cat2write lines

DESCRIPTION

@@ -41,7 +41,7 @@ Suggests:
     knitr,
     pkgbuild,
     pkgload,
-    roxygen2 (>= 7.0.1),
+    roxygen2 (>= 6.0.1),
     rmarkdown,
     rstudioapi
 RoxygenNote: 7.1.1

NEWS.md

@@ -65,7 +65,7 @@ instead.
 
 (Github issue/PR numbers in parentheses)
 
-* New [vignette](http://mc-stan.org/rstantools/articles/) walking through the package creation process. (#9) (thanks to Stefan Siegert)
+* New [vignette](https://mc-stan.org/rstantools/articles/) walking through the package creation process. (#9) (thanks to Stefan Siegert)
 
 * `rstan_package_skeleton()` now calls `usethis::create_package()` instead of `utils::package.skeleton()`. (#28)
 

R/init_cpp.R

@@ -36,35 +36,26 @@ init_cpp <- function(name, path) {
   if (!missing(path))
     file <- file.path(path, file)
 
-  cat(
-    "// Generated by the rstantools package\n\n",
+  writeLines(c(
+    "// Generated by the rstantools package",
+    "", "",
     "#include <R.h>",
     "#include <Rinternals.h>",
     "#include <R_ext/Rdynload.h>",
     "#include <R_ext/Visibility.h>",
     "#include <Rversion.h>",
-    sep = "\n",
-    file = file,
-    append = FALSE
-  )
-
-  cat(
-    "\n\nstatic const R_CallMethodDef CallEntries[] = {",
+    "", "",
+    "static const R_CallMethodDef CallEntries[] = {",
     "  {NULL, NULL, 0}",
     "};",
-    sep = "\n",
-    file = file,
-    append = TRUE
-  )
-
-  cat(
-    paste0("\n\nvoid attribute_visible R_init_", name, "(DllInfo *dll) {"),
+    "", "",
+    paste0("void attribute_visible R_init_", name, "(DllInfo *dll) {"),
     "  // next line is necessary to avoid a NOTE from R CMD check",
     "  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);",
     "  R_useDynamicSymbols(dll, TRUE); // necessary for .onLoad() to work",
-    "}",
-    sep = "\n",
-    file = file,
-    append = TRUE
+    "}"
+    ),
+    con = file
   )
+  return(invisible(NULL))
 }

R/rstan_create_package.R

@@ -236,12 +236,11 @@ rstan_create_package <- function(path,
   message("Configuring Stan compile and module export instructions ...")
   rstan_config(pkgdir)
 
-  cat(
-    readLines(.system_file("Read_and_delete_me")), "\n",
-    file = file.path(pkgdir, "Read-and-delete-me"),
-    sep = "\n",
-    append = TRUE
-  )
+  # open = "at" implies text is appended
+  con <- file(file.path(pkgdir, "Read-and-delete-me"), open = "at")
+  writeLines(readLines(.system_file("Read_and_delete_me")), con)
+  close(con)
+
   message(
     domain = NA,
     sprintf(

R/rstan_package_utils.R

@@ -98,24 +98,8 @@
     if (acc) {
       # create/overwrite file
       if (msg) message("Adding ", basename(dest_file), " file ...")
-      cat(file_lines, sep = "\n", file = dest_file) # can't this fail?
+      writeLines(file_lines, con = dest_file)
     }
   }
-  ## acc <- has_file && !is_stanfile # create stan file if acc = TRUE
-  ## if (acc) {
-  ##   # non-stan file found: don't overwrite
-  ##   if (warn) .warning_nowrite(file.path(basename(pkgdir), ...))
-  ## } else {
-  ##   # stan file found: only overwrite if changed
-  ##   if (noedit && (file_lines[1] != noedit_msg)) {
-  ##     # add "noedit" to top of file
-  ##     file_lines <- c(noedit_msg, "", file_lines)
-  ##   }
-  ##   old_lines <- readLines(dest_file)
-  ##   acc <- !identical(old_lines, file_lines)
-  ##   if (acc) {
-  ##     cat(file_lines, sep = "\n", file = dest_file) # can't this fail?
-  ##   }
-  ## }
   invisible(acc)
 }

R/update_description.R

@@ -73,11 +73,6 @@
   if(acc) {
     if(msg) message("Updating DESCRIPTION ...")
     desc_pkg$write()
-    ## cat(desc_pkg$str(normalize = FALSE), "\n",
-    ##     file = file.path(pkgdir, "DESCRIPTION"))
-    ## dep_fields <- dep_fields[dep_fields %in% colnames(desc_pkg)]
-    ## write.dcf(desc_pkg, file = file.path(pkgdir, "DESCRIPTION"),
-    ##           keep.white = dep_fields)
   }
   if(!auto_config && msg) {
     if(has_rstantools) {

R/use_rstan.R

@@ -136,11 +136,10 @@ use_rstan <- function(pkgdir = ".", license = TRUE, auto_config = TRUE) {
   if (.is_generic_namespace(namespc)) {
     # automatically update default NAMESPACE
     if (msg) message("Updating NAMESPACE ...")
-    cat("# Generated by roxygen2: fake comment so roxygen2 overwrites silently.",
-        namespc[!grepl("^#", namespc)],
-        req_lines,
-        file = file.path(pkgdir, "NAMESPACE"),
-        sep = "\n")
+    writeLines(c("# Generated by roxygen2: fake comment so roxygen2 overwrites silently.",
+                 namespc[!grepl("^#", namespc)],
+                 req_lines),
+                 con = file.path(pkgdir, "NAMESPACE"))
     acc <- TRUE # namespace was modified
   } else {
     # print message stating required dependencies

tests/testthat/RStanTest/test-rstan_package_skeleton_plus.R

@@ -82,11 +82,11 @@ file.copy(from = "test-postsamp.R",
 # roxygen2 can't overwrite NAMESPACE unless it created it,
 # so trick it into thinking it did
 # (and add the rstan stuff or else you get errors...)
-cat("# Generated by roxygen2: do not edit by hand",
-    "",
-    "import(Rcpp,methods)",
-    "useDynLib(RStanTest, .registration = TRUE)", sep = "\n",
-    file = file.path(pkg_path, pkg_name, "NAMESPACE"))
+writeLines(c("# Generated by roxygen2: do not edit by hand",
+             "",
+             "import(Rcpp,methods)",
+             "useDynLib(RStanTest, .registration = TRUE)"),
+           con = file.path(pkg_path, pkg_name, "NAMESPACE"))
 
 roxygen2::roxygenize(pkg_name) # run roxygen2
 utils::install.packages(pkg_name, repos = NULL, type = "source")

tests/testthat/test-rstan_config.R

@@ -99,16 +99,16 @@ test_that("Unmodified Stan src files are not overwritten", {
 
 # fake .o files
 invisible(sapply(gsub("\\.stan$", "", basename(stan_files)), function(sf) {
-  cat("fake .o file\n",
-      file = file.path(pkg_dest_path, "src",
-                       rstantools:::.stan_prefix(sf, ".o")))
+  writeLines("fake .o file",
+             con = file.path(pkg_dest_path, "src",
+                             rstantools:::.stan_prefix(sf, ".o")))
 }))
 
 # dummy src files
 src_files <- c("foo.cpp", "stanExports_foo.txt", "abcstanExports_foo.cc")
 invisible(sapply(src_files, function(sf) {
-  cat("// fake source file\n",
-      file = file.path(pkg_dest_path, "src", sf))
+  writeLines("// fake source file\n",
+             con = file.path(pkg_dest_path, "src", sf))
 }))
 
 

vignettes/developer-guidelines.Rmd

@@ -6,7 +6,7 @@ output:
   rmarkdown::html_vignette:
     toc: true
 vignette: >
-  %\VignetteIndexEntry{Developer Guidelines}
+  %\VignetteIndexEntry{Guidelines for Developers of R Packages Interfacing with Stan}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -17,7 +17,7 @@ One of the coolest things about working on a project like Stan has been seeing
 some of our users begin to develop tools for making Stan more accessible to
 audiences that may otherwise not benefit from what Stan offers. In particular,
 recently we have started seeing a growing number of R packages that provide
-high-level interfaces to Stan, using the [__rstan__](https://mc-stan.org/rstan) 
+high-level interfaces to Stan, using the [__rstan__](https://mc-stan.org/rstan/) 
 package for estimating models without requiring that the user be familiar with 
 the Stan modeling language itself.
 
@@ -56,7 +56,7 @@ package should be an exception definitely let us know.
 which you should use to create the basic structure of your package. (As of
 `v2.0.0` this replaces the `rstan_package_skeleton` function.) This will set up
 a package with functionality for pre-compiled Stan programs, in the style of the
-[__rstanarm__](https://mc-stan.org/rstanarm) package (source code:
+[__rstanarm__](https://mc-stan.org/rstanarm/) package (source code:
 https://github.com/stan-dev/rstanarm).
 
 * Use version control (e.g., git).
@@ -171,10 +171,10 @@ decent grammar and actual sentences wherever possible.
 
 ### Recommended resources
 
-* Hadley Wickham's [book on R packages](http://r-pkgs.had.co.nz/). If you are 
-interested in developing an R package that interfaces with Stan but are not an 
-experienced package developer, we recommend Hadley's book, which is free to read
-online. Even if you are an experienced developer of R packages, Hadley's book is
+* Hadley Wickham and Jenny Bryan's [book on R packages](https://r-pkgs.org/). If you 
+are interested in developing an R package that interfaces with Stan but are not an 
+experienced package developer, we recommend this book, which is free to read
+online. Even if you are an experienced developer of R packages, the book is
 still a great resource.
 
 * If you need help setting up your package or have questions about these 

vignettes/minimal-rstan-package.Rmd

@@ -30,7 +30,7 @@ if(dir.exists(PATH)) {
 
 In this vignette we will walk through the steps necessary for creating an
 R package that depends on Stan by creating a package with one function
-that fits a simple linear regression. Before continuing, we recommend that you first read the other vignette [_Guidelines for Developers of R Packages Interfacing with Stan_](http://mc-stan.org/rstantools/articles/developer-guidelines.html).
+that fits a simple linear regression. Before continuing, we recommend that you first read the other vignette [_Guidelines for Developers of R Packages Interfacing with Stan_](https://mc-stan.org/rstantools/articles/developer-guidelines.html).
 
 ## Creating the package skeleton
 
@@ -156,7 +156,7 @@ model {
   y ~ normal(intercept + beta * x, sigma);
 }
 "
-cat(stan_prog, file = file.path(PATH, "inst", "stan", "lm.stan"))
+writeLines(stan_prog, con = file.path(PATH, "inst", "stan", "lm.stan"))
 rstan_config(PATH)
 ```
 
@@ -213,7 +213,7 @@ lm_stan <- function(x, y, ...) {
   return(out)
 }
 "
-cat(Rcode, file = file.path(PATH, "R", "lm_stan.R"))
+writeLines(Rcode, con = file.path(PATH, "R", "lm_stan.R"))
 ```
 
 When __roxygen2__ documentation is enabled, a top-level package file
@@ -236,17 +236,18 @@ information about the package.
 With __roxygen__ documentation enabled, we need to generate the documentation
 for `lm_stan` and update the `NAMESPACE` so the function is exported, i.e.,
 available to users when the package is installed.  This can be done with the
-function `roxygen2::roxygenize()`.
+function `roxygen2::roxygenize()`, which needs to be called twice initially.
 
+```{r, results = "hide"}
+example(source) # defines the sourceDir() function
+```
 ```{r, eval = FALSE}
-try(roxygen2::roxygenize(load_code = roxygen2::load_source), silent = TRUE)
-pkgbuild::compile_dll()
+try(roxygen2::roxygenize(load_code = sourceDir), silent = TRUE)
 roxygen2::roxygenize()
 ```
 ```{r, echo=FALSE}
-try(roxygen2::roxygenize(PATH, load_code = roxygen2::load_source), silent = TRUE)
+try(roxygen2::roxygenize(PATH, load_code = sourceDir), silent = TRUE)
 rm(lm_stan)
-pkgbuild::compile_dll(PATH)
 roxygen2::roxygenize(PATH)
 ```
 
@@ -320,6 +321,6 @@ The following steps are required if one is using `devtools`:
 
 * Ask a question at the [Stan Forums](https://discourse.mc-stan.org/)
 
-* [R packages](http://r-pkgs.had.co.nz/) by Hadley Wickham provides a solid
-foundation in R package development as well as the release process.
+* [R packages](https://r-pkgs.org/) by Hadley Wickham and Jenny Bryan provides
+a solid foundation in R package development as well as the release process.