From 8a082a515a08dc46c5dae9ab36d6d4ffdcfebadc Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Tue, 20 Jul 2021 08:37:37 +0100
Subject: [PATCH 1/7] only check the scripts and report_sources folders with
 list_deps

---
 R/list_deps.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/list_deps.R b/R/list_deps.R
index 28668d2..7cdd459 100644
--- a/R/list_deps.R
+++ b/R/list_deps.R
@@ -22,9 +22,14 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
 
   tmp <- suppressMessages(validate_factory(factory))
   root <- tmp$root
+  config <- as.data.frame(read.dcf(file.path(root, "factory_config")))
+  report_sources <- config$report_sources
+  root_report_sources <- file.path(root, report_sources)
+  root_scripts <- file.path(root, "scripts")
+  root_to_check <- c(root_report_sources, root_scripts)
 
   # Find dependencies in R files
-  r_files <- list.files(root, pattern = "\\.[Rr]$", recursive = TRUE, full.names = TRUE)
+  r_files <- list.files(root_to_check, pattern = "\\.[Rr]$", recursive = TRUE, full.names = TRUE)
   r_files_deps <- character(0)
   if (length(r_files) && check_r) {
     r_files_deps <- list_r_file_deps(r_files)
@@ -34,7 +39,7 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   # dependencies of code that is actually run are returned.
   op <- options(knitr.purl.inline = TRUE)
   on.exit(options(op))
-  rmd_files <- list.files(root, pattern = "\\.[Rr]md$", recursive = TRUE, full.names = TRUE)
+  rmd_files <- list.files(root_to_check, pattern = "\\.[Rr]md$", recursive = TRUE, full.names = TRUE)
   if (exclude_readme) {
     readme <- list.files(pattern = "README\\.Rmd", recursive = TRUE, ignore.case = TRUE, full.names = TRUE)
     rmd_files <- rmd_files[!rmd_files %in% readme]

From 8b1ca1d1f2bd54df8c96739d8c4bb446a1554be3 Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Tue, 20 Jul 2021 08:56:55 +0100
Subject: [PATCH 2/7] change binary argument to compare due to deprecation in
 testthat

---
 tests/testthat/test-compile_reports.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-compile_reports.R b/tests/testthat/test-compile_reports.R
index 734144d..6d862cd 100644
--- a/tests/testthat/test-compile_reports.R
+++ b/tests/testthat/test-compile_reports.R
@@ -25,7 +25,7 @@ test_that("test parameteriesed report output", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "param_report_check.md", compare = compare_file_text)
 })
 
 test_that("test ignore_case works report output", {
@@ -54,7 +54,7 @@ test_that("test ignore_case works report output", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "param_report_check.md", compare = compare_file_text)
 
   # Should error if not case insensitive
   expect_error(
@@ -98,7 +98,7 @@ test_that("test output folder gets recreated if not there", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "outputs_deleted_param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "outputs_deleted_param_report_check.md", compare = compare_file_text)
 })
 
 
@@ -127,7 +127,7 @@ test_that("parameteriesed report with missing param output but input", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "missing_param_report_check.md", binary = FALSE)
+  expect_snapshot_file(md_file, "missing_param_report_check.md", compare = compare_file_text)
 })
 
 test_that("non parameteriesed report with param input", {
@@ -155,7 +155,7 @@ test_that("non parameteriesed report with param input", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "nonparameterised_with_params.md", binary = FALSE)
+  expect_snapshot_file(md_file, "nonparameterised_with_params.md", compare = compare_file_text)
 })
 
 test_that("parameteriesed report with missing param (but in environment)", {
@@ -184,7 +184,7 @@ test_that("parameteriesed report with missing param (but in environment)", {
   md_file <- grep("\\.md", list_outputs(f), value = TRUE)
   md_file <- path(f, "outputs", md_file)
 
-  expect_snapshot_file(md_file, "missing_param_but_envir.md", binary = FALSE)
+  expect_snapshot_file(md_file, "missing_param_but_envir.md", compare = compare_file_text)
 })
 
 

From ff746b6ca30179a6bf2f30ae3c5ba61776d24a8e Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Tue, 20 Jul 2021 10:35:16 +0100
Subject: [PATCH 3/7] update list_deps documentation

---
 R/list_deps.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/list_deps.R b/R/list_deps.R
index 7cdd459..fca2c6b 100644
--- a/R/list_deps.R
+++ b/R/list_deps.R
@@ -1,7 +1,7 @@
 #' List dependencies of reports within a factory
 #'
-#' This function can be used to list package dependencies based of the reports
-#'   and R scripts within the factory.
+#' List package dependencies based on the reports and scripts within the
+#'   report_sources and scripts directories respectively.
 #'
 #' @inheritParams compile_reports
 #' @param missing A logical indicating if only missing dependencies should be

From 1788cfdce0fdaba52cea443068d76a15bd954bf0 Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Tue, 20 Jul 2021 10:35:38 +0100
Subject: [PATCH 4/7] update NEWS for list_deps

---
 NEWS.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index a672394..2d5f2ac 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,8 @@
 # reportfactory (development version)
 
+* `list_deps()` now only checks the `report_sources` and `scripts` folders for
+  package dependencies.
+
 # reportfactory 0.3.1
 
 * Fixed `list_deps()`, which was broken due to major changes in the

From 76d1f22dce0e3563d2f0119bf9eb7987484dc272 Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Fri, 30 Jul 2021 15:05:00 +0100
Subject: [PATCH 5/7] tidying

---
 R/internals.R |  6 ++++++
 R/list_deps.R | 31 +++++++++++++++++++++++++++----
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/R/internals.R b/R/internals.R
index b2e1021..4d7c0ad 100644
--- a/R/internals.R
+++ b/R/internals.R
@@ -37,6 +37,8 @@ factory_root <- function(directory = ".") {
   root
 }
 
+# -------------------------------------------------------------------------
+
 #' check whether a vector is "integer-like" to a given precision
 #'
 #' @param x vector to check
@@ -47,6 +49,8 @@ is.wholenumber <- function(x, tol = .Machine$double.eps^0.5)  {
   all(abs(x - round(x)) < tol)
 }
 
+# -------------------------------------------------------------------------
+
 #' copy a file from the skeleton directory
 #'
 #' @param file name of the file you want to copy
@@ -58,6 +62,7 @@ copy_skeleton_file <- function(file, dest) {
   file.copy(f, dest)
 }
 
+# -------------------------------------------------------------------------
 
 #' Change part of the front yaml matter from an Rmarkdown file
 #'
@@ -103,6 +108,7 @@ change_yaml_matter <- function(input_file, ..., output_file) {
   }
 }
 
+# -------------------------------------------------------------------------
 
 #' Return rows of one data.frame not in another
 #'
diff --git a/R/list_deps.R b/R/list_deps.R
index fca2c6b..31af1b8 100644
--- a/R/list_deps.R
+++ b/R/list_deps.R
@@ -29,7 +29,13 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   root_to_check <- c(root_report_sources, root_scripts)
 
   # Find dependencies in R files
-  r_files <- list.files(root_to_check, pattern = "\\.[Rr]$", recursive = TRUE, full.names = TRUE)
+  r_files <- list.files(
+    root_to_check,
+    pattern = "\\.[Rr]$",
+    recursive = TRUE,
+    full.names = TRUE
+  )
+
   r_files_deps <- character(0)
   if (length(r_files) && check_r) {
     r_files_deps <- list_r_file_deps(r_files)
@@ -39,9 +45,19 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   # dependencies of code that is actually run are returned.
   op <- options(knitr.purl.inline = TRUE)
   on.exit(options(op))
-  rmd_files <- list.files(root_to_check, pattern = "\\.[Rr]md$", recursive = TRUE, full.names = TRUE)
+  rmd_files <- list.files(
+    root_to_check,
+    pattern = "\\.[Rr]md$",
+    recursive = TRUE,
+    full.names = TRUE
+  )
   if (exclude_readme) {
-    readme <- list.files(pattern = "README\\.Rmd", recursive = TRUE, ignore.case = TRUE, full.names = TRUE)
+    readme <- list.files(
+      pattern = "README\\.Rmd",
+      recursive = TRUE,
+      ignore.case = TRUE,
+      full.names = TRUE
+    )
     rmd_files <- rmd_files[!rmd_files %in% readme]
   }
 
@@ -56,7 +72,12 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
     fe <- file(fefil, "w")
     sink(fe, type = "message")
     mapply(
-      function(x,y) try(knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0), silent = TRUE),
+      function(x,y) {
+        try(
+          knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0),
+          silent = TRUE
+        )
+      } ,
       rmd_files,
       fd
     )
@@ -74,6 +95,8 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   deps
 }
 
+# -------------------------------------------------------------------------
+
 list_r_file_deps <- function(filepaths) {
 
   dat <- vapply(

From 4c3ff1ea43591bf233d4668b3b3eb8a1773db010 Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Mon, 9 Aug 2021 10:05:50 +0100
Subject: [PATCH 6/7] Default to simple readLines parsing or reports and
 scripts

---
 R/list_deps.R                     | 93 ++++++++++++++++++-------------
 inst/skeletons/example_report.Rmd |  4 ++
 man/list_deps.Rd                  | 13 ++++-
 tests/testthat/test-list_deps.R   | 38 ++++++++++---
 4 files changed, 98 insertions(+), 50 deletions(-)

diff --git a/R/list_deps.R b/R/list_deps.R
index 31af1b8..d6fc9cb 100644
--- a/R/list_deps.R
+++ b/R/list_deps.R
@@ -11,6 +11,11 @@
 #'   checked. Note that this will error if the script cannot be parsed.
 #' @param exclude_readme If TRUE (default) README files will not be checked for
 #'   dependencies.
+#' @param parse_first If `TRUE` code will first be parsed for validity and
+#'   unevaluated Rmd chunks will not be checked for dependencies. The default
+#'   value is `FALSE` and, in this case, files will simply be checked line by
+#'   line for calls to `library`, `require` or use of double, `::`, and triple,
+#'   `:::` function calls.
 #'
 #' @note This function requires that any R scripts present in the factory are
 #'   valid syntax else the function will error.
@@ -18,7 +23,8 @@
 #' @return A character vector of package dependencies.
 #'
 #' @export
-list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_readme = TRUE) {
+list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE,
+                      exclude_readme = TRUE, parse_first = FALSE) {
 
   tmp <- suppressMessages(validate_factory(factory))
   root <- tmp$root
@@ -28,7 +34,7 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
   root_scripts <- file.path(root, "scripts")
   root_to_check <- c(root_report_sources, root_scripts)
 
-  # Find dependencies in R files
+  # List of R files
   r_files <- list.files(
     root_to_check,
     pattern = "\\.[Rr]$",
@@ -36,18 +42,9 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
     full.names = TRUE
   )
 
-  r_files_deps <- character(0)
-  if (length(r_files) && check_r) {
-    r_files_deps <- list_r_file_deps(r_files)
-  }
-
-  # Find dependencies in Rmd files. We knit the files first to ensure only
-  # dependencies of code that is actually run are returned.
-  op <- options(knitr.purl.inline = TRUE)
-  on.exit(options(op))
+  # List of Rmd files
   rmd_files <- list.files(
-    root_to_check,
-    pattern = "\\.[Rr]md$",
+    root_to_check, pattern = "\\.[Rr]md$",
     recursive = TRUE,
     full.names = TRUE
   )
@@ -61,31 +58,45 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
     rmd_files <- rmd_files[!rmd_files %in% readme]
   }
 
+  # Find R file dependencies
+  r_files_deps <- character(0)
+  if (length(r_files) && check_r) {
+    r_files_deps <- list_r_file_deps(r_files, parse = parse_first)
+  }
+
+  # Find Rmd file dependencies
+  op <- options(knitr.purl.inline = TRUE)
+  on.exit(options(op))
   rmd_files_deps <- character(0)
   if (length(rmd_files)) {
-    d <- tempdir()
-    fd <- sub(pattern = "(.*)\\..*$", replacement = "\\1", basename(rmd_files))
-    fd <- vapply(fd, function(x) file.path(d, x), character(1))
-    on.exit(unlink(fd), add = TRUE)
-    fefil <- tempfile()
-    on.exit(unlink(fefil), add = TRUE)
-    fe <- file(fefil, "w")
-    sink(fe, type = "message")
-    mapply(
-      function(x,y) {
-        try(
-          knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0),
-          silent = TRUE
-        )
-      } ,
-      rmd_files,
-      fd
-    )
-    sink(type = "message")
-    close(fe)
-    rmd_files_deps <- c("rmarkdown", list_r_file_deps(fd))
+    if (parse_first) {
+      d <- tempdir()
+      fd <- sub(pattern = "(.*)\\..*$", replacement = "\\1", basename(rmd_files))
+      fd <- vapply(fd, function(x) file.path(d, x), character(1))
+      on.exit(unlink(fd), add = TRUE)
+      fefil <- tempfile()
+      on.exit(unlink(fefil), add = TRUE)
+      fe <- file(fefil, "w")
+      sink(fe, type = "message")
+      mapply(
+        function(x,y) {
+          try(
+            knitr::purl(input = x, output = y, quiet = TRUE, documentation = 0),
+            silent = TRUE
+          )
+        } ,
+        rmd_files,
+        fd
+      )
+      sink(type = "message")
+      close(fe)
+      rmd_files_deps <- c("rmarkdown", list_r_file_deps(fd, parse = TRUE))
+    } else {
+      rmd_files_deps <- c("rmarkdown", list_r_file_deps(rmd_files, parse = FALSE))
+    }
   }
 
+  # return unique dependencies
   deps <- unique(c(r_files_deps, rmd_files_deps))
   if (missing) {
     installed <- basename(find.package(deps))
@@ -97,13 +108,15 @@ list_deps <- function(factory = ".", missing = FALSE, check_r = TRUE, exclude_re
 
 # -------------------------------------------------------------------------
 
-list_r_file_deps <- function(filepaths) {
+list_r_file_deps <- function(filepaths, parse = FALSE) {
 
-  dat <- vapply(
-    filepaths,
-    function(x) paste(as.character(parse(x)), collapse = "\n"),
-    character(1)
-  )
+  if (parse) {
+    f <- function(x) paste(as.character(parse(x)), collapse = "\n")
+  } else {
+    f <- function(x) paste(readLines(x), collapse = "\n")
+  }
+
+  dat <- vapply(filepaths, f, character(1))
 
   colon_string <- r"---{([a-zA-Z][\w.]*)(?=:{2,3})}---"
   colon_greg <- gregexpr(colon_string, dat, perl = TRUE)
diff --git a/inst/skeletons/example_report.Rmd b/inst/skeletons/example_report.Rmd
index f10636b..5f4fff8 100644
--- a/inst/skeletons/example_report.Rmd
+++ b/inst/skeletons/example_report.Rmd
@@ -12,6 +12,10 @@ output:
 knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, fig.width = 8, fig.height = 6, dpi = 70)
 ```
 
+```{r, eval = FALSE}
+base::mean(c(1,2))
+```
+
 This is an example report to illustrate how `reportfactory` can be used.
 It loads the `fs` library purely for demonstration purposes. 
 
diff --git a/man/list_deps.Rd b/man/list_deps.Rd
index 75b0389..8da0c4f 100644
--- a/man/list_deps.Rd
+++ b/man/list_deps.Rd
@@ -8,7 +8,8 @@ list_deps(
   factory = ".",
   missing = FALSE,
   check_r = TRUE,
-  exclude_readme = TRUE
+  exclude_readme = TRUE,
+  parse_first = FALSE
 )
 }
 \arguments{
@@ -24,13 +25,19 @@ checked. Note that this will error if the script cannot be parsed.}
 
 \item{exclude_readme}{If TRUE (default) README files will not be checked for
 dependencies.}
+
+\item{parse_first}{If \code{TRUE} code will first be parsed for validity and
+unevaluated Rmd chunks will not be checked for dependencies. The default
+value is \code{FALSE} and, in this case, files will simply be checked line by
+line for calls to \code{library}, \code{require} or use of double, \code{::}, and triple,
+\code{:::} function calls.}
 }
 \value{
 A character vector of package dependencies.
 }
 \description{
-This function can be used to list package dependencies based of the reports
-and R scripts within the factory.
+List package dependencies based on the reports and scripts within the
+report_sources and scripts directories respectively.
 }
 \note{
 This function requires that any R scripts present in the factory are
diff --git a/tests/testthat/test-list_deps.R b/tests/testthat/test-list_deps.R
index 8fa3066..5179842 100644
--- a/tests/testthat/test-list_deps.R
+++ b/tests/testthat/test-list_deps.R
@@ -1,6 +1,6 @@
 library(fs)
 
-test_that("list_deps works", {
+test_that("non parsing list_deps works", {
 
   f <- new_factory(path = path_temp(), move_in = FALSE)
   on.exit(dir_delete(f))
@@ -9,13 +9,37 @@ test_that("list_deps works", {
   file_copy(path("test_reports", "package_calls.Rmd"), path(f, "report_sources"))
   file_copy(path("test_reports", "example.R"), path(f, "report_sources"))
 
-  expected_deps_package_calls <- c("purrr", "readxl", "fs", "rmarkdown", "utils", "yaml", "callr", "rprojroot")
+  # non parsed expected_deps
+  expected_deps_package_calls_rmd <- c("purrr", "readxl", "fs", "rmarkdown")
+  expected_deps_example_r <- c("fs", "yaml", "callr", "utils", "rprojroot")
+  expected_deps_example_report <- c("base", "knitr", "fs")
+  expected_deps <- c(expected_deps_package_calls_rmd,
+                     expected_deps_example_r,
+                     expected_deps_example_report)
 
-  expected_deps_example_report <- c("knitr", "fs", "rmarkdown")
-  expected_deps_readme <- "rmarkdown"
-  expected_deps <- c(expected_deps_package_calls,
-                     expected_deps_example_report,
-                     expected_deps_readme)
   deps <- list_deps(f)
   expect_equal(sort(deps), sort(unique(expected_deps)))
 })
+
+
+test_that("parsing list_deps works", {
+
+  f <- new_factory(path = path_temp(), move_in = FALSE)
+  on.exit(dir_delete(f))
+
+  # copy test reports over (as this has inline code)
+  file_copy(path("test_reports", "package_calls.Rmd"), path(f, "report_sources"))
+  file_copy(path("test_reports", "example.R"), path(f, "report_sources"))
+
+  # non parsed expected_deps
+  expected_deps_package_calls_rmd <- c("purrr", "readxl", "fs", "rmarkdown")
+  expected_deps_example_r <- c("fs", "yaml", "callr", "utils", "rprojroot")
+  expected_deps_example_report <- c("knitr", "fs")
+  expected_deps <- c(expected_deps_package_calls_rmd,
+                     expected_deps_example_r,
+                     expected_deps_example_report)
+
+  deps <- list_deps(f, parse_first = TRUE)
+  expect_equal(sort(deps), sort(unique(expected_deps)))
+})
+

From 6262868620d928d05e91c82e1cae0cb509434a83 Mon Sep 17 00:00:00 2001
From: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Date: Mon, 9 Aug 2021 12:58:16 +0100
Subject: [PATCH 7/7] CRAN prep

---
 DESCRIPTION      | 2 +-
 NEWS.md          | 2 +-
 cran-comments.md | 6 ++----
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fbcd83c..dda3bd4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: reportfactory
 Title: Lightweight Infrastructure for Handling Multiple R Markdown Documents
-Version: 0.3.1.9000
+Version: 0.4.0
 Authors@R: c(
   person("Thibaut", "Jombart", role = "aut", email = "thibautjombart@gmail.com"),
   person("Amy", "Gimma", role = "ctb", email = "amyg225@gmail.com"),
diff --git a/NEWS.md b/NEWS.md
index 9a993f5..f3783fb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# reportfactory (development version)
+# reportfactory 0.4.0
 
 * `list_deps()` now only checks the `report_sources` and `scripts` folders for
   package dependencies.
diff --git a/cran-comments.md b/cran-comments.md
index 27aff2b..83282b9 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,8 +1,6 @@
-# Reason for update
-* Fixes due to breaking changes in the upstream checkpoint package.
-
 # Tested on
-* Fedora 34, R Under development (unstable) (2021-06-16 r80504)
+* Fedora 34, R Under development (unstable) (2021-08-09 r80724)
+* Winbuilder, R Under development (unstable) (2021-08-05 r80717)
 
 ## R CMD check results for above environments
 Status: OK