Merge pull request #38 from mayer79/release_candidate

Release candidate

.Rbuildignore

@@ -1,5 +1,11 @@
-^.*\.Rproj$
-^\.Rproj\.user$
+^LICENSE\.md$
+^packaging.R$
+[.]Rproj$
+^backlog$
+^cran-comments.md$
+^logo.png$
 ^cran-comments\.md$
 ^doc$
-^Meta$
+^Meta$
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -6,3 +6,4 @@ doc
 Meta
 /doc/
 /Meta/
+inst/doc

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: missRanger
 Title: Fast Imputation of Missing Values
-Version: 2.1.4
-Date: 2021-05-19
+Version: 2.1.5
+Date: 2022-01-29
 Authors@R: 
  person(given = "Michael",
  family = "Mayer",
@@ -22,25 +22,25 @@ Description: Alternative implementation of the beautiful 'MissForest'
  to do multiple imputation when repeating the call to missRanger(). A
  formula interface allows to control which variables should be imputed
  by which.
-License: GPL(>= 2)
-URL: https://github.com/mayer79/missRanger
-BugReports: https://github.com/mayer79/missRanger/issues
+License: GPL (>= 2)
 Depends: 
  R (>= 3.5.0)
-VignetteBuilder: 
- knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
+URL: https://github.com/mayer79/missRanger
+BugReports: https://github.com/mayer79/missRanger/issues
 Imports: 
  ranger,
  FNN,
  stats,
  utils
 Suggests: 
- knitr,
- dplyr,
  mice,
- rmarkdown,
+ dplyr,
  survival,
- testthat
+ knitr,
+ rmarkdown,
+ testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Config/testthat/edition: 3

NEWS.md

@@ -1,12 +1,20 @@
+# missRanger 2.1.5
+
+Maintenance release,
+
+- switching to testthat 3,
+- changing the package structure, and
+- bringing vignettes into right order.
+
 # missRanger 2.1.4
 
 ## Minor changes
 
 - Now using progress bar instead of "." to show progress (when verbose = 1).
 
-# missRanger 2.1.2 & 2.1.3
+# missRanger 2.1.2 and 2.1.3
 
-## Maintainance update
+## Maintenance update
 
 - Fixing failing unit tests.
 

README.md

@@ -15,7 +15,7 @@ install.packages("missRanger")
 Latest version from github:
 ``` r
 library(devtools)
-install_github("mayer79/missRanger", subdir = "release/missRanger")
+install_github("mayer79/missRanger")
 ```
 
 ## Examples

cran-comments.md

@@ -1,32 +1,25 @@
-## Re-Re-Re-Resubmission
+This is a maintenance release, switching to 
 
-I don't get rid of the note on LazyData. Do I simply need to remove that line in the description file?
+- testthat 3,
+- modifying vignette order,
+- improving the way how the package is being updated/generated.
 
-## Re-Re-Resubmission
+## R CMD check results seem okay
 
-Note from incoming pre-checks:
+checking for unstated dependencies in examples ... OK
+ WARNING
+ 'qpdf' is needed for checks on size reduction of PDFs
 
-* checking LazyData ... NOTE
- 'LazyData' is specified without a 'data' directory
-
-I have now set LazyData to false. 
+## Online check results seem okay (2 notes below)
 
-## Re-Resubmission
-
-This is an update of the resubmission to fix one failing unit test, see e-mail below. I overlooked additional unit tests failures on M1Mac. I don't really know what is going on. However, they all seem to be related to a smallish dataset. I have replaced it with a larger dataset and hope the problems will vanish.
-
-## Resubmission:
-
-Fixing a failing unit test on Solaris which needs to be fixed according to Brian's e-mail below:
-
-"
-Dear maintainer,
-
-Please see the problems shown on
-<https://cran.r-project.org/web/checks/check_results_missRanger.html>.
-
-Please correct before 2021-04-04 to safely retain your package on CRAN.
-
-The CRAN Team
-"
+- check_win_devel()
+- check_rhub()
 
+Found the following (possibly) invalid DOIs:
+ DOI: 10.1093/bioinformatics/btr597
+ From: DESCRIPTION
+ Status: Forbidden
+ Message: 403
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+ 'lastMiKTeXException'

packaging.R

@@ -1,26 +1,21 @@
-#=====================================================================================
-# BUILD THE PACKAGE
-#=====================================================================================
+#=============================================================================
+# Put together the package
+#=============================================================================
 
-if (FALSE) {
- library(ranger)
- library(FNN)
- lapply(list.files("R", full.names = TRUE), source)
-}
+# WORKFLOW: UPDATE EXISTING PACKAGE
+# 1) Modify package content and documentation.
+# 2) Increase package number in "use_description" below.
+# 3) Go through this script and carefully answer "no" if a "use_*" function
+# asks to overwrite the existing files. Or just skip that function call.
 
 library(usethis)
-library(devtools)
 
-# Create a new package
-dir.create(file.path("release"))
-pkg <- file.path("release", "missRanger")
-
-create_package(
- pkg,
+# Sketch of description file
+use_description(
  fields = list(
  Title = "Fast Imputation of Missing Values",
  Type = "Package",
- Version = "2.1.4",
+ Version = "2.1.5",
  Date = Sys.Date(),
  Description = "Alternative implementation of the beautiful 'MissForest' algorithm used to impute 
  mixed-type data sets by chaining random forests, introduced by Stekhoven, D.J. and 
@@ -33,87 +28,78 @@ create_package(
  repeating the call to missRanger(). 
  A formula interface allows to control which variables should be imputed by which.",
  `Authors@R` = "person('Michael', 'Mayer', email = '[email protected]', role = c('aut', 'cre', 'cph'))",
- URL = "https://github.com/mayer79/missRanger",
- BugReports = "https://github.com/mayer79/missRanger/issues",
  Depends = "R (>= 3.5.0)",
- VignetteBuilder = "knitr",
- License = "GPL(>= 2)",
  LazyData = NULL,
- Maintainer = "Michael Mayer <[email protected]>"),
- open = FALSE)
+ Maintainer = "Michael Mayer <[email protected]>"
+ ),
+ roxygen = TRUE
+)
+
+use_gpl_license(2)
+use_github_links() # use this if this project is on github
 
-file.copy(file.path(pkg, "DESCRIPTION"), to = getwd(), overwrite = TRUE)
-# Use package has no option to look for pkg, so we first copy description from pkg, modify it and move back
+# Your files that do not belong to the package itself (others are added by "use_* function")
+use_build_ignore(c("^packaging.R$", "[.]Rproj$", "^backlog$",
+ "^cran-comments.md$", "^logo.png$"), escape = FALSE)
+
+# Required external packages
 use_package("FNN", "imports")
 use_package("ranger", "Imports")
 use_package("stats", "Imports")
 use_package("utils", "Imports")
 
 use_package("dplyr", "Suggests")
-use_package("knitr", "Suggests")
 use_package("mice", "Suggests")
-use_package("rmarkdown", "Suggests")
 use_package("survival", "Suggests")
-use_package("testthat", "Suggests")
-
-# Set up other files -------------------------------------------------
-# use_readme_md()
-# use_news_md()
-# use_cran_comments()
-# use_testthat()
-
-# Copy readme etc.
-file.copy(c(".Rbuildignore", "NEWS.md", "README.md", 
- "cran-comments.md", "DESCRIPTION"), 
- pkg, overwrite = TRUE)
-
-# Copy R scripts and document them
-if (!dir.exists(file.path(pkg, "R"))) {
- dir.create(file.path(pkg, "R"))
-}
-file.copy(list.files("R", full.names = TRUE), file.path(pkg, "R"), overwrite = TRUE)
-devtools::document(pkg)
 
-# Logo
+# If your code uses the pipe operator %>%
+# use_pipe()
+
+# If your package contains data. Google how to document
+# use_data()
+
+# Add short docu in Markdown (without running R code)
+use_readme_md()
+
+# Longer docu in RMarkdown (with running R code). Often quite similar to readme.
+use_vignette("missRanger")
+use_vignette("multiple_imputation")
+use_vignette("working_with_censoring")
+
+# If you want to add unit tests
+use_testthat()
+# use_test("test-missRanger.R")
+
+# On top of NEWS.md, describe changes made to the package
+use_news_md()
+
+# Add logo
 use_logo("logo.png")
-dir.create(file.path(pkg, "man", "figures"))
-file.copy(file.path("man", "figures", "logo.png"),
- file.path(pkg, "man", "figures", "logo.png"), overwrite = TRUE)
 
-# Tests
-if (!dir.exists(file.path(pkg, "tests"))) {
- dir.create(file.path(pkg, "tests"))
-}
-file.copy("tests", pkg, recursive = TRUE)
-test(pkg)
-
-if (TRUE) {
- # Copy vignette
- # use_vignette(name = "missRanger", title = "missRanger")
- dir.create(file.path(pkg, "vignettes"))
- dir.create(file.path(pkg, "doc"))
- dir.create(file.path(pkg, "Meta"))
- file.copy(list.files("vignettes", full.names = TRUE),
- file.path(pkg, "vignettes"), overwrite = TRUE)
-
- devtools::build_vignettes(pkg)
-}
+# If package goes to CRAN: infos (check results etc.) for CRAN
+use_cran_comments()
 
-# Check
-check(pkg, manual = TRUE, cran = TRUE)
 
-# Create
-# build(pkg)
+#=============================================================================
+# Finish package building (can use fresh session)
+#=============================================================================
 
-# Install
-# install(pkg)
+library(devtools)
 
-check_win_devel(pkg)
+document()
+test()
+build_vignettes()
+check(manual = TRUE, cran = TRUE)
+build()
+# build(binary = TRUE)
+install()
 
-rhub::check_for_cran(pkg)
-rhub::check_on_windows(pkg)
-rhub::check_on_linux(pkg)
-rhub::check_on_macos(pkg)
-rhub::check_on_solaris(pkg)
+# Run only if package is public(!) and should go to CRAN
+if (FALSE) {
+ check_win_devel()
+ check_rhub()
 
-devtools::release(pkg)
+ # Wait until above checks are passed without relevant notes/warnings
+ # then submit to CRAN
+ release()
+}