19.1Mb
+Specified C++11: please drop specification unless essential
 ```
 
-The package makes extensive use of compiled code to improve performance.
+The package makes extensive use of C++11 code throughout.
 
 
 ```

inst/CITATION

@@ -1,18 +1,10 @@
-citHeader("To cite jackalope in publications use:")
-
-citEntry(entry = "Article",
-  title        = "{jackalope}: a swift, versatile phylogenomic and high-throughput sequencing simulator",
-  author       = personList(as.person("Lucas A. Nell")),
-  journal      = "{Molecular Ecology Resources}",
-  year         = "2020",
-  volume       = "20",
-  number       = "4",
-  pages        = "1132--1140",
-  url          = "https://doi.org/10.1111/1755-0998.13173",
-  doi          = "10.1111/1755-0998.13173",
-  textVersion  =
-  paste("Nell, Lucas A (2020).",
-        "jackalope: a swift, versatile phylogenomic and high-throughput sequencing simulator.",
-        "Molecular Ecology Resources 20(4): 1132-1140.",
-        "doi: 10.1111/1755-0998.13173.")
+bibentry(bibtype = "Article",
+    title        = "{jackalope}: a swift, versatile phylogenomic and high-throughput sequencing simulator",
+    author       = person(c("Lucas", "A"), "Nell", role = "aut"),
+    journal      = "Molecular Ecology Resources",
+    year         = 2020,
+    volume       = 20,
+    number       = 4,
+    pages        = "1132--1140",
+    doi          = "10.1111/1755-0998.13173"
 )