From 20c91afe55c6ded68cc096bef805f6cd645c0852 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 15:57:55 +0200
Subject: [PATCH 01/13] add extra_deps argument

---
 R/check.R                         | 12 ++--
 R/deps_installation_proposal.R    | 11 ++++
 R/desc_utils.R                    | 94 +++++++++++++++++++++++++++----
 man/deparse_dep_str.Rd            | 22 ++++++++
 man/deparse_ver_str.Rd            | 21 +++++++
 man/deps_check.Rd                 |  8 +++
 man/deps_installation_proposal.Rd | 28 +++++++--
 man/desc_add_extra_deps.Rd        | 27 +++++++++
 man/version_from_desc.Rd          |  2 +-
 9 files changed, 205 insertions(+), 20 deletions(-)
 create mode 100644 man/deparse_dep_str.Rd
 create mode 100644 man/deparse_ver_str.Rd
 create mode 100644 man/desc_add_extra_deps.Rd

diff --git a/R/check.R b/R/check.R
index ef4442bf..13f6c3b9 100644
--- a/R/check.R
+++ b/R/check.R
@@ -19,11 +19,12 @@
 #' x$ip
 #' x$check
 max_deps_check <- function(path,
+                           extra_deps = character(),
                            config = list(),
                            build_args = character(),
                            check_args = character(),
                            ...) {
-  ip <- new_max_deps_installation_proposal(path, config)
+  ip <- new_max_deps_installation_proposal(path, extra_deps, config)
   execute_ip(ip, path, check_args, build_args, ...)
 }
 
@@ -35,11 +36,12 @@ max_deps_check <- function(path,
 #' x$ip
 #' x$check
 release_deps_check <- function(path,
+                               extra_deps = character(),
                                config = list(),
                                build_args = character(),
                                check_args = character(),
                                ...) {
-  ip <- new_release_deps_installation_proposal(path, config)
+  ip <- new_release_deps_installation_proposal(path, extra_deps, config)
   execute_ip(ip, path, check_args, build_args, ...)
 }
 
@@ -51,11 +53,12 @@ release_deps_check <- function(path,
 #' x$ip
 #' x$check
 min_cohort_deps_check <- function(path,
+                                  extra_deps = character(),
                                   config = list(),
                                   build_args = character(),
                                   check_args = character(),
                                   ...) {
-  ip <- new_min_cohort_deps_installation_proposal(path, config)
+  ip <- new_min_cohort_deps_installation_proposal(path, extra_deps, config)
   execute_ip(ip, path, check_args, build_args, ...)
 }
 
@@ -67,11 +70,12 @@ min_cohort_deps_check <- function(path,
 #' x$ip
 #' x$check
 min_isolated_deps_check <- function(path,
+                                    extra_deps = character(),
                                     config = list(),
                                     build_args = character(),
                                     check_args = character(),
                                     ...) {
-  ip <- new_min_isolated_deps_installation_proposal(path, config)
+  ip <- new_min_isolated_deps_installation_proposal(path, extra_deps, config)
   execute_ip(ip, path, check_args, build_args, ...)
 }
 
diff --git a/R/deps_installation_proposal.R b/R/deps_installation_proposal.R
index 3cde74a6..793bb875 100644
--- a/R/deps_installation_proposal.R
+++ b/R/deps_installation_proposal.R
@@ -39,6 +39,9 @@
 #' Please see also [`pkgdepends::pkg_config`] and [`pak::pak-config`] for other configuration possibilities.
 #'
 #' @param path (`string`) path to the package sources
+#' @param extra_deps (`character(1)`) Extra dependencies specified similarly to the `DESCRIPTION` file, i.e.
+#' `"<package name> (<operator> <version>)"` where both `<operator>` and `<version>` are optional.
+#' Multiple entries are possible separated by `";"`.
 #' @param config (`list`) configuration options. See [`pkgdepends::pkg_config`] for details.
 #' `"dependencies"` and `"library"` elements are overwritten by package level defaults.
 #'
@@ -54,6 +57,7 @@
 #' x$solve()
 #' x$get_solution()
 new_max_deps_installation_proposal <- function(path, # nolint
+                                               extra_deps = character(0L),
                                                config = list()) {
   path <- normalizePath(path)
   config <- append_config(default_config(), config)
@@ -71,6 +75,7 @@ new_max_deps_installation_proposal <- function(path, # nolint
   new_refs_str <- map_key_character(new_refs, "ref")
 
   d <- desc_cond_set_refs(d, new_refs_str)
+  d <- desc_add_extra_deps(d, extra_deps)
 
   res <- desc_to_ip(d, config)
   class(res) <- c("max_deps_installation_proposal", "deps_installation_proposal", class(res))
@@ -85,6 +90,7 @@ new_max_deps_installation_proposal <- function(path, # nolint
 #' x$solve()
 #' x$get_solution()
 new_release_deps_installation_proposal <- function(path, # nolint
+                                                   extra_deps = character(0L),
                                                    config = list()) {
   path <- normalizePath(path)
   config <- append_config(default_config(), config)
@@ -102,6 +108,7 @@ new_release_deps_installation_proposal <- function(path, # nolint
   new_refs_str <- map_key_character(new_refs, "ref")
 
   d <- desc_cond_set_refs(d, new_refs_str)
+  d <- desc_add_extra_deps(d, extra_deps)
   d <- desc_remotes_cleanup(d)
 
   res <- desc_to_ip(d, config)
@@ -118,6 +125,7 @@ new_release_deps_installation_proposal <- function(path, # nolint
 #' solve_ip(x)
 #' x$get_solution()
 new_min_cohort_deps_installation_proposal <- function(path, # nolint
+                                                      extra_deps = character(0L),
                                                       config = list()) {
   path <- normalizePath(path)
   config <- append_config(default_config(), config)
@@ -155,6 +163,7 @@ new_min_cohort_deps_installation_proposal <- function(path, # nolint
   )
   new_refs_str <- map_key_character(new_refs, "ref")
   d <- desc_cond_set_refs(d, new_refs_str)
+  d <- desc_add_extra_deps(d, extra_deps)
   d <- desc_remotes_cleanup(d)
 
   # find PPM snapshot
@@ -222,6 +231,7 @@ new_min_cohort_deps_installation_proposal <- function(path, # nolint
 #' solve_ip(x)
 #' x$get_solution()
 new_min_isolated_deps_installation_proposal <- function(path, # nolint
+                                                        extra_deps = character(0L),
                                                         config = list()) {
   path <- normalizePath(path)
   config <- append_config(default_config(), config)
@@ -262,6 +272,7 @@ new_min_isolated_deps_installation_proposal <- function(path, # nolint
   new_refs_str <- map_key_character(new_refs, "ref")
 
   d <- desc_cond_set_refs(d, new_refs_str)
+  d <- desc_add_extra_deps(d, extra_deps)
   d <- desc_remotes_cleanup(d)
 
   res <- desc_to_ip(d, config)
diff --git a/R/desc_utils.R b/R/desc_utils.R
index dcfc43fc..28d0e5f9 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -122,6 +122,78 @@ desc_cond_set_refs <- function(d, refs) {
   return(invisible(d))
 }
 
+#' Adds extra dependencies to the `desc` object.
+#'
+#' This will add dependencies to the `Imports` field.
+#'
+#' @param d (`desc`) DESCRIPTION object from [desc::desc]
+#' @param x (`character(1)`) Extra dependencies specified similarly to the `DESCRIPTION` file, i.e.
+#' `"<package name> (<operator> <version>)"` where both `<operator>` and `<version>` are optional.
+#' Multiple entries are possible separated by `";"`.
+#'
+#' @return `desc` object with added dependencies.
+#'
+#' @keywords internal
+#'
+#' @examples
+#' d <- desc::desc(cmd = "!new")
+#' d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3); bar (== 2.3.4)")
+#' d$get_deps()
+desc_add_extra_deps <- function(d, x) {
+  if (length(x)) {
+    for (x_i in strsplit(x, ";")[[1]]) {
+      x_i_deparsed <- deparse_dep_str(trimws(x_i))
+      d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
+    }
+  }
+  return(invisible(d))
+}
+
+#' Deparse a dependency string
+#'
+#' @param x (`character`) Dependency string in form of `<package name> (<operator> <version>)`. See examples.
+#'
+#' @return `list` with `package`, `op`, `op_ver` and `ver_str` fields.
+#'
+#' @keywords internal
+#'
+#' @examples
+#' verdepcheck:::deparse_dep_str("foo")
+#' verdepcheck:::deparse_dep_str("foo (>= 1.2.3)")
+deparse_dep_str <- function(x) {
+  x <- trimws(strsplit(x, "\\(")[[1]])
+  package <- x[1]
+  ver_str <- gsub("\\)$", "", x[2])
+  ver_str_deparsed <- deparse_ver_str(ver_str)
+  list(
+    package = x[1],
+    op = ver_str_deparsed$op,
+    op_ver = ver_str_deparsed$op_ver,
+    ver_str = ver_str
+  )
+}
+#' Deparse a version string
+#'
+#' @param x (`character`) Version string in form of `<operator> <version>`. See examples.
+#'
+#' @return `list` with `op` and `op_ver` fields.
+#'
+#' @keywords internal
+#'
+#' @examples
+#' verdepcheck:::deparse_ver_str(">= 1.2.3")
+deparse_ver_str <- function(x) {
+  x <- trimws(x)
+  if (x == "*" || x == "") {
+    return(list(op = "", op_ver = ""))
+  }
+  split_vec <- strsplit(x, " ")[[1]]
+  list(
+    op = split_vec[1],
+    op_ver = split_vec[2]
+  )
+}
+
 #' Create `installation_plan` object from `desc` object
 #' @importFrom pkgdepends new_pkg_installation_proposal
 #' @keywords internal
@@ -137,7 +209,7 @@ desc_to_ip <- function(d, config) {
 }
 
 #' Get package version from description
-#' @param d (`desc`) DESCRIPTION object from [desc::description]
+#' @param d (`desc`) DESCRIPTION object from [desc::desc]
 #' @param pkg_name (`character`) Package name
 #' @keywords internal
 #'
@@ -152,20 +224,20 @@ desc_to_ip <- function(d, config) {
 version_from_desc <- function(d, pkg_name) {
   all_deps <- d$get_deps()
 
-  version <- (all_deps$version[all_deps$package == pkg_name])[[1]]
-  result <- list(
+  ver_str <- (all_deps$version[all_deps$package == pkg_name])[[1]]
+
+  res <- list(
     package = pkg_name,
-    version_str = version,
+    ver_str = ver_str,
     op = "",
     op_ver = ""
   )
-  if (version == "*" || trimws(version) == "") {
-    return(result)
-  }
-  split_vec <- strsplit(version, " ")[[1]]
-  result$op <- split_vec[1]
-  result$op_ver <- split_vec[2]
-  result
+
+  ver_str_deparsed <- deparse_ver_str(ver_str)
+  res$op <- ver_str_deparsed$op
+  res$op_ver <- ver_str_deparsed$op_ver
+
+  res
 }
 
 #' Filter for package versions that comply with an operator and version
diff --git a/man/deparse_dep_str.Rd b/man/deparse_dep_str.Rd
new file mode 100644
index 00000000..b8065a13
--- /dev/null
+++ b/man/deparse_dep_str.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/desc_utils.R
+\name{deparse_dep_str}
+\alias{deparse_dep_str}
+\title{Deparse a dependency string}
+\usage{
+deparse_dep_str(x)
+}
+\arguments{
+\item{x}{(\code{character}) Dependency string in form of \verb{<package name> (<operator> <version>)}. See examples.}
+}
+\value{
+\code{list} with \code{package}, \code{op}, \code{op_ver} and \code{ver_str} fields.
+}
+\description{
+Deparse a dependency string
+}
+\examples{
+verdepcheck:::deparse_dep_str("foo")
+verdepcheck:::deparse_dep_str("foo (>= 1.2.3)")
+}
+\keyword{internal}
diff --git a/man/deparse_ver_str.Rd b/man/deparse_ver_str.Rd
new file mode 100644
index 00000000..cc8c3559
--- /dev/null
+++ b/man/deparse_ver_str.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/desc_utils.R
+\name{deparse_ver_str}
+\alias{deparse_ver_str}
+\title{Deparse a version string}
+\usage{
+deparse_ver_str(x)
+}
+\arguments{
+\item{x}{(\code{character}) Version string in form of \verb{<operator> <version>}. See examples.}
+}
+\value{
+\code{list} with \code{op} and \code{op_ver} fields.
+}
+\description{
+Deparse a version string
+}
+\examples{
+verdepcheck:::deparse_ver_str(">= 1.2.3")
+}
+\keyword{internal}
diff --git a/man/deps_check.Rd b/man/deps_check.Rd
index 2d450648..c4b119e2 100644
--- a/man/deps_check.Rd
+++ b/man/deps_check.Rd
@@ -9,6 +9,7 @@
 \usage{
 max_deps_check(
   path,
+  extra_deps = character(),
   config = list(),
   build_args = character(),
   check_args = character(),
@@ -17,6 +18,7 @@ max_deps_check(
 
 release_deps_check(
   path,
+  extra_deps = character(),
   config = list(),
   build_args = character(),
   check_args = character(),
@@ -25,6 +27,7 @@ release_deps_check(
 
 min_cohort_deps_check(
   path,
+  extra_deps = character(),
   config = list(),
   build_args = character(),
   check_args = character(),
@@ -33,6 +36,7 @@ min_cohort_deps_check(
 
 min_isolated_deps_check(
   path,
+  extra_deps = character(),
   config = list(),
   build_args = character(),
   check_args = character(),
@@ -42,6 +46,10 @@ min_isolated_deps_check(
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
+\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+Multiple entries are possible separated by \code{";"}.}
+
 \item{config}{(\code{list}) configuration options. See \code{\link[pkgdepends:pkg_config]{pkgdepends::pkg_config}} for details.
 \code{"dependencies"} and \code{"library"} elements are overwritten by package level defaults.}
 
diff --git a/man/deps_installation_proposal.Rd b/man/deps_installation_proposal.Rd
index b468b30f..ed7033d3 100644
--- a/man/deps_installation_proposal.Rd
+++ b/man/deps_installation_proposal.Rd
@@ -8,17 +8,37 @@
 \alias{new_min_isolated_deps_installation_proposal}
 \title{Create installation proposal using various dependency strategies}
 \usage{
-new_max_deps_installation_proposal(path, config = list())
+new_max_deps_installation_proposal(
+  path,
+  extra_deps = character(0L),
+  config = list()
+)
 
-new_release_deps_installation_proposal(path, config = list())
+new_release_deps_installation_proposal(
+  path,
+  extra_deps = character(0L),
+  config = list()
+)
 
-new_min_cohort_deps_installation_proposal(path, config = list())
+new_min_cohort_deps_installation_proposal(
+  path,
+  extra_deps = character(0L),
+  config = list()
+)
 
-new_min_isolated_deps_installation_proposal(path, config = list())
+new_min_isolated_deps_installation_proposal(
+  path,
+  extra_deps = character(0L),
+  config = list()
+)
 }
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
+\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+Multiple entries are possible separated by \code{";"}.}
+
 \item{config}{(\code{list}) configuration options. See \code{\link[pkgdepends:pkg_config]{pkgdepends::pkg_config}} for details.
 \code{"dependencies"} and \code{"library"} elements are overwritten by package level defaults.}
 }
diff --git a/man/desc_add_extra_deps.Rd b/man/desc_add_extra_deps.Rd
new file mode 100644
index 00000000..9442e28c
--- /dev/null
+++ b/man/desc_add_extra_deps.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/desc_utils.R
+\name{desc_add_extra_deps}
+\alias{desc_add_extra_deps}
+\title{Adds extra dependencies to the \code{desc} object.}
+\usage{
+desc_add_extra_deps(d, x)
+}
+\arguments{
+\item{d}{(\code{desc}) DESCRIPTION object from \link[desc:desc]{desc::desc}}
+
+\item{x}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
+\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+Multiple entries are possible separated by \code{";"}.}
+}
+\value{
+\code{desc} object with added dependencies.
+}
+\description{
+This will add dependencies to the \code{Imports} field.
+}
+\examples{
+d <- desc::desc(cmd = "!new")
+d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3); bar (== 2.3.4)")
+d$get_deps()
+}
+\keyword{internal}
diff --git a/man/version_from_desc.Rd b/man/version_from_desc.Rd
index 76f9f27b..78ad7988 100644
--- a/man/version_from_desc.Rd
+++ b/man/version_from_desc.Rd
@@ -7,7 +7,7 @@
 version_from_desc(d, pkg_name)
 }
 \arguments{
-\item{d}{(\code{desc}) DESCRIPTION object from \link[desc:description]{desc::description}}
+\item{d}{(\code{desc}) DESCRIPTION object from \link[desc:desc]{desc::desc}}
 
 \item{pkg_name}{(\code{character}) Package name}
 }

From 536d2df200d52c2557efd0fb65b49bdd20a99d3b Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 16:31:37 +0200
Subject: [PATCH 02/13] more robust against NA

---
 R/desc_utils.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 28d0e5f9..def2671d 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -164,6 +164,9 @@ deparse_dep_str <- function(x) {
   x <- trimws(strsplit(x, "\\(")[[1]])
   package <- x[1]
   ver_str <- gsub("\\)$", "", x[2])
+  if (is.na(ver_str)) {
+    ver_str <- ""
+  }
   ver_str_deparsed <- deparse_ver_str(ver_str)
   list(
     package = x[1],
@@ -184,7 +187,7 @@ deparse_dep_str <- function(x) {
 #' verdepcheck:::deparse_ver_str(">= 1.2.3")
 deparse_ver_str <- function(x) {
   x <- trimws(x)
-  if (x == "*" || x == "") {
+  if (is.na(x) || length(x) == 0 || x == "*" || x == "") {
     return(list(op = "", op_ver = ""))
   }
   split_vec <- strsplit(x, " ")[[1]]

From 183f50720093e7982c6e54641474498f7d3e5644 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 17:12:36 +0200
Subject: [PATCH 03/13] handle missing ver better

---
 R/desc_utils.R                    | 7 ++++---
 man/deps_check.Rd                 | 4 ++--
 man/deps_installation_proposal.Rd | 4 ++--
 man/desc_add_extra_deps.Rd        | 7 ++++---
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index def2671d..842da2b8 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -137,11 +137,12 @@ desc_cond_set_refs <- function(d, refs) {
 #'
 #' @examples
 #' d <- desc::desc(cmd = "!new")
-#' d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3); bar (== 2.3.4)")
+#' d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3)")
+#' d <- verdepcheck:::desc_add_extra_deps(d, "bar (>= 2.3.4); baz (>= 3.4.5)")
 #' d$get_deps()
 desc_add_extra_deps <- function(d, x) {
   if (length(x)) {
-    for (x_i in strsplit(x, ";")[[1]]) {
+    for (x_i in trimws(strsplit(x, ";")[[1]])) {
       x_i_deparsed <- deparse_dep_str(trimws(x_i))
       d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
     }
@@ -165,7 +166,7 @@ deparse_dep_str <- function(x) {
   package <- x[1]
   ver_str <- gsub("\\)$", "", x[2])
   if (is.na(ver_str)) {
-    ver_str <- ""
+    ver_str <- "*"
   }
   ver_str_deparsed <- deparse_ver_str(ver_str)
   list(
diff --git a/man/deps_check.Rd b/man/deps_check.Rd
index c4b119e2..ce7b59bc 100644
--- a/man/deps_check.Rd
+++ b/man/deps_check.Rd
@@ -46,8 +46,8 @@ min_isolated_deps_check(
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
-\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
-\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 
 \item{config}{(\code{list}) configuration options. See \code{\link[pkgdepends:pkg_config]{pkgdepends::pkg_config}} for details.
diff --git a/man/deps_installation_proposal.Rd b/man/deps_installation_proposal.Rd
index ed7033d3..246f8541 100644
--- a/man/deps_installation_proposal.Rd
+++ b/man/deps_installation_proposal.Rd
@@ -35,8 +35,8 @@ new_min_isolated_deps_installation_proposal(
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
-\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
-\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 
 \item{config}{(\code{list}) configuration options. See \code{\link[pkgdepends:pkg_config]{pkgdepends::pkg_config}} for details.
diff --git a/man/desc_add_extra_deps.Rd b/man/desc_add_extra_deps.Rd
index 9442e28c..eca12566 100644
--- a/man/desc_add_extra_deps.Rd
+++ b/man/desc_add_extra_deps.Rd
@@ -9,8 +9,8 @@ desc_add_extra_deps(d, x)
 \arguments{
 \item{d}{(\code{desc}) DESCRIPTION object from \link[desc:desc]{desc::desc}}
 
-\item{x}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, e.g.
-\code{"<package name> (<operator> <version>)"} where both \code{operator} and \code{version} are optional.
+\item{x}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 }
 \value{
@@ -21,7 +21,8 @@ This will add dependencies to the \code{Imports} field.
 }
 \examples{
 d <- desc::desc(cmd = "!new")
-d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3); bar (== 2.3.4)")
+d <- verdepcheck:::desc_add_extra_deps(d, "foo (>= 1.2.3)")
+d <- verdepcheck:::desc_add_extra_deps(d, "bar (>= 2.3.4); baz (>= 3.4.5)")
 d$get_deps()
 }
 \keyword{internal}

From 4efae8158cf190ed4bd1895d6b42da5764328504 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 17:29:26 +0200
Subject: [PATCH 04/13] add debug statements

---
 R/desc_utils.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 842da2b8..48ba7ecd 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -141,6 +141,10 @@ desc_cond_set_refs <- function(d, refs) {
 #' d <- verdepcheck:::desc_add_extra_deps(d, "bar (>= 2.3.4); baz (>= 3.4.5)")
 #' d$get_deps()
 desc_add_extra_deps <- function(d, x) {
+  cat("desc_add_extra_deps: \n")
+  cat(x)
+  cat("\n")
+
   if (length(x)) {
     for (x_i in trimws(strsplit(x, ";")[[1]])) {
       x_i_deparsed <- deparse_dep_str(trimws(x_i))
@@ -162,6 +166,10 @@ desc_add_extra_deps <- function(d, x) {
 #' verdepcheck:::deparse_dep_str("foo")
 #' verdepcheck:::deparse_dep_str("foo (>= 1.2.3)")
 deparse_dep_str <- function(x) {
+  cat("deparse_dep_str: \n")
+  cat(x)
+  cat("\n")
+
   x <- trimws(strsplit(x, "\\(")[[1]])
   package <- x[1]
   ver_str <- gsub("\\)$", "", x[2])
@@ -187,6 +195,10 @@ deparse_dep_str <- function(x) {
 #' @examples
 #' verdepcheck:::deparse_ver_str(">= 1.2.3")
 deparse_ver_str <- function(x) {
+  cat("deparse_ver_str: \n")
+  cat(x)
+  cat("\n")
+
   x <- trimws(x)
   if (is.na(x) || length(x) == 0 || x == "*" || x == "") {
     return(list(op = "", op_ver = ""))

From db76e14e529c07b641265620e3ef2cbfe9c9370f Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 18:00:12 +0200
Subject: [PATCH 05/13] more debug statements

---
 R/desc_utils.R | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 48ba7ecd..638a508f 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -143,11 +143,24 @@ desc_cond_set_refs <- function(d, refs) {
 desc_add_extra_deps <- function(d, x) {
   cat("desc_add_extra_deps: \n")
   cat(x)
+  cat("strsplit:\n")
+  cat(strsplit(x, ";")[[1]])
+  cat("\n")
+  cat(trimws(strsplit(x, ";")[[1]]))
   cat("\n")
 
   if (length(x)) {
     for (x_i in trimws(strsplit(x, ";")[[1]])) {
-      x_i_deparsed <- deparse_dep_str(trimws(x_i))
+      cat("x_i: \n")
+      cat(x_i)
+      cat("\n")
+
+      x_i_deparsed <- deparse_dep_str(x_i)
+
+      cat("x_i_deparsed: \n")
+      cat(x_i_deparsed)
+      cat("\n")
+
       d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
     }
   }

From ebf0fa3332585a0d163cdf0cf80c8b92aa9c9cda Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 18:12:50 +0200
Subject: [PATCH 06/13] more debug statements

---
 R/desc_utils.R | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 638a508f..4ec091f9 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -143,10 +143,18 @@ desc_cond_set_refs <- function(d, refs) {
 desc_add_extra_deps <- function(d, x) {
   cat("desc_add_extra_deps: \n")
   cat(x)
+  cat("\n")
   cat("strsplit:\n")
   cat(strsplit(x, ";")[[1]])
   cat("\n")
-  cat(trimws(strsplit(x, ";")[[1]]))
+  cat("strsplit (fixed):\n")
+  cat(strsplit(x, ";", fixed = TRUE)[[1]])
+  cat("\n")
+  cat("strsplit (perl):\n")
+  cat(strsplit(x, ";", perl = TRUE)[[1]])
+  cat("\n")
+  cat("strsplit (useBytes):\n")
+  cat(strsplit(x, ";", useBytes = TRUE)[[1]])
   cat("\n")
 
   if (length(x)) {
@@ -156,11 +164,6 @@ desc_add_extra_deps <- function(d, x) {
       cat("\n")
 
       x_i_deparsed <- deparse_dep_str(x_i)
-
-      cat("x_i_deparsed: \n")
-      cat(x_i_deparsed)
-      cat("\n")
-
       d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
     }
   }

From 5640d65b27604c9388f3d53c0c00971bbbace7f0 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 18:21:06 +0200
Subject: [PATCH 07/13] escape semicolon

---
 R/desc_utils.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 4ec091f9..02548415 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -145,20 +145,20 @@ desc_add_extra_deps <- function(d, x) {
   cat(x)
   cat("\n")
   cat("strsplit:\n")
-  cat(strsplit(x, ";")[[1]])
+  cat(strsplit(x, "\\;")[[1]])
   cat("\n")
   cat("strsplit (fixed):\n")
-  cat(strsplit(x, ";", fixed = TRUE)[[1]])
+  cat(strsplit(x, "\\;", fixed = TRUE)[[1]])
   cat("\n")
   cat("strsplit (perl):\n")
-  cat(strsplit(x, ";", perl = TRUE)[[1]])
+  cat(strsplit(x, "\\;", perl = TRUE)[[1]])
   cat("\n")
   cat("strsplit (useBytes):\n")
-  cat(strsplit(x, ";", useBytes = TRUE)[[1]])
+  cat(strsplit(x, "\\;", useBytes = TRUE)[[1]])
   cat("\n")
 
   if (length(x)) {
-    for (x_i in trimws(strsplit(x, ";")[[1]])) {
+    for (x_i in trimws(strsplit(x, "\\;")[[1]])) {
       cat("x_i: \n")
       cat(x_i)
       cat("\n")

From b42798df02adf8e25e683027b4e6a290b9c8432a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 18:29:51 +0200
Subject: [PATCH 08/13] more debug statements

---
 R/desc_utils.R | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 02548415..9eb8502d 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -142,19 +142,15 @@ desc_cond_set_refs <- function(d, refs) {
 #' d$get_deps()
 desc_add_extra_deps <- function(d, x) {
   cat("desc_add_extra_deps: \n")
-  cat(x)
-  cat("\n")
+  print(x)
   cat("strsplit:\n")
-  cat(strsplit(x, "\\;")[[1]])
-  cat("\n")
+  print(strsplit(x, "\\;"))
   cat("strsplit (fixed):\n")
-  cat(strsplit(x, "\\;", fixed = TRUE)[[1]])
-  cat("\n")
+  print(strsplit(x, "\\;", fixed = TRUE))
   cat("strsplit (perl):\n")
-  cat(strsplit(x, "\\;", perl = TRUE)[[1]])
-  cat("\n")
+  print(strsplit(x, "\\;", perl = TRUE))
   cat("strsplit (useBytes):\n")
-  cat(strsplit(x, "\\;", useBytes = TRUE)[[1]])
+  print(strsplit(x, "\\;", useBytes = TRUE))
   cat("\n")
 
   if (length(x)) {

From f381c5a26c1861a98cac489bdb60126c1b757c81 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 20 Jun 2024 18:47:54 +0200
Subject: [PATCH 09/13] rm debug prints

---
 R/desc_utils.R | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index 9eb8502d..bdb556ae 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -141,24 +141,8 @@ desc_cond_set_refs <- function(d, refs) {
 #' d <- verdepcheck:::desc_add_extra_deps(d, "bar (>= 2.3.4); baz (>= 3.4.5)")
 #' d$get_deps()
 desc_add_extra_deps <- function(d, x) {
-  cat("desc_add_extra_deps: \n")
-  print(x)
-  cat("strsplit:\n")
-  print(strsplit(x, "\\;"))
-  cat("strsplit (fixed):\n")
-  print(strsplit(x, "\\;", fixed = TRUE))
-  cat("strsplit (perl):\n")
-  print(strsplit(x, "\\;", perl = TRUE))
-  cat("strsplit (useBytes):\n")
-  print(strsplit(x, "\\;", useBytes = TRUE))
-  cat("\n")
-
   if (length(x)) {
     for (x_i in trimws(strsplit(x, "\\;")[[1]])) {
-      cat("x_i: \n")
-      cat(x_i)
-      cat("\n")
-
       x_i_deparsed <- deparse_dep_str(x_i)
       d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
     }
@@ -178,10 +162,6 @@ desc_add_extra_deps <- function(d, x) {
 #' verdepcheck:::deparse_dep_str("foo")
 #' verdepcheck:::deparse_dep_str("foo (>= 1.2.3)")
 deparse_dep_str <- function(x) {
-  cat("deparse_dep_str: \n")
-  cat(x)
-  cat("\n")
-
   x <- trimws(strsplit(x, "\\(")[[1]])
   package <- x[1]
   ver_str <- gsub("\\)$", "", x[2])
@@ -207,10 +187,6 @@ deparse_dep_str <- function(x) {
 #' @examples
 #' verdepcheck:::deparse_ver_str(">= 1.2.3")
 deparse_ver_str <- function(x) {
-  cat("deparse_ver_str: \n")
-  cat(x)
-  cat("\n")
-
   x <- trimws(x)
   if (is.na(x) || length(x) == 0 || x == "*" || x == "") {
     return(list(op = "", op_ver = ""))

From bc6ed21322079ab23a6c05c9e041223a5d068096 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 21 Jun 2024 11:12:07 +0200
Subject: [PATCH 10/13] fix docs; spelling and urlchecker

---
 _pkgdown.yml                            |  1 +
 inst/WORDLIST                           |  6 +-----
 vignettes/run_with_docker_container.Rmd | 10 +++++-----
 3 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 124a04b8..abaecc0b 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -13,6 +13,7 @@ articles:
   - title: Articles
     navbar: ~
     contents:
+      - matches("*")
 
 reference:
   - title: Dependency Check
diff --git a/inst/WORDLIST b/inst/WORDLIST
index 6fc5163c..d98ed468 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,7 +1,3 @@
-behaviour
 CMD
-cran
-deps
+RStudio
 pre
-ver
-verdepcheck
diff --git a/vignettes/run_with_docker_container.Rmd b/vignettes/run_with_docker_container.Rmd
index ada4f56b..e80359fb 100644
--- a/vignettes/run_with_docker_container.Rmd
+++ b/vignettes/run_with_docker_container.Rmd
@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 ```
 
 `verdepcheck` can be used within a docker container to consistently check the version dependencies of an R package.
-This vignette demonstrates how to run the [`r-verdepcheck-action`](https://github.com/insightsengineering/r-verdepcheck-action) Github workflow locally with a minimal setup.
+This vignette demonstrates how to run the [`r-verdepcheck-action`](https://github.com/insightsengineering/r-verdepcheck-action) GitHub workflow locally with a minimal setup.
 
 1. Download the docker image
 1. Run the docker container
@@ -29,7 +29,7 @@ _Note_: that you can skip the container setup and run the code below in your loc
 
 ### Pull and run the docker image
 
-The docker image used in this vignette is available on the Github Container Registry (ghcr.io) and is being used by the Insights Engineering R packages (such as `teal` and `tern`).
+The docker image used in this vignette is available on the GitHub Container Registry ([`ghcr.io`](https://ghcr.io)) and is being used by the Insights Engineering R packages (such as `teal` and `tern`).
 
 ```bash
 docker pull ghcr.io/insightsengineering/rstudio:latest
@@ -38,7 +38,7 @@ docker run --rm -p 8787:8787 -e PASSWORD=test -v ./:/workspace/project ghcr.io/i
 
 ### Open the RStudio in the browser
 
-Navigate to [http://localhost:8787](http://localhost:8788) and login with the username `rstudio` and password `test`.
+Navigate to [`http://localhost:8787`] and login with the username `rstudio` and password `test`.
 
 ### Clean `pkgcache` cache before repeated runs
 
@@ -49,7 +49,7 @@ In order to avoid using cached downloads from the previous run, it is recommend
 rm -rf /home/rstudio/.cache/R/pkgcache
 ```
 
-_note_: The location of the pkgcache directory may vary depending on the operation system.
+_note_: The location of the `pkgcache` directory may vary depending on the operation system.
 Use the R command `pkgcache::pkg_cache_summary()` to find its location in your system.
 
 ### Run the code below inside the container
@@ -87,7 +87,7 @@ system2(
     "clone",
     depth,
     ref,
-    sprintf("https://github.com/%s", github_id),
+    paste0("https://github.com/", github_id),
     repo_path
   ) |> purrr::compact() # remove empty arguments if they are NULL
 )

From b90ae5f878978adcf4f3e7c085c63e5adeafa8d7 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 24 Jun 2024 17:59:40 +0200
Subject: [PATCH 11/13] raise error if dep exists; add tests

---
 R/desc_utils.R                   |  3 +++
 tests/testthat/test-desc_utils.R | 12 ++++++++++++
 2 files changed, 15 insertions(+)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index bdb556ae..a84acbc2 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -144,6 +144,9 @@ desc_add_extra_deps <- function(d, x) {
   if (length(x)) {
     for (x_i in trimws(strsplit(x, "\\;")[[1]])) {
       x_i_deparsed <- deparse_dep_str(x_i)
+      if (any(d$get_deps()$package == x_i_deparsed$package)) {
+        stop("Cannot add extra dependency '", x_i_deparsed$package, "' as it already exists in DESCRIPTION file.")
+      }
       d$set_dep(x_i_deparsed$package, "Imports", x_i_deparsed$ver_str)
     }
   }
diff --git a/tests/testthat/test-desc_utils.R b/tests/testthat/test-desc_utils.R
index f7388d73..a363daf4 100644
--- a/tests/testthat/test-desc_utils.R
+++ b/tests/testthat/test-desc_utils.R
@@ -150,6 +150,18 @@ test_that("desc_remotes_cleanup accepts no Config/Need/verdepcheck", {
   expect_contains(clean_d$get_remotes(), "tidyverse/dplyr@*release")
 })
 
+test_that("desc_add_extra_deps will add extra dependencies", {
+  d <- desc::desc("!new")
+  d <- desc_add_extra_deps(d, "foo (>= 1.2.3)")
+  expect_contains(d$get_deps(), data.frame(type = "Imports", package = "foo", version = ">= 1.2.3"))
+})
+
+test_that("desc_add_extra_deps raises error for already existing package", {
+  d <- desc::desc("!new")
+  d$set_dep("foo", "Imports", ">= 1.2.3")
+  expect_error(desc_add_extra_deps(d, "foo (>= 1.2.3)"), "already exists")
+})
+
 test_that("get_desc_field_pkgs allows for no Config/Needs/verdepcheck", {
   d <- desc::desc(
     file = verdepcheck:::local_description(

From d9967798cb8b90ee189514dc64468d0b72e5271a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 24 Jun 2024 18:03:08 +0200
Subject: [PATCH 12/13] docs wording

---
 R/deps_installation_proposal.R    | 2 +-
 man/deps_check.Rd                 | 2 +-
 man/deps_installation_proposal.Rd | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/deps_installation_proposal.R b/R/deps_installation_proposal.R
index 793bb875..b9e40730 100644
--- a/R/deps_installation_proposal.R
+++ b/R/deps_installation_proposal.R
@@ -39,7 +39,7 @@
 #' Please see also [`pkgdepends::pkg_config`] and [`pak::pak-config`] for other configuration possibilities.
 #'
 #' @param path (`string`) path to the package sources
-#' @param extra_deps (`character(1)`) Extra dependencies specified similarly to the `DESCRIPTION` file, i.e.
+#' @param extra_deps (`character(1)`) Extra dependencies specified similarly as in the `DESCRIPTION` file, i.e.
 #' `"<package name> (<operator> <version>)"` where both `<operator>` and `<version>` are optional.
 #' Multiple entries are possible separated by `";"`.
 #' @param config (`list`) configuration options. See [`pkgdepends::pkg_config`] for details.
diff --git a/man/deps_check.Rd b/man/deps_check.Rd
index ce7b59bc..88cd6040 100644
--- a/man/deps_check.Rd
+++ b/man/deps_check.Rd
@@ -46,7 +46,7 @@ min_isolated_deps_check(
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
-\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly as in the \code{DESCRIPTION} file, i.e.
 \code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 
diff --git a/man/deps_installation_proposal.Rd b/man/deps_installation_proposal.Rd
index 246f8541..6e6af34b 100644
--- a/man/deps_installation_proposal.Rd
+++ b/man/deps_installation_proposal.Rd
@@ -35,7 +35,7 @@ new_min_isolated_deps_installation_proposal(
 \arguments{
 \item{path}{(\code{string}) path to the package sources}
 
-\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\item{extra_deps}{(\code{character(1)}) Extra dependencies specified similarly as in the \code{DESCRIPTION} file, i.e.
 \code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 

From 994e0de9539f0d8171ebd75266094d84ae71c7ac Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 24 Jun 2024 18:04:31 +0200
Subject: [PATCH 13/13] docs cont.

---
 R/desc_utils.R             | 2 +-
 man/desc_add_extra_deps.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/desc_utils.R b/R/desc_utils.R
index a84acbc2..492be862 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -127,7 +127,7 @@ desc_cond_set_refs <- function(d, refs) {
 #' This will add dependencies to the `Imports` field.
 #'
 #' @param d (`desc`) DESCRIPTION object from [desc::desc]
-#' @param x (`character(1)`) Extra dependencies specified similarly to the `DESCRIPTION` file, i.e.
+#' @param x (`character(1)`) Extra dependencies specified similarly as in the `DESCRIPTION` file, i.e.
 #' `"<package name> (<operator> <version>)"` where both `<operator>` and `<version>` are optional.
 #' Multiple entries are possible separated by `";"`.
 #'
diff --git a/man/desc_add_extra_deps.Rd b/man/desc_add_extra_deps.Rd
index eca12566..065ec758 100644
--- a/man/desc_add_extra_deps.Rd
+++ b/man/desc_add_extra_deps.Rd
@@ -9,7 +9,7 @@ desc_add_extra_deps(d, x)
 \arguments{
 \item{d}{(\code{desc}) DESCRIPTION object from \link[desc:desc]{desc::desc}}
 
-\item{x}{(\code{character(1)}) Extra dependencies specified similarly to the \code{DESCRIPTION} file, i.e.
+\item{x}{(\code{character(1)}) Extra dependencies specified similarly as in the \code{DESCRIPTION} file, i.e.
 \code{"<package name> (<operator> <version>)"} where both \verb{<operator>} and \verb{<version>} are optional.
 Multiple entries are possible separated by \code{";"}.}
 }