Merge pull request #131 from ropensci/document

Set install = FALSE by default for document()

R/processData.R

@@ -717,7 +717,7 @@ project_data_path <- function(file = NULL) {
 #' @rdname document
 #' @title Build documentation for a data package using DataPackageR.
 #' @param path \code{character} the path to the data package source root.
-#' @param install \code{logical} install and reload the package. (default TRUE)
+#' @param install \code{logical} install the package. (default FALSE)
 #' @param ... additional arguments to \code{install}
 #' @returns Called for side effects. Returns TRUE on successful exit.
 #' @export
@@ -745,10 +745,10 @@ project_data_path <- function(file = NULL) {
 #' # call package_build to run the "foo.Rmd" processing and
 #' # build a data package.
 #' package_build(file.path(tempdir(), pname), install = FALSE)
-#' document(path = file.path(tempdir(), pname), install=FALSE)
+#' document(path = file.path(tempdir(), pname), install = FALSE)
 #' }
 #' }
-document <- function(path = ".", install = TRUE, ...) {
+document <- function(path = ".", install = FALSE, ...) {
   if (getOption('DataPackageR_verbose', TRUE)) cat("\n")
   usethis::proj_set(path = path)
   path <- usethis::proj_get()

README.Rmd

@@ -196,29 +196,30 @@ datapackage_skeleton(
 # These will be added to the NEWS.md file along with the DataVersion in the package source directory.
 # If the build is run in non-interactive mode, the description will read
 # "Package built in non-interactive mode". You may update it later.
-dir.create(file.path(tempdir(),"lib"))
-package_build(packageName = file.path(tempdir(),"mtcars20"), install = FALSE,
-              lib = file.path(tempdir(),"lib"))
+package_build(packageName = file.path(tempdir(),"mtcars20"))
 
 # Update the autogenerated roxygen documentation in data-raw/documentation.R. 
 # edit(file.path(tempdir(),"mtcars20","R","mtcars20.R"))
 
 # 4. Rebuild the documentation.
-document(file.path(tempdir(),"mtcars20"), install = FALSE,
-         lib = file.path(tempdir(),"lib"))
+document(file.path(tempdir(),"mtcars20"))
 
 # Let's use the package we just created.
-install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"), type = "source", repos = NULL)
-library(mtcars20)
+# During actual use, the temporary library does not need to be specified.
+temp_lib <- file.path(tempdir(),"lib")
+dir.create(temp_lib)
+install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"),
+                 type = "source", repos = NULL, lib = temp_lib)
+library(mtcars20, lib.loc = temp_lib)
 data("cars_over_20") # load the data
-cars_over_20  # Now we can use it.
-?cars_over_20 # See the documentation you wrote in data-raw/documentation.R.
 
 # We have our dataset!
 # Since we preprocessed it,
 # it is clean and under the 5 MB limit for data in packages.
 cars_over_20
 
+?cars_over_20 # See the documentation you wrote in data-raw/documentation.R.
+
 # We can easily check the version of the data
 data_version("mtcars20")
 

README.md

@@ -234,8 +234,8 @@ datapackage_skeleton(
   code_files = processing_code, 
   r_object_names = "cars_over_20", 
   path = tempdir()) 
-#> ✔ Creating 'C:/Users/dslager/AppData/Local/Temp/RtmpSCRvVa/mtcars20/'
-#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpSCRvVa/mtcars20'
+#> ✔ Creating 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20/'
+#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20'
 #> ✔ Creating 'R/'
 #> ✔ Writing 'DESCRIPTION'
 #> Package: mtcars20
@@ -251,7 +251,7 @@ datapackage_skeleton(
 #> RoxygenNote: 7.3.1
 #> ✔ Writing 'NAMESPACE'
 #> ✔ Setting active project to '<no active project>'
-#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpSCRvVa/mtcars20'
+#> ✔ Setting active project to 'C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20'
 #> ✔ Added DataVersion string to 'DESCRIPTION'
 #> ✔ Creating 'data-raw/'
 #> ✔ Creating 'data/'
@@ -266,9 +266,7 @@ datapackage_skeleton(
 # These will be added to the NEWS.md file along with the DataVersion in the package source directory.
 # If the build is run in non-interactive mode, the description will read
 # "Package built in non-interactive mode". You may update it later.
-dir.create(file.path(tempdir(),"lib"))
-package_build(packageName = file.path(tempdir(),"mtcars20"), install = FALSE,
-              lib = file.path(tempdir(),"lib"))
+package_build(packageName = file.path(tempdir(),"mtcars20"))
 #> 
 #> ✔ 1 data set(s) created by subsetCars.Rmd
 #> • cars_over_20
@@ -281,13 +279,13 @@ package_build(packageName = file.path(tempdir(),"mtcars20"), install = FALSE,
 #> Writing 'mtcars20.Rd'
 #> Writing 'cars_over_20.Rd'
 #> ── R CMD build ─────────────────────────────────────────────────────────────────
-#>          checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpSCRvVa\mtcars20/DESCRIPTION' ...  ✔  checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpSCRvVa\mtcars20/DESCRIPTION'
+#>          checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpuqBumR\mtcars20/DESCRIPTION' ...  ✔  checking for file 'C:\Users\dslager\AppData\Local\Temp\RtmpuqBumR\mtcars20/DESCRIPTION' (341ms)
 #>       ─  preparing 'mtcars20':
 #>    checking DESCRIPTION meta-information ...     checking DESCRIPTION meta-information ...   ✔  checking DESCRIPTION meta-information
 #>       ─  checking for LF line-endings in source and make files and shell scripts
 #>       ─  checking for empty or unneeded directories
 #>       ─  looking to see if a 'data/datalist' file should be added
-#>   ─  building 'mtcars20_1.0.tar.gz'
+#>       ─  building 'mtcars20_1.0.tar.gz'
 #>      
 #> Next Steps 
 #> 1. Update your package documentation. 
@@ -300,34 +298,25 @@ package_build(packageName = file.path(tempdir(),"mtcars20"), install = FALSE,
 #>    - Set up a github repository for your pacakge. 
 #>    - Add the github repository as a remote of your local package repository. 
 #>    -  git push  your local repository to gitub.
-#> [1] "C:/Users/dslager/AppData/Local/Temp/RtmpSCRvVa/mtcars20_1.0.tar.gz"
+#> [1] "C:/Users/dslager/AppData/Local/Temp/RtmpuqBumR/mtcars20_1.0.tar.gz"
 
 # Update the autogenerated roxygen documentation in data-raw/documentation.R. 
 # edit(file.path(tempdir(),"mtcars20","R","mtcars20.R"))
 
 # 4. Rebuild the documentation.
-document(file.path(tempdir(),"mtcars20"), install = FALSE,
-         lib = file.path(tempdir(),"lib"))
+document(file.path(tempdir(),"mtcars20"))
 #> ℹ Updating mtcars20 documentation
 #> ℹ Loading mtcars20
 #> [1] TRUE
 
 # Let's use the package we just created.
-install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"), type = "source", repos = NULL)
-#> Installing package into 'C:/Users/dslager/AppData/Local/Temp/Rtmpk5QUs0/temp_libpath1af01866231b'
-#> (as 'lib' is unspecified)
-library(mtcars20)
+# During actual use, the temporary library does not need to be specified.
+temp_lib <- file.path(tempdir(),"lib")
+dir.create(temp_lib)
+install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"),
+                 type = "source", repos = NULL, lib = temp_lib)
+library(mtcars20, lib.loc = temp_lib)
 data("cars_over_20") # load the data
-cars_over_20  # Now we can use it.
-#>    speed dist
-#> 44    22   66
-#> 45    23   54
-#> 46    24   70
-#> 47    24   92
-#> 48    24   93
-#> 49    24  120
-#> 50    25   85
-?cars_over_20 # See the documentation you wrote in data-raw/documentation.R.
 
 # We have our dataset!
 # Since we preprocessed it,
@@ -342,6 +331,8 @@ cars_over_20
 #> 49    24  120
 #> 50    25   85
 
+?cars_over_20 # See the documentation you wrote in data-raw/documentation.R.
+
 # We can easily check the version of the data
 data_version("mtcars20")
 #> [1] '0.1.0'

tests/testthat/test-document.R

@@ -50,6 +50,7 @@ NULL
     close(connection)
     expect_true(
       document(file.path(tempdir, "subsetCars"),
+               install = TRUE,
                lib = temp_libpath,
                quiet = ! getOption('DataPackageR_verbose', TRUE))
     )

vignettes/Using_DataPackageR.Rmd

@@ -1,6 +1,5 @@
 ---
 title: "Using DataPackageR"
-author: "Greg Finak <gfinak@fredhutch.org>"
 date: "`r Sys.Date()`"
 output: 
   rmarkdown::html_vignette:
@@ -153,13 +152,7 @@ This will be converted to an Rmd file with a proper yaml header, which will then
 Once the skeleton framework is set up, run the preprocessing code to build `cars_over_20`, and reproducibly enclose it in a package.
 
 ```{r , eval = rmarkdown::pandoc_available()}
-dir.create(file.path(tempdir(),"lib"))
-
-DataPackageR:::package_build(
-  file.path(tempdir(),"mtcars20"),
-  install = TRUE,
-  lib = file.path(tempdir(),"lib")
-)
+DataPackageR::package_build(file.path(tempdir(),"mtcars20"))
 ```
 
 ### Documenting your data set changes in NEWS.
@@ -216,8 +209,7 @@ The autogenerated documentation source is in the `documentation.R` file in `data
 You should update this file to properly document your objects. Then rebuild the documentation:
 
 ```{r rebuild_docs, eval = rmarkdown::pandoc_available()}
-dir.create(file.path(tempdir(),"lib")) # a temporary library directory
-document(file.path(tempdir(),"mtcars20"), lib = file.path(tempdir(),"lib"))
+DataPackageR::document(file.path(tempdir(),"mtcars20"))
 ```
 
 Updating documentation does not reprocess the data.
@@ -244,8 +236,12 @@ The data set documentation will be accessible via `?cars_over_20`, and the data
 # Create a temporary library to install into.
 dir.create(file.path(tempdir(),"lib"))
 
-# Let's use the package we just created.
-install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"), type = "source", repos = NULL, lib = file.path(tempdir(),"lib"))
+# Let's install the package we just created.
+# This can also be done with with `install = TRUE` in package_build() or document().
+
+install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"),
+                 type = "source", repos = NULL,
+                 lib = file.path(tempdir(),"lib"))
 lns <- loadNamespace
 if (!"package:mtcars20"%in%search())
   attachNamespace(lns('mtcars20',lib.loc = file.path(tempdir(),"lib"))) #use library() in your code

vignettes/YAML_Configuration_Details.Rmd

@@ -1,6 +1,5 @@
 ---
 title: "YAML Configuration Details"
-author: "Greg Finak <gfinak@fredhutch.org>"
 date: "`r Sys.Date()`"
 output: 
   rmarkdown::html_vignette: