From 417e1c8904bafe72464dd6f6f78b15f17113e0a7 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 19 Apr 2024 18:22:36 +0200
Subject: [PATCH 01/19] various enhancements

---
 NAMESPACE                      |   2 +
 R/desc_utils.R                 |   1 +
 R/get_ref.R                    | 138 +++++++++++++++++++++------------
 R/solve.R                      |   5 ++
 R/utils.R                      |   2 +-
 man/cli_pb_init.Rd             |   4 +-
 man/get_ref_min.Rd             |   8 +-
 man/get_release_date.Rd        |   7 +-
 man/get_version.Rd             |  31 ++++++++
 tests/testthat/setup-options.R |  20 +++++
 10 files changed, 157 insertions(+), 61 deletions(-)
 create mode 100644 man/get_version.Rd
 create mode 100644 tests/testthat/setup-options.R

diff --git a/NAMESPACE b/NAMESPACE
index ea456ab2..ea79ffc3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ S3method(get_release_date,remote_ref)
 S3method(get_release_date,remote_ref_cran)
 S3method(get_release_date,remote_ref_github)
 S3method(get_release_date,remote_ref_standard)
+S3method(get_version,remote_ref)
 S3method(solve_ip,deps_installation_proposal)
 S3method(solve_ip,min_isolated_deps_installation_proposal)
 export(check_ip)
@@ -20,6 +21,7 @@ export(get_ref_min)
 export(get_ref_min_incl_cran)
 export(get_ref_release)
 export(get_release_date)
+export(get_version)
 export(install_ip)
 export(max_deps_check)
 export(min_cohort_deps_check)
diff --git a/R/desc_utils.R b/R/desc_utils.R
index 80983b3c..dcfc43fc 100644
--- a/R/desc_utils.R
+++ b/R/desc_utils.R
@@ -128,6 +128,7 @@ desc_cond_set_refs <- function(d, refs) {
 desc_to_ip <- function(d, config) {
   temp_desc <- tempfile()
   d$write(temp_desc)
+  cli::cli_alert_info(paste0("Creating temporary DESCRIPTION file: ", cli::col_blue(temp_desc)))
 
   pkgdepends::new_pkg_installation_proposal(
     refs = paste0("deps::", temp_desc),
diff --git a/R/get_ref.R b/R/get_ref.R
index 9171cf9a..302e5192 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -79,7 +79,7 @@ get_ref_min <- function(remote_ref, op = "", op_ver = "") {
 #' @rdname get_ref_min
 #' @exportS3Method get_ref_min remote_ref
 #' @examples
-#' verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
+#' get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
 get_ref_min.remote_ref <- function(remote_ref, op = "", op_ver = "") {
   remote_ref
 }
@@ -94,9 +94,9 @@ get_ref_min.remote_ref <- function(remote_ref, op = "", op_ver = "") {
 #' @importFrom pkgdepends parse_pkg_ref
 #' @importFrom stats setNames
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
-#' verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("cran::dplyr"))
+#' get_ref_min(pkgdepends::parse_pkg_ref("cran::dplyr"))
 get_ref_min.remote_ref_cran <- function(remote_ref, op = "", op_ver = "") {
-  if (remote_ref$atleast == "" && remote_ref$version != "") {
+  if (remote_ref$version != "") {
     return(remote_ref)
   }
 
@@ -107,7 +107,7 @@ get_ref_min.remote_ref_cran <- function(remote_ref, op = "", op_ver = "") {
   pv <- filter_valid_version(pv, op, op_ver)
   min_ver <- Filter(function(x) x == min(pv), pv)
 
-  new_ref <- sprintf("%s@%s", remote_ref$ref, names(min_ver)) # @TODO deparse, add ver, parse again
+  new_ref <- sprintf("%s@%s", remote_ref$package, names(min_ver))
   tryCatch(
     pkgdepends::parse_pkg_ref(new_ref),
     error = function(err) {
@@ -127,7 +127,7 @@ get_ref_min.remote_ref_cran <- function(remote_ref, op = "", op_ver = "") {
 #' @rdname get_ref_min
 #' @exportS3Method get_ref_min remote_ref_standard
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
-#' verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))
+#' get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))
 get_ref_min.remote_ref_standard <- function(remote_ref, op = "", op_ver = "") {
   get_ref_min.remote_ref_cran(remote_ref, op, op_ver)
 }
@@ -140,7 +140,7 @@ get_ref_min.remote_ref_standard <- function(remote_ref, op = "", op_ver = "") {
 #' @importFrom pkgdepends parse_pkg_ref
 #'
 #' @examplesIf gh::gh_token() != ""
-#' verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("cran/dplyr"))
+#' get_ref_min(pkgdepends::parse_pkg_ref("cran/dplyr"))
 get_ref_min.remote_ref_github <- function(remote_ref, op = "", op_ver = "") {
   if (remote_ref$commitish != "") {
     return(remote_ref)
@@ -285,22 +285,50 @@ get_ref_max <- function(remote_ref) {
 #' @importFrom pkgdepends parse_pkg_ref
 #' @export
 get_ref_release <- function(remote_ref) {
+  # create list of ref candidates to check
+  # return the one of the highest version
+  # this is a named list of character with version values and refs names
+  ref_candidates <- list()
   if (check_if_on_cran(remote_ref)) {
-    return(pkgdepends::parse_pkg_ref(remote_ref$package))
+    cran_ref <- remote_ref$package
+    cran_ver <- get_version(pkgdepends::parse_pkg_ref(cran_ref))
+    ref_candidates <- append(ref_candidates, setNames(list(cran_ver), cran_ref))
   }
   if (inherits(remote_ref, "remote_ref_github")) {
+    gh_release_ref <- cond_parse_pkg_ref_release(remote_ref)
+    gh_release_ver <- get_version(gh_release_ref)
+    ref_candidates <- c(ref_candidates, setNames(list(gh_release_ver), gh_release_ref$ref))
+
     if (!is.null(remote_ref$commitish) && remote_ref$commitish != "") {
-      return(remote_ref)
+      gh_commitish_ref <- remote_ref
+      gh_commitish_ver <- get_version(gh_commitish_ref)
+      ref_candidates <- c(ref_candidates, setNames(list(gh_commitish_ver), gh_commitish_ref$ref))
     }
     if (!is.null(remote_ref$pull) && remote_ref$pull != "") {
-      return(remote_ref)
+      gh_pull_ref <- remote_ref
+      gh_pull_ver <- get_version(gh_pull_ref)
+      ref_candidates <- c(ref_candidates, setNames(list(gh_pull_ver), gh_pull_ref$ref))
     }
-    if (!is.null(remote_ref$release) && remote_ref$release != "") {
-      return(cond_parse_pkg_ref_release(remote_ref))
+  } else {
+    input_ref <- remote_ref$ref
+    input_ver <- get_version(remote_ref)
+    ref_candidates <- c(ref_candidates, setNames(list(input_ver), input_ref))
+  }
+
+  if (length(ref_candidates) == 0 || all(is.na(ref_candidates))) {
+    return(remote_ref)
+  } else {
+    max_ver <- ref_candidates[[1]]
+    max_ref <- names(ref_candidates[1])
+    for (i in 2:length(ref_candidates)) {
+      i_ver <- ref_candidates[[i]]
+      i_ref <- names(ref_candidates[i])
+      if (!is.na(i_ver) && i_ver > max_ver) {
+        max_ref <- i_ref
+      }
     }
-    return(cond_parse_pkg_ref_release(remote_ref))
+    return(pkgdepends::parse_pkg_ref(max_ref))
   }
-  return(remote_ref)
 }
 
 #' @importFrom pkgdepends parse_pkg_ref
@@ -335,66 +363,78 @@ cond_parse_pkg_ref_release <- function(remote_ref) {
   }
 }
 
+#' Get package version.
+#'
+#' @inheritParams get_ref_min
+#' @returns Package version created with `package_version`.
+#'
+#' @export
+get_version <- function(remote_ref) {
+  UseMethod("get_version", remote_ref)
+}
+
+#' @rdname get_version
+#' @importFrom pkgdepends::new_pkg_deps
+#' @exportS3Method get_version remote_ref
+#' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
+#' get_version(pkgdepends::parse_pkg_ref("dplyr"))
+#' get_version(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
+#' get_version(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
+get_version.remote_ref <- function(remote_ref, op = "", op_ver = "") {
+  x <- pkgdepends::new_pkg_deps(remote_ref$ref, config = list(dependencies = FALSE))
+  x$solve()
+  if (x$get_solution()$status == "FAILED") {
+    return(NA)
+  } else {
+    as.package_version(x$get_resolution()[1, "version"])
+  }
+}
+
+
 #' Get release date.
 #'
 #' @inheritParams get_ref_min
-#' @inherit get_ref_min return
+#' @returns Date
 #'
 #' @export
 get_release_date <- function(remote_ref) {
   UseMethod("get_release_date", remote_ref)
 }
 
-#' Get release date from GitHub references
-#'
 #' @rdname get_release_date
 #' @exportS3Method get_release_date remote_ref_github
 #' @importFrom gh gh_gql
 #'
 #' @examplesIf gh::gh_token() != ""
-#' remote_ref <- pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0")
-#' get_release_date(remote_ref)
+#' get_release_date(pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0"))
 get_release_date.remote_ref_github <- function(remote_ref) {
+  x <- pkgdepends::new_pkg_deps(remote_ref$ref, config = list(dependencies = FALSE))
+  x$solve()
+  if (x$get_solution()$status == "FAILED") {
+    return(as.Date(NA))
+  }
+
+  sha <- x$get_resolution()[1, "extra"][[1]]$remotesha
+  if (is.null(sha)) {
+    return(as.Date(NA))
+  }
+
   gql_query <- sprintf("{
     repository(owner: \"%s\", name: \"%s\") {
-      refs(refPrefix: \"refs/tags/\", query: \"%s\", first: 100) {
-        edges {
-        	node {
-          	name
-            target {
-              ... on Commit {
-                committedDate
-              }
-            }
-          }
+      object(oid: \"%s\") {
+        ... on Commit {
+          committedDate
         }
       }
     }
-  }", remote_ref$username, remote_ref$repo, remote_ref$commitish)
+  }", remote_ref$username, remote_ref$repo, sha)
 
   resp <- try(gh::gh_gql(gql_query), silent = TRUE)
-  if (inherits(resp, "try-error") || is.null(resp$data$repository$refs$edges)) {
-    return(as.Date(NA_real_))
-  }
-
-  result <- vapply(
-    resp$data$repository$refs$edges,
-    function(x) {
-      if (x$node$name != remote_ref$commitish) {
-        return(as.Date(NA_real_))
-      }
-      as.Date(x$node$target$committedDate)
-    },
-    double(1)
-  )
-
-  result <- Filter(function(el) !is.na(el) && !is.null(el), result)
-
-  if (length(result) == 0) {
-    return(as.Date(NA_real_))
+  if (inherits(resp, "try-error") || is.null(resp$data$repository$object$committedDate)) {
+    return(as.Date(NA))
   }
 
-  max(as.Date(result))
+  as.Date(resp$data$repository$object$committedDate)
 }
 
 #' Get release date from GitHub references
diff --git a/R/solve.R b/R/solve.R
index 2fd25c1a..e681b84e 100644
--- a/R/solve.R
+++ b/R/solve.R
@@ -71,6 +71,11 @@ solve_ip.min_isolated_deps_installation_proposal <- function(ip) { # nolint
 
   new_res <- do.call(rbind, deps_res)
 
+  if (is.null(new_res)) {
+    ip$solve()
+    return(invisible(ip))
+  }
+
   # Keep only top versions in calculated resolution (new_res).
   #  Very large resolution tables can become problematic and take a long to
   #  converge to a solution.
diff --git a/R/utils.R b/R/utils.R
index 94d79282..a563a065 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -86,7 +86,7 @@ resolve_ppm_snapshot <- function(pkg_ref_str, operator, pkg_version) {
   i_res
 }
 
-#' Create `cli` progress bar for resolving versions.
+#' Create `cli` progress bar to print status to the console.
 #' @importFrom cli col_blue col_yellow cli_progress_bar col_green pb_current pb_elapsed pb_eta pb_extra
 #' pb_spin pb_total style_bold symbol
 #' @keywords internal
diff --git a/man/cli_pb_init.Rd b/man/cli_pb_init.Rd
index 62a5daa9..85fd0d9d 100644
--- a/man/cli_pb_init.Rd
+++ b/man/cli_pb_init.Rd
@@ -2,11 +2,11 @@
 % Please edit documentation in R/utils.R
 \name{cli_pb_init}
 \alias{cli_pb_init}
-\title{Create \code{cli} progress bar for resolving versions.}
+\title{Create \code{cli} progress bar to print status to the console.}
 \usage{
 cli_pb_init(type, total, ...)
 }
 \description{
-Create \code{cli} progress bar for resolving versions.
+Create \code{cli} progress bar to print status to the console.
 }
 \keyword{internal}
diff --git a/man/get_ref_min.Rd b/man/get_ref_min.Rd
index e81310bb..dd630224 100644
--- a/man/get_ref_min.Rd
+++ b/man/get_ref_min.Rd
@@ -42,15 +42,15 @@ and then \code{\link[gh:gh]{gh::gh()}} to download \code{DESCRIPTION} file and t
 }
 }
 \examples{
-verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
+get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
 \dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("cran::dplyr"))
+get_ref_min(pkgdepends::parse_pkg_ref("cran::dplyr"))
 \dontshow{\}) # examplesIf}
 \dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))
+get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))
 \dontshow{\}) # examplesIf}
 \dontshow{if (gh::gh_token() != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-verdepcheck:::get_ref_min(pkgdepends::parse_pkg_ref("cran/dplyr"))
+get_ref_min(pkgdepends::parse_pkg_ref("cran/dplyr"))
 \dontshow{\}) # examplesIf}
 }
 \seealso{
diff --git a/man/get_release_date.Rd b/man/get_release_date.Rd
index d36fe28f..9aba4136 100644
--- a/man/get_release_date.Rd
+++ b/man/get_release_date.Rd
@@ -16,19 +16,16 @@ get_release_date(remote_ref)
 \item{remote_ref}{(\code{remote_ref}) object created with \code{\link[pkgdepends:parse_pkg_refs]{pkgdepends::parse_pkg_ref()}}}
 }
 \value{
-(\code{remote_ref}) object with the package reference
+Date
 }
 \description{
 Get release date.
 
-Get release date from GitHub references
-
 Get release date from GitHub references
 }
 \examples{
 \dontshow{if (gh::gh_token() != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-remote_ref <- pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0")
-get_release_date(remote_ref)
+get_release_date(pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0"))
 \dontshow{\}) # examplesIf}
 \dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 remote_ref <- pkgdepends::parse_pkg_ref("dplyr@1.1.0")
diff --git a/man/get_version.Rd b/man/get_version.Rd
new file mode 100644
index 00000000..bc26b7c0
--- /dev/null
+++ b/man/get_version.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_ref.R
+\name{get_version}
+\alias{get_version}
+\alias{get_version.remote_ref}
+\title{Get package version.}
+\usage{
+get_version(remote_ref)
+
+\method{get_version}{remote_ref}(remote_ref, op = "", op_ver = "")
+}
+\arguments{
+\item{remote_ref}{(\code{remote_ref}) object created with \code{\link[pkgdepends:parse_pkg_refs]{pkgdepends::parse_pkg_ref()}}}
+
+\item{op}{(\code{character(1)}) optional, version condition comparison operator (e.g. \code{">"}, \code{">="})}
+
+\item{op_ver}{(\code{character(1)}) optional, version number against which \code{op} argument is applied}
+}
+\value{
+Package version created with \code{package_version}.
+}
+\description{
+Get package version.
+}
+\examples{
+\dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+get_version(pkgdepends::parse_pkg_ref("dplyr"))
+get_version(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
+get_version(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
+\dontshow{\}) # examplesIf}
+}
diff --git a/tests/testthat/setup-options.R b/tests/testthat/setup-options.R
new file mode 100644
index 00000000..78be1f9b
--- /dev/null
+++ b/tests/testthat/setup-options.R
@@ -0,0 +1,20 @@
+# `opts_partial_match_old` is left for exclusions due to partial matching in dependent packages (i.e. not fixable here)
+# it might happen that it is not used right now, but it is left for possible future use
+# use with: `withr::with_options(opts_partial_match_old, { ... })` inside the test
+opts_partial_match_old <- list(
+  warnPartialMatchDollar = getOption("warnPartialMatchDollar"),
+  warnPartialMatchArgs = getOption("warnPartialMatchArgs"),
+  warnPartialMatchAttr = getOption("warnPartialMatchAttr")
+)
+opts_partial_match_new <- list(
+  warnPartialMatchDollar = TRUE,
+  warnPartialMatchArgs = TRUE,
+  warnPartialMatchAttr = TRUE
+)
+
+if (isFALSE(getFromNamespace("on_cran", "testthat")()) && requireNamespace("withr", quietly = TRUE)) {
+  withr::local_options(
+    opts_partial_match_new,
+    .local_envir = testthat::teardown_env()
+  )
+}

From c38a12779e11542c85a644c9407ee3cecb130254 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 19 Apr 2024 18:40:36 +0200
Subject: [PATCH 02/19] rcmdcheck fixes

---
 R/get_ref.R        | 6 +++---
 man/get_version.Rd | 6 +-----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index 302e5192..ec063d83 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -374,13 +374,13 @@ get_version <- function(remote_ref) {
 }
 
 #' @rdname get_version
-#' @importFrom pkgdepends::new_pkg_deps
+#' @importFrom pkgdepends new_pkg_deps
 #' @exportS3Method get_version remote_ref
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
 #' get_version(pkgdepends::parse_pkg_ref("dplyr"))
 #' get_version(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
 #' get_version(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
-get_version.remote_ref <- function(remote_ref, op = "", op_ver = "") {
+get_version.remote_ref <- function(remote_ref) {
   x <- pkgdepends::new_pkg_deps(remote_ref$ref, config = list(dependencies = FALSE))
   x$solve()
   if (x$get_solution()$status == "FAILED") {
@@ -483,7 +483,7 @@ get_cran_data <- function(package) {
     if (is.null(pkgenv$cache_db)) {
       pkgenv$cache_db <- tools::CRAN_package_db()
     }
-    db <- subset(pkgenv$cache_db, Package == package)
+    db <- subset(pkgenv$cache_db, pkgenv$cache_db$Package == package)
     cran_current <- data.frame(
       type = "cran",
       package = package,
diff --git a/man/get_version.Rd b/man/get_version.Rd
index bc26b7c0..1a668b01 100644
--- a/man/get_version.Rd
+++ b/man/get_version.Rd
@@ -7,14 +7,10 @@
 \usage{
 get_version(remote_ref)
 
-\method{get_version}{remote_ref}(remote_ref, op = "", op_ver = "")
+\method{get_version}{remote_ref}(remote_ref)
 }
 \arguments{
 \item{remote_ref}{(\code{remote_ref}) object created with \code{\link[pkgdepends:parse_pkg_refs]{pkgdepends::parse_pkg_ref()}}}
-
-\item{op}{(\code{character(1)}) optional, version condition comparison operator (e.g. \code{">"}, \code{">="})}
-
-\item{op_ver}{(\code{character(1)}) optional, version number against which \code{op} argument is applied}
 }
 \value{
 Package version created with \code{package_version}.

From 4f9120c09262ac361a100f4525e88b4c4ebf7e38 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 19 Apr 2024 18:45:14 +0200
Subject: [PATCH 03/19] docs

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index 98a8849f..124a04b8 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -35,3 +35,4 @@ reference:
     contents:
       - starts_with("get_ref_")
       - get_release_date
+      - get_version

From af186e1794fbb8f2e7ca38ed86a0ddbec7029499 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 13 May 2024 17:00:28 +0200
Subject: [PATCH 04/19] more robust in case no release is found

---
 R/get_ref.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index ec063d83..3dade134 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -296,8 +296,10 @@ get_ref_release <- function(remote_ref) {
   }
   if (inherits(remote_ref, "remote_ref_github")) {
     gh_release_ref <- cond_parse_pkg_ref_release(remote_ref)
-    gh_release_ver <- get_version(gh_release_ref)
-    ref_candidates <- c(ref_candidates, setNames(list(gh_release_ver), gh_release_ref$ref))
+    if (!is.null(gh_release_ref)) {
+      gh_release_ver <- get_version(gh_release_ref)
+      ref_candidates <- c(ref_candidates, setNames(list(gh_release_ver), gh_release_ref$ref))
+    }
 
     if (!is.null(remote_ref$commitish) && remote_ref$commitish != "") {
       gh_commitish_ref <- remote_ref
@@ -320,7 +322,7 @@ get_ref_release <- function(remote_ref) {
   } else {
     max_ver <- ref_candidates[[1]]
     max_ref <- names(ref_candidates[1])
-    for (i in 2:length(ref_candidates)) {
+    for (i in seq_along(ref_candidates)) {
       i_ver <- ref_candidates[[i]]
       i_ref <- names(ref_candidates[i])
       if (!is.na(i_ver) && i_ver > max_ver) {
@@ -337,7 +339,7 @@ get_ref_release <- function(remote_ref) {
 cond_parse_pkg_ref_release <- function(remote_ref) {
   has_release <- function(remote_ref) {
     isFALSE(inherits(
-      try(remotes::github_remote(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo))),
+      try(remotes::github_remote(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo)), silent = TRUE),
       "try-error"
     ))
   }

From 9f0d7ec0a4823723910347c6ac68713dc7dcb4d2 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 13 May 2024 17:01:19 +0200
Subject: [PATCH 05/19] test: force use binaries to avoid building and
 compilation

---
 R/utils.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/utils.R b/R/utils.R
index a563a065..38f186aa 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -10,6 +10,7 @@ pkgenv <- new.env(parent = emptyenv())
 default_config <- function() {
   list(
     dependencies = c(.desc_field, pkgdepends::as_pkg_dependencies(TRUE)$direct),
+    cran_mirror = pak::repo_resolve("PPM@latest"),
     library = tempfile()
   )
 }

From b3596eb60c3f361e4d138af318a83981dd4547c0 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 13 May 2024 17:14:43 +0200
Subject: [PATCH 06/19] use pkgcache instead of pak; docs

---
 R/utils.R                | 4 ++--
 man/map_key_character.Rd | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 38f186aa..6e2df40b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -10,7 +10,7 @@ pkgenv <- new.env(parent = emptyenv())
 default_config <- function() {
   list(
     dependencies = c(.desc_field, pkgdepends::as_pkg_dependencies(TRUE)$direct),
-    cran_mirror = pak::repo_resolve("PPM@latest"),
+    cran_mirror = pkgcache::repo_resolve("PPM@latest"),
     library = tempfile()
   )
 }
@@ -169,7 +169,7 @@ local_description <- function(pkg_list = c(pkgdepends = "Import"),
 #' Support function to reduce repetitive code
 #'
 #' @param x (`list`) list of lists where each internal list contain the same key
-#' @param field (`character(1)`) key of field to retrieve
+#' @param key (`character(1)`) key of field to retrieve
 #'
 #' @keywords internal
 #'
diff --git a/man/map_key_character.Rd b/man/map_key_character.Rd
index 05e6c552..f89fd78e 100644
--- a/man/map_key_character.Rd
+++ b/man/map_key_character.Rd
@@ -10,7 +10,7 @@ map_key_character(x, key)
 \arguments{
 \item{x}{(\code{list}) list of lists where each internal list contain the same key}
 
-\item{field}{(\code{character(1)}) key of field to retrieve}
+\item{key}{(\code{character(1)}) key of field to retrieve}
 }
 \description{
 Support function to reduce repetitive code

From 06238c3f73106c8555e964f34940a4c270131924 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Mon, 13 May 2024 17:26:06 +0200
Subject: [PATCH 07/19] add  to its own Config/Needs/verdepcheck

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3c5574e8..e01867f3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,6 +31,7 @@ Suggests:
     pingr,
     testthat (>= 3.0.4)
 Config/Needs/verdepcheck:
+    r-lib/cli,
     r-lib/desc,
     r-lib/gh,
     r-lib/pkgcache,

From 8229d4d428aa913141b19be5f8d2985e88a4e87e Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Tue, 14 May 2024 18:39:28 +0200
Subject: [PATCH 08/19] use binary repo for min_isolated

---
 R/utils.R | 41 ++++++++++++++---------------------------
 1 file changed, 14 insertions(+), 27 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 6e2df40b..6ef83f8f 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -31,35 +31,22 @@ base_pkgs <- function() {
 #' get_ppm_snapshot_by_date("2023-08-01")
 #' get_ppm_snapshot_by_date(Sys.Date() + 10)
 get_ppm_snapshot_by_date <- function(date) {
-  fallback_repo <- file.path(pkgcache::ppm_repo_url(), "latest")
-  if (is.na(date) || is.infinite(date)) {
-    return(fallback_repo)
-  }
-
-  snaps <- pkgcache::ppm_snapshots()
-  res <- as.character(as.Date(utils::head(
-    snaps[as.Date(snaps$date) > as.Date(date), "date"],
-    1
-  )))
-  if (length(res) == 0) {
-    warning(sprintf(
-      paste0(
-        "Cannot find PPM snapshot for date after %s.",
-        " Will use latest ppm snapshot instead."
-      ),
-      as.character(date)
-    ))
-    return(fallback_repo)
-  }
-  parse_ppm_url(res)
-}
-
-#' @importFrom pkgcache ppm_repo_url
-parse_ppm_url <- function(snapshot) {
-  file.path(pkgcache::ppm_repo_url(), snapshot)
+  tryCatch({
+    # https://github.com/r-lib/pkgcache/issues/110
+    # pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
+    snaps <- pkgcache::ppm_snapshots()
+    date_snap <- as.character(snaps[as.Date(snaps$date) > as.Date(date), "date"][1])
+    if (length(date_snap) == 0) {
+      stop("No PPM snapshot found for the given date.")
+    }
+    file.path(pkgcache::ppm_repo_url(), date_snap)
+    gsub("latest", date_snap, pkgcache::repo_resolve("PPM@latest"))
+  }, error = function(err) {
+    pkgcache::repo_resolve("PPM@latest")
+  })
 }
 
-#' Resolve the dependencies of package based on the release date + 1
+#' Resolve the dependencies of a package based on its release date + 1.
 #'
 #' @importFrom pkgdepends new_pkg_deps parse_pkg_ref
 #' @keywords internal

From a10eef96539d30661816016c7139afbb1ce59d2d Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 14 May 2024 16:41:38 +0000
Subject: [PATCH 09/19] [skip style] [skip vbump] Restyle files

---
 R/utils.R | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 6ef83f8f..5a222580 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -31,19 +31,22 @@ base_pkgs <- function() {
 #' get_ppm_snapshot_by_date("2023-08-01")
 #' get_ppm_snapshot_by_date(Sys.Date() + 10)
 get_ppm_snapshot_by_date <- function(date) {
-  tryCatch({
-    # https://github.com/r-lib/pkgcache/issues/110
-    # pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
-    snaps <- pkgcache::ppm_snapshots()
-    date_snap <- as.character(snaps[as.Date(snaps$date) > as.Date(date), "date"][1])
-    if (length(date_snap) == 0) {
-      stop("No PPM snapshot found for the given date.")
+  tryCatch(
+    {
+      # https://github.com/r-lib/pkgcache/issues/110
+      # pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
+      snaps <- pkgcache::ppm_snapshots()
+      date_snap <- as.character(snaps[as.Date(snaps$date) > as.Date(date), "date"][1])
+      if (length(date_snap) == 0) {
+        stop("No PPM snapshot found for the given date.")
+      }
+      file.path(pkgcache::ppm_repo_url(), date_snap)
+      gsub("latest", date_snap, pkgcache::repo_resolve("PPM@latest"))
+    },
+    error = function(err) {
+      pkgcache::repo_resolve("PPM@latest")
     }
-    file.path(pkgcache::ppm_repo_url(), date_snap)
-    gsub("latest", date_snap, pkgcache::repo_resolve("PPM@latest"))
-  }, error = function(err) {
-    pkgcache::repo_resolve("PPM@latest")
-  })
+  )
 }
 
 #' Resolve the dependencies of a package based on its release date + 1.

From 0dfd27e94c7f5ae28e4913d600a91651e31e9868 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 14 May 2024 16:41:46 +0000
Subject: [PATCH 10/19] [skip roxygen] [skip vbump] Roxygen Man Pages Auto
 Update

---
 man/resolve_ppm_snapshot.Rd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/resolve_ppm_snapshot.Rd b/man/resolve_ppm_snapshot.Rd
index 11b8613c..977c3ec5 100644
--- a/man/resolve_ppm_snapshot.Rd
+++ b/man/resolve_ppm_snapshot.Rd
@@ -2,11 +2,11 @@
 % Please edit documentation in R/utils.R
 \name{resolve_ppm_snapshot}
 \alias{resolve_ppm_snapshot}
-\title{Resolve the dependencies of package based on the release date + 1}
+\title{Resolve the dependencies of a package based on its release date + 1.}
 \usage{
 resolve_ppm_snapshot(pkg_ref_str, operator, pkg_version)
 }
 \description{
-Resolve the dependencies of package based on the release date + 1
+Resolve the dependencies of a package based on its release date + 1.
 }
 \keyword{internal}

From 44554bd40539a42da340cb21b4df67bb34756bc5 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Tue, 14 May 2024 18:52:18 +0200
Subject: [PATCH 11/19] lint

---
 R/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index 5a222580..68359e39 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -34,7 +34,7 @@ get_ppm_snapshot_by_date <- function(date) {
   tryCatch(
     {
       # https://github.com/r-lib/pkgcache/issues/110
-      # pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
+      # uncomment this: pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
       snaps <- pkgcache::ppm_snapshots()
       date_snap <- as.character(snaps[as.Date(snaps$date) > as.Date(date), "date"][1])
       if (length(date_snap) == 0) {

From c15cb55e52e328139fd366cb33c180d9aed662ba Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 16 May 2024 11:36:44 +0200
Subject: [PATCH 12/19] Update R/get_ref.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
---
 R/get_ref.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_ref.R b/R/get_ref.R
index 3dade134..a058aafa 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -327,6 +327,7 @@ get_ref_release <- function(remote_ref) {
       i_ref <- names(ref_candidates[i])
       if (!is.na(i_ver) && i_ver > max_ver) {
         max_ref <- i_ref
+        max_ver <- i_ver
       }
     }
     return(pkgdepends::parse_pkg_ref(max_ref))

From aea4aa8458918d7a1487a51a4af775e3c85564a2 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 16 May 2024 11:37:11 +0200
Subject: [PATCH 13/19] Update R/get_ref.R
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
---
 R/get_ref.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index a058aafa..92e0dff5 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -292,7 +292,7 @@ get_ref_release <- function(remote_ref) {
   if (check_if_on_cran(remote_ref)) {
     cran_ref <- remote_ref$package
     cran_ver <- get_version(pkgdepends::parse_pkg_ref(cran_ref))
-    ref_candidates <- append(ref_candidates, setNames(list(cran_ver), cran_ref))
+    ref_candidates <- c(ref_candidates, setNames(list(cran_ver), cran_ref))
   }
   if (inherits(remote_ref, "remote_ref_github")) {
     gh_release_ref <- cond_parse_pkg_ref_release(remote_ref)

From 39e04f2a8b92ea486a64c730dbdef33877cd3f2b Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 16 May 2024 11:40:17 +0200
Subject: [PATCH 14/19] review comments; other minor stuff

---
 R/get_ref.R                                   | 59 ++++++++-----------
 R/solve.R                                     |  4 +-
 R/utils.R                                     |  2 +-
 man/get_desc_from_gh.Rd                       |  2 +
 man/get_ref_release.Rd                        |  6 ++
 man/get_release_date.Rd                       |  2 +-
 .../test-deps_installation_proposal.R         |  8 +--
 7 files changed, 42 insertions(+), 41 deletions(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index 92e0dff5..8319aab1 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -14,7 +14,7 @@ get_ref_min_incl_cran <- function(remote_ref, op = "", op_ver = "") {
 }
 
 #' @rdname get_ref_min_incl_cran
-#' @exportS3Method get_ref_min_incl_cran remote_ref
+#' @export
 #' @examples
 #' verdepcheck:::get_ref_min_incl_cran(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
@@ -25,7 +25,7 @@ get_ref_min_incl_cran.remote_ref <- function(remote_ref, op = "", op_ver = "") {
 
 #' @rdname get_ref_min_incl_cran
 #' @importFrom pkgdepends parse_pkg_ref
-#' @exportS3Method get_ref_min_incl_cran remote_ref_github
+#' @export
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
 #' verdepcheck:::get_ref_min_incl_cran(pkgdepends::parse_pkg_ref("cran/dplyr"))
 get_ref_min_incl_cran.remote_ref_github <- function(remote_ref, op = "", op_ver = "") {
@@ -77,7 +77,7 @@ get_ref_min <- function(remote_ref, op = "", op_ver = "") {
 }
 
 #' @rdname get_ref_min
-#' @exportS3Method get_ref_min remote_ref
+#' @export
 #' @examples
 #' get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
 get_ref_min.remote_ref <- function(remote_ref, op = "", op_ver = "") {
@@ -88,7 +88,7 @@ get_ref_min.remote_ref <- function(remote_ref, op = "", op_ver = "") {
 #' to obtain historical data.
 #'
 #' @rdname get_ref_min
-#' @exportS3Method get_ref_min remote_ref_cran
+#' @export
 #' @importFrom cli cli_alert_danger
 #' @importFrom pkgcache cran_archive_list meta_cache_list
 #' @importFrom pkgdepends parse_pkg_ref
@@ -101,7 +101,7 @@ get_ref_min.remote_ref_cran <- function(remote_ref, op = "", op_ver = "") {
   }
 
   x_pkg_cache <- pkgcache::meta_cache_list(remote_ref$package)
-  x_pkg_cache_archive <- pkgcache::cran_archive_list(package = remote_ref$package)
+  x_pkg_cache_archive <- pkgcache::cran_archive_list(packages = remote_ref$package)
   pv <- unique(c(x_pkg_cache_archive$version, x_pkg_cache$version))
   pv <- stats::setNames(package_version(pv), pv)
   pv <- filter_valid_version(pv, op, op_ver)
@@ -125,7 +125,7 @@ get_ref_min.remote_ref_cran <- function(remote_ref, op = "", op_ver = "") {
 }
 
 #' @rdname get_ref_min
-#' @exportS3Method get_ref_min remote_ref_standard
+#' @export
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
 #' get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))
 get_ref_min.remote_ref_standard <- function(remote_ref, op = "", op_ver = "") {
@@ -136,7 +136,7 @@ get_ref_min.remote_ref_standard <- function(remote_ref, op = "", op_ver = "") {
 #' and then [`gh::gh()`] to download `DESCRIPTION` file and then read package version.
 #'
 #' @rdname get_ref_min
-#' @exportS3Method get_ref_min remote_ref_github
+#' @export
 #' @importFrom pkgdepends parse_pkg_ref
 #'
 #' @examplesIf gh::gh_token() != ""
@@ -254,7 +254,7 @@ get_gh_tags <- function(org, repo, max_date = Sys.Date() + 1, min_date = as.Date
 #' @importFrom gh gh
 #' @keywords internal
 #'
-#' @examples
+#' @examplesIf gh::gh_token() != ""
 #' verdepcheck:::get_desc_from_gh("tidyverse", "dplyr")
 #' verdepcheck:::get_desc_from_gh("tidyverse", "dplyr", "v1.1.0")
 get_desc_from_gh <- function(org, repo, ref = "") {
@@ -284,6 +284,10 @@ get_ref_max <- function(remote_ref) {
 #'
 #' @importFrom pkgdepends parse_pkg_ref
 #' @export
+#'
+#' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
+#' get_ref_release(pkgdepends::parse_pkg_ref("dplyr"))
+#' get_ref_release(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
 get_ref_release <- function(remote_ref) {
   # create list of ref candidates to check
   # return the one of the highest version
@@ -301,15 +305,13 @@ get_ref_release <- function(remote_ref) {
       ref_candidates <- c(ref_candidates, setNames(list(gh_release_ver), gh_release_ref$ref))
     }
 
-    if (!is.null(remote_ref$commitish) && remote_ref$commitish != "") {
-      gh_commitish_ref <- remote_ref
-      gh_commitish_ver <- get_version(gh_commitish_ref)
-      ref_candidates <- c(ref_candidates, setNames(list(gh_commitish_ver), gh_commitish_ref$ref))
-    }
-    if (!is.null(remote_ref$pull) && remote_ref$pull != "") {
-      gh_pull_ref <- remote_ref
-      gh_pull_ver <- get_version(gh_pull_ref)
-      ref_candidates <- c(ref_candidates, setNames(list(gh_pull_ver), gh_pull_ref$ref))
+    if (
+      (!is.null(remote_ref$commitish) && remote_ref$commitish != "") ||
+        (!is.null(remote_ref$pull) && remote_ref$pull != "")
+    ) {
+      gh_ref <- remote_ref
+      gh_ver <- get_version(gh_ref)
+      ref_candidates <- c(ref_candidates, setNames(list(gh_ver), gh_ref$ref))
     }
   } else {
     input_ref <- remote_ref$ref
@@ -338,6 +340,8 @@ get_ref_release <- function(remote_ref) {
 #' @importFrom remotes github_remote
 #' @keywords internal
 cond_parse_pkg_ref_release <- function(remote_ref) {
+  stopifnot(inherits(remote_ref, "remote_ref_github"))
+
   has_release <- function(remote_ref) {
     isFALSE(inherits(
       try(remotes::github_remote(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo)), silent = TRUE),
@@ -345,18 +349,7 @@ cond_parse_pkg_ref_release <- function(remote_ref) {
     ))
   }
   parse_pkg_ref_remote <- function(remote_ref) {
-    # temporary fix for https://github.com/r-lib/pkgdepends/issues/275#issuecomment-1461787363
-    # @TODO: replace it with below one-liner if fixed
-    # parse_pkg_ref(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo)) # nolint
-    pkgdepends::parse_pkg_ref(
-      sprintf(
-        "%s=%s/%s@%s",
-        remote_ref$package,
-        remote_ref$username,
-        remote_ref$repo,
-        remotes::github_remote(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo))$ref
-      )
-    )
+    parse_pkg_ref(sprintf("%s/%s@*release", remote_ref$username, remote_ref$repo)) # nolint
   }
 
   if (has_release(remote_ref)) {
@@ -378,7 +371,7 @@ get_version <- function(remote_ref) {
 
 #' @rdname get_version
 #' @importFrom pkgdepends new_pkg_deps
-#' @exportS3Method get_version remote_ref
+#' @export
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
 #' get_version(pkgdepends::parse_pkg_ref("dplyr"))
 #' get_version(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
@@ -405,10 +398,10 @@ get_release_date <- function(remote_ref) {
 }
 
 #' @rdname get_release_date
-#' @exportS3Method get_release_date remote_ref_github
+#' @export
 #' @importFrom gh gh_gql
 #'
-#' @examplesIf gh::gh_token() != ""
+#' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != "" && gh::gh_token() != ""
 #' get_release_date(pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0"))
 get_release_date.remote_ref_github <- function(remote_ref) {
   x <- pkgdepends::new_pkg_deps(remote_ref$ref, config = list(dependencies = FALSE))
@@ -443,7 +436,7 @@ get_release_date.remote_ref_github <- function(remote_ref) {
 #' Get release date from GitHub references
 #'
 #' @rdname get_release_date
-#' @exportS3Method get_release_date remote_ref_cran
+#' @export
 #'
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
 #' remote_ref <- pkgdepends::parse_pkg_ref("dplyr@1.1.0")
diff --git a/R/solve.R b/R/solve.R
index e681b84e..9b5d9185 100644
--- a/R/solve.R
+++ b/R/solve.R
@@ -9,7 +9,7 @@ solve_ip <- function(ip) {
   UseMethod("solve_ip", ip)
 }
 
-#' @exportS3Method solve_ip deps_installation_proposal
+#' @export
 solve_ip.deps_installation_proposal <- function(ip) {
   ip$solve()
   resolve_ignoring_release_remote(ip)
@@ -24,7 +24,7 @@ solve_ip.deps_installation_proposal <- function(ip) {
 #'
 #' @importFrom stats na.omit
 #'
-#' @exportS3Method solve_ip min_isolated_deps_installation_proposal
+#' @export
 solve_ip.min_isolated_deps_installation_proposal <- function(ip) { # nolint
   ip$resolve()
   res <- ip$get_resolution()
diff --git a/R/utils.R b/R/utils.R
index 68359e39..5593412b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -15,7 +15,7 @@ default_config <- function() {
   )
 }
 append_config <- function(x1, x2) {
-  append(x1, x2)[unique(c(names(x1), names(x2)))]
+  modifyList(x1, x2)
 }
 
 #' @importFrom utils installed.packages
diff --git a/man/get_desc_from_gh.Rd b/man/get_desc_from_gh.Rd
index 2bf134a7..2122706a 100644
--- a/man/get_desc_from_gh.Rd
+++ b/man/get_desc_from_gh.Rd
@@ -10,7 +10,9 @@ get_desc_from_gh(org, repo, ref = "")
 Get DESCRIPTION from GitHub Repository
 }
 \examples{
+\dontshow{if (gh::gh_token() != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 verdepcheck:::get_desc_from_gh("tidyverse", "dplyr")
 verdepcheck:::get_desc_from_gh("tidyverse", "dplyr", "v1.1.0")
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/get_ref_release.Rd b/man/get_ref_release.Rd
index d7bcd39c..21d92028 100644
--- a/man/get_ref_release.Rd
+++ b/man/get_ref_release.Rd
@@ -15,3 +15,9 @@ get_ref_release(remote_ref)
 \description{
 Get reference to the release version of the package.
 }
+\examples{
+\dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+get_ref_release(pkgdepends::parse_pkg_ref("dplyr"))
+get_ref_release(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
+\dontshow{\}) # examplesIf}
+}
diff --git a/man/get_release_date.Rd b/man/get_release_date.Rd
index 9aba4136..47beab33 100644
--- a/man/get_release_date.Rd
+++ b/man/get_release_date.Rd
@@ -24,7 +24,7 @@ Get release date.
 Get release date from GitHub references
 }
 \examples{
-\dontshow{if (gh::gh_token() != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "" && gh::gh_token() != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 get_release_date(pkgdepends::parse_pkg_ref("tidyverse/dplyr@v1.1.0"))
 \dontshow{\}) # examplesIf}
 \dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
diff --git a/tests/testthat/test-deps_installation_proposal.R b/tests/testthat/test-deps_installation_proposal.R
index aa21d985..2bd255bc 100644
--- a/tests/testthat/test-deps_installation_proposal.R
+++ b/tests/testthat/test-deps_installation_proposal.R
@@ -235,8 +235,8 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles tern an
   withr::defer(unlink(x$get_config()$library))
 
   x <- test_proposal_common(x, "tern", "source", "0.8.3", NULL)
-  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip = FALSE)
-  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip = FALSE)
+  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip_flag = FALSE)
 })
 
 # Test for encapsulation isssue where another dependency (primary or in the tree)
@@ -259,8 +259,8 @@ test_that("new_min_isolated_deps_installation_proposal correctly resolves a diff
   withr::defer(unlink(x$get_config()$library))
 
   x <- test_proposal_common(x, "tern", "source", "0.8.3", NULL)
-  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip = FALSE)
-  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip = FALSE)
+  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip_flag = FALSE)
 })
 
 # #################################################################

From 2bb3914ec401e541712477a2a61c614fa5703161 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Thu, 16 May 2024 12:01:41 +0200
Subject: [PATCH 15/19] rm platform arg

---
 tests/testthat/helper.R                       |  8 +---
 .../test-deps_installation_proposal.R         | 42 +++++++++----------
 2 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 30d14488..4defb0fa 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -30,8 +30,6 @@ skip_if_empty_gh_token <- function() {
 #' @param x (`pkg_installation_proposal` object) Valid proposal created by one
 #' of the available methods.
 #' @param pkg_name (`string`) Name of package that is being tested for version.
-#' @param platform (optional `string`) Name of the platform, should be 'source' in
-#' most cases.
 #' @param pkg_ver_target (optional `string`) version that is expected to be in the
 #' proposal. A `NULL` value indicates to use the latest version on CRAN or a
 #' GitHub repository reference
@@ -45,7 +43,6 @@ skip_if_empty_gh_token <- function() {
 #' @keywords internal
 test_proposal_common <- function(x,
                                  pkg_name = "pkgdepends",
-                                 platform = "source",
                                  pkg_ver_target = NULL,
                                  pkg_gh_str = NULL,
                                  solve_ip_flag = TRUE) {
@@ -60,7 +57,7 @@ test_proposal_common <- function(x,
 
   x_solution_pkg <- subset(
     x_solution,
-    package == pkg_name & platform == "source"
+    package == pkg_name
   )
 
   expect_true(nrow(x_solution_pkg) >= 1)
@@ -95,7 +92,6 @@ test_proposal_common <- function(x,
 #' @keywords internal
 test_proposal_common_bioc <- function(x,
                                       pkg_name = "pkgdepends",
-                                      platform = "source",
                                       solve_ip_flag = TRUE) {
   expect_s3_class(x, "pkg_installation_proposal")
 
@@ -108,7 +104,7 @@ test_proposal_common_bioc <- function(x,
 
   x_solution_pkg <- subset(
     x_solution,
-    package == pkg_name & platform == "source"
+    package == pkg_name
   )
 
   expect_true(nrow(x_solution_pkg) >= 1)
diff --git a/tests/testthat/test-deps_installation_proposal.R b/tests/testthat/test-deps_installation_proposal.R
index 2bd255bc..d9263da1 100644
--- a/tests/testthat/test-deps_installation_proposal.R
+++ b/tests/testthat/test-deps_installation_proposal.R
@@ -6,7 +6,7 @@ test_that("new_max_deps_installation_proposal correctly handles standard referen
   x <- new_max_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, NULL)
+  test_proposal_common(x, "pkgdepends", NULL, NULL)
 })
 
 test_that("new_release_deps_installation_proposal correctly handles standard reference", {
@@ -17,7 +17,7 @@ test_that("new_release_deps_installation_proposal correctly handles standard ref
   x <- new_release_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, NULL)
+  test_proposal_common(x, "pkgdepends", NULL, NULL)
 })
 
 test_that("new_min_isolated_installation_proposal correctly handles standard reference", {
@@ -28,7 +28,7 @@ test_that("new_min_isolated_installation_proposal correctly handles standard ref
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.1.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.1.0", NULL)
 })
 
 test_that("new_min_cohort_deps_installation_proposal correctly handles standard reference", {
@@ -39,7 +39,7 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles standard
   x <- new_min_cohort_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.1.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.1.0", NULL)
 })
 
 # #################################################################
@@ -69,7 +69,7 @@ test_that("new_max_deps_installation_proposal correctly handles <org>/<repo> ref
   x <- new_max_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, remote_str)
+  test_proposal_common(x, "pkgdepends", NULL, remote_str)
 })
 
 test_that("new_max_deps_installation_proposal correctly handles <org>/<repo>@*release reference", {
@@ -85,7 +85,7 @@ test_that("new_max_deps_installation_proposal correctly handles <org>/<repo>@*re
   x <- new_max_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, remote_str)
+  test_proposal_common(x, "pkgdepends", NULL, remote_str)
 })
 
 test_that("new_max_deps_installation_proposal correctly handles <org>/<repo>@<tag> ref. (particular remote tag)", {
@@ -101,7 +101,7 @@ test_that("new_max_deps_installation_proposal correctly handles <org>/<repo>@<ta
   x <- new_max_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.3.2", remote_str)
+  test_proposal_common(x, "pkgdepends", "0.3.2", remote_str)
 })
 
 test_that("new_max_deps_installation_proposal correctly handles <org>/<repo> ref. (without Config/Need/verdpcheck)", {
@@ -113,7 +113,7 @@ test_that("new_max_deps_installation_proposal correctly handles <org>/<repo> ref
   x <- new_max_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, remote_str)
+  test_proposal_common(x, "pkgdepends", NULL, remote_str)
 })
 
 test_that("new_release_deps_installation_proposal correctly handles <org>/<repo> reference", {
@@ -125,7 +125,7 @@ test_that("new_release_deps_installation_proposal correctly handles <org>/<repo>
   x <- new_release_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", NULL, NULL)
+  test_proposal_common(x, "pkgdepends", NULL, NULL)
 })
 
 test_that("new_min_cohort_deps_installation_proposal correctly handles <org>/<repo> reference", {
@@ -137,7 +137,7 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles <org>/<re
   x <- new_min_cohort_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.1.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.1.0", NULL)
 })
 
 test_that("new_min_deps_installation_proposal correctly handles <org>/<repo> reference", {
@@ -154,7 +154,7 @@ test_that("new_min_deps_installation_proposal correctly handles <org>/<repo> ref
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.1.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.1.0", NULL)
 })
 
 # ################################################################
@@ -179,7 +179,7 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles \">=\"
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.2.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.2.0", NULL)
 })
 
 test_that("new_min_isolated_deps_installation_proposal correctly handles \">=\" dependency for standard reference", {
@@ -190,7 +190,7 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles \">=\"
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.2.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.2.0", NULL)
 })
 
 test_that("new_min_cohort_deps_installation_proposal correctly handles \">=\" dependency for <org>/<repo> reference", {
@@ -201,7 +201,7 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles \">=\" de
   x <- new_min_cohort_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.2.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.2.0", NULL)
 })
 
 test_that("new_min_cohort_deps_installation_proposal correctly handles \">=\" dependency for standard reference", {
@@ -212,7 +212,7 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles \">=\" de
   x <- new_min_cohort_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  test_proposal_common(x, "pkgdepends", "source", "0.2.0", NULL)
+  test_proposal_common(x, "pkgdepends", "0.2.0", NULL)
 })
 
 test_that("new_min_isolated_deps_installation_proposal correctly handles tern and rtables", {
@@ -234,9 +234,9 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles tern an
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  x <- test_proposal_common(x, "tern", "source", "0.8.3", NULL)
-  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip_flag = FALSE)
-  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "tern", "0.8.3", NULL)
+  test_proposal_common(x, "rtables", "0.6.1", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "formatters", "0.5.0", NULL, solve_ip_flag = FALSE)
 })
 
 # Test for encapsulation isssue where another dependency (primary or in the tree)
@@ -258,9 +258,9 @@ test_that("new_min_isolated_deps_installation_proposal correctly resolves a diff
   x <- new_min_isolated_deps_installation_proposal(d_std_path)
   withr::defer(unlink(x$get_config()$library))
 
-  x <- test_proposal_common(x, "tern", "source", "0.8.3", NULL)
-  x <- test_proposal_common(x, "rtables", "source", "0.6.1", NULL, solve_ip_flag = FALSE)
-  test_proposal_common(x, "formatters", "source", "0.5.0", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "tern", "0.8.3", NULL)
+  test_proposal_common(x, "rtables", "0.6.1", NULL, solve_ip_flag = FALSE)
+  test_proposal_common(x, "formatters", "0.5.0", NULL, solve_ip_flag = FALSE)
 })
 
 # #################################################################

From 0bbe250fdaafe2150acfe0ae4ff6d0aba5717b7a Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 17 May 2024 11:29:08 +0200
Subject: [PATCH 16/19] fix tests

---
 R/get_ref.R                                   | 55 ++++++++++---------
 R/utils.R                                     |  2 +-
 .../test-deps_installation_proposal.R         | 10 +---
 tests/testthat/test-get_ref.R                 |  4 +-
 tests/testthat/test-utils.R                   |  5 +-
 5 files changed, 36 insertions(+), 40 deletions(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index 8319aab1..2bc46d40 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -468,32 +468,37 @@ get_release_date.remote_ref <- function(remote_ref) {
 #' verdepcheck:::get_cran_data("dplyr")
 #' verdepcheck:::get_cran_data("SummarizedExperiment")
 get_cran_data <- function(package) {
-  cran_archive <- pkgcache::cran_archive_list(packages = package)[, c(
-    "package", "version", "mtime"
-  )]
-  cran_current <- pkgcache::meta_cache_list(packages = package)[, c(
-    "type", "package", "version", "published"
-  )]
-  if (all(is.na(cran_current$published))) {
-    # workaround of https://github.com/r-lib/pkgcache/issues/109
-    if (is.null(pkgenv$cache_db)) {
-      pkgenv$cache_db <- tools::CRAN_package_db()
-    }
-    db <- subset(pkgenv$cache_db, pkgenv$cache_db$Package == package)
-    cran_current <- data.frame(
-      type = "cran",
-      package = package,
-      version = db$Version,
-      published = as.POSIXct(db$`Date/Publication`)
-    )
-  }
+  cran_archive <- pkgcache::cran_archive_list(packages = package)[, c("package", "version", "mtime")]
+  cran_current <- head(
+    pkgcache::meta_cache_list(packages = package)[, c("type", "package", "version", "published")],
+    1
+  )
 
-  # Bioc custom logic as packages in Bioconductor do not return a published date
-  #  this will be immediately obsolete if {pkgcache} starts to return a non-NA value
-  #  note: a date is required for the `min_cohort` strategy
-  bioc_na_mtime_ix <- is.na(cran_current$published) & cran_current$type == "bioc"
-  if (NROW(cran_current[bioc_na_mtime_ix, ]) > 0) {
-    cran_current[bioc_na_mtime_ix, "published"] <- Sys.Date()
+  # handle missing dates
+  if (nrow(cran_current > 0)) {
+    if (is.na(cran_current$published)) {
+      if (cran_current$type == "cran") {
+        # in general, this should not happen for cran - https://github.com/r-lib/pkgcache/issues/109
+        # this is a temporary workaround
+        if (is.null(pkgenv$cache_db)) {
+          pkgenv$cache_db <- tools::CRAN_package_db()
+        }
+        db <- subset(pkgenv$cache_db, pkgenv$cache_db$Package == package)
+        cran_current <- data.frame(
+          type = "cran",
+          package = package,
+          version = db$Version[1],
+          published = as.POSIXct(db$`Date/Publication`[1])
+        )
+      } else if (cran_current$type == "bioc") {
+        cran_current <- data.frame(
+          type = "bioc",
+          package = package,
+          version = cran_current$version,
+          published = Sys.Date()
+        )
+      }
+    }
   }
 
   # Remove extra columns
diff --git a/R/utils.R b/R/utils.R
index 5593412b..89f44219 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -36,7 +36,7 @@ get_ppm_snapshot_by_date <- function(date) {
       # https://github.com/r-lib/pkgcache/issues/110
       # uncomment this: pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1)))
       snaps <- pkgcache::ppm_snapshots()
-      date_snap <- as.character(snaps[as.Date(snaps$date) > as.Date(date), "date"][1])
+      date_snap <- as.character(head(snaps[as.Date(snaps$date) > as.Date(date), "date"], 1))
       if (length(date_snap) == 0) {
         stop("No PPM snapshot found for the given date.")
       }
diff --git a/tests/testthat/test-deps_installation_proposal.R b/tests/testthat/test-deps_installation_proposal.R
index d9263da1..8eb903bc 100644
--- a/tests/testthat/test-deps_installation_proposal.R
+++ b/tests/testthat/test-deps_installation_proposal.R
@@ -289,10 +289,7 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles Bioc pack
 
   d_std_path <- local_description(list(SummarizedExperiment = "Import"))
 
-  expect_warning(
-    x <- new_min_cohort_deps_installation_proposal(d_std_path),
-    "Cannot find PPM snapshot"
-  )
+  x <- new_min_cohort_deps_installation_proposal(d_std_path)
 
   withr::defer(unlink(x$get_config()$library))
 
@@ -309,10 +306,7 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles Bioc pa
 
   withr::defer(unlink(x$get_config()$library))
 
-  expect_warning(
-    test_proposal_common_bioc(x, "SummarizedExperiment"),
-    "Cannot find PPM snapshot"
-  )
+  test_proposal_common_bioc(x, "SummarizedExperiment")
 })
 
 test_that("new_release_deps_installation_proposal correctly handles Bioc package", {
diff --git a/tests/testthat/test-get_ref.R b/tests/testthat/test-get_ref.R
index 6c5ac605..524da724 100644
--- a/tests/testthat/test-get_ref.R
+++ b/tests/testthat/test-get_ref.R
@@ -24,7 +24,7 @@ test_that("get_release_date.remote_ref_github will only retrieve 1 date for rlan
   expect_identical(as.Date(result), as.Date("2022-01-20T16:47:02Z"))
 })
 
-test_that("get_release_date.remote_ref_github will retrieve missing date (NA) for rlang@0.0.0", {
+test_that("get_release_date.remote_ref_github will retrieve missing date (NA) for r-lib/rlang@v0.0.0", {
   skip_if_offline()
   skip_if_empty_gh_token()
 
@@ -37,7 +37,7 @@ test_that("get_release_date.remote_ref_github will retrieve missing date (NA) fo
   expect_s3_class(result, "Date")
 })
 
-test_that("get_release_date.remote_ref_cran will retrieve missing date (NA) for rlang@0.0.0", {
+test_that("get_release_date.remote_ref_cran will retrieve missing date (NA) for package.does.not.exist@1.1.0", {
   skip_if_offline()
   skip_if_empty_gh_token()
 
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 1e30911d..6bf3a044 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -101,10 +101,7 @@ test_that("get_ppm_snapshot_by_date will accept NA", {
 test_that("get_ppm_snapshot_by_date will accept dates in the future", {
   skip_if_offline()
   auxiliary_fun <- function(days = 0) {
-    expect_warning(
-      expect_latest_ppm(get_ppm_snapshot_by_date(Sys.Date())),
-      "Cannot find PPM snapshot for date"
-    )
+    expect_latest_ppm(get_ppm_snapshot_by_date(Sys.Date()))
   }
 
   auxiliary_fun(0)

From 412e3260c1e44f0a592dea1610949b859a3688a5 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Fri, 17 May 2024 16:18:31 +0200
Subject: [PATCH 17/19] rename get_cran_data to get_release_data; more accurate
 release date for bioc packages

---
 NAMESPACE                                     |  1 +
 R/get_ref.R                                   | 16 ++++++++++------
 man/{get_cran_data.Rd => get_release_data.Rd} | 14 +++++++-------
 tests/testthat/test-get_ref.R                 |  4 ++--
 4 files changed, 20 insertions(+), 15 deletions(-)
 rename man/{get_cran_data.Rd => get_release_data.Rd} (52%)

diff --git a/NAMESPACE b/NAMESPACE
index ea79ffc3..9e205165 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -49,6 +49,7 @@ importFrom(cli,symbol)
 importFrom(desc,desc)
 importFrom(gh,gh)
 importFrom(gh,gh_gql)
+importFrom(jsonlite,fromJSON)
 importFrom(pkgcache,cran_archive_list)
 importFrom(pkgcache,meta_cache_list)
 importFrom(pkgcache,ppm_repo_url)
diff --git a/R/get_ref.R b/R/get_ref.R
index 2bc46d40..b017ac27 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -443,7 +443,7 @@ get_release_date.remote_ref_github <- function(remote_ref) {
 #' get_release_date.remote_ref_cran(remote_ref)
 get_release_date.remote_ref_cran <- function(remote_ref) {
   result <- subset(
-    get_cran_data(remote_ref$package),
+    get_release_data(remote_ref$package),
     package_version(version, strict = FALSE) == package_version(remote_ref$version, strict = FALSE),
     select = "mtime"
   )[[1]][1]
@@ -460,14 +460,16 @@ get_release_date.remote_ref <- function(remote_ref) {
   as.Date(NA_real_)
 }
 
-#' Get CRAN/Bioconductor metadata information on packages
+#' Get data for CRAN/Bioconductor package releases
 #'
 #' @importFrom pkgcache cran_archive_list meta_cache_list
+#' @importFrom jsonlite fromJSON
+#'
 #' @keywords internal
 #' @examplesIf Sys.getenv("R_USER_CACHE_DIR", "") != ""
-#' verdepcheck:::get_cran_data("dplyr")
-#' verdepcheck:::get_cran_data("SummarizedExperiment")
-get_cran_data <- function(package) {
+#' verdepcheck:::get_release_data("dplyr")
+#' verdepcheck:::get_release_data("SummarizedExperiment")
+get_release_data <- function(package) {
   cran_archive <- pkgcache::cran_archive_list(packages = package)[, c("package", "version", "mtime")]
   cran_current <- head(
     pkgcache::meta_cache_list(packages = package)[, c("type", "package", "version", "published")],
@@ -491,11 +493,13 @@ get_cran_data <- function(package) {
           published = as.POSIXct(db$`Date/Publication`[1])
         )
       } else if (cran_current$type == "bioc") {
+        url <- sprintf("https://packagemanager.posit.co/__api__/repos/4/packages/%s?bioc_version=%s", package, pkgcache::bioc_version())
+        release_date <- as.POSIXct(jsonlite::fromJSON(readLines(url, warn = FALSE))$occurred)
         cran_current <- data.frame(
           type = "bioc",
           package = package,
           version = cran_current$version,
-          published = Sys.Date()
+          published = release_date
         )
       }
     }
diff --git a/man/get_cran_data.Rd b/man/get_release_data.Rd
similarity index 52%
rename from man/get_cran_data.Rd
rename to man/get_release_data.Rd
index 34e6f37d..3860b7fb 100644
--- a/man/get_cran_data.Rd
+++ b/man/get_release_data.Rd
@@ -1,18 +1,18 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/get_ref.R
-\name{get_cran_data}
-\alias{get_cran_data}
-\title{Get CRAN/Bioconductor metadata information on packages}
+\name{get_release_data}
+\alias{get_release_data}
+\title{Get data for CRAN/Bioconductor package releases}
 \usage{
-get_cran_data(package)
+get_release_data(package)
 }
 \description{
-Get CRAN/Bioconductor metadata information on packages
+Get data for CRAN/Bioconductor package releases
 }
 \examples{
 \dontshow{if (Sys.getenv("R_USER_CACHE_DIR", "") != "") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-verdepcheck:::get_cran_data("dplyr")
-verdepcheck:::get_cran_data("SummarizedExperiment")
+verdepcheck:::get_release_data("dplyr")
+verdepcheck:::get_release_data("SummarizedExperiment")
 \dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/tests/testthat/test-get_ref.R b/tests/testthat/test-get_ref.R
index 524da724..70cd32ed 100644
--- a/tests/testthat/test-get_ref.R
+++ b/tests/testthat/test-get_ref.R
@@ -62,10 +62,10 @@ test_that("get_release_date with any class other than remote_ref.{github,cran,st
   expect_s3_class(result, "Date")
 })
 
-test_that("get_cran_data returns date for Bioconductor", {
+test_that("get_release_data returns date for Bioconductor", {
   skip_if_offline()
 
-  expect_false(any(is.na(get_cran_data("SummarizedExperiment")$mtime)))
+  expect_false(any(is.na(get_release_data("SummarizedExperiment")$mtime)))
 })
 
 test_that("get_ref_release returns a CRAN remote_reference if package exists", {

From 35be885ffa024eb29bb4a7e2dac872575b1882d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 20 May 2024 19:17:45 -0400
Subject: [PATCH 18/19] fix: add jsonlite to description

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index e01867f3..62c3049c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,6 +18,7 @@ Imports:
     cli (>= 3.6.0),
     desc (>= 1.2),
     gh,
+    jsonlite,
     pkgcache (>= 2.1.0),
     pkgdepends (>= 0.5.0),
     rcmdcheck,
@@ -34,6 +35,7 @@ Config/Needs/verdepcheck:
     r-lib/cli,
     r-lib/desc,
     r-lib/gh,
+    jeroen/jsonlite,
     r-lib/pkgcache,
     r-lib/pkgdepends,
     r-lib/rcmdcheck,

From 8a41033aed6cde5aba5d9de6eabe8fd8e51dca25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 20 May 2024 19:18:00 -0400
Subject: [PATCH 19/19] fix: linter error

---
 R/get_ref.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/get_ref.R b/R/get_ref.R
index b017ac27..33332b87 100644
--- a/R/get_ref.R
+++ b/R/get_ref.R
@@ -493,7 +493,11 @@ get_release_data <- function(package) {
           published = as.POSIXct(db$`Date/Publication`[1])
         )
       } else if (cran_current$type == "bioc") {
-        url <- sprintf("https://packagemanager.posit.co/__api__/repos/4/packages/%s?bioc_version=%s", package, pkgcache::bioc_version())
+        url <- sprintf(
+          "https://packagemanager.posit.co/__api__/repos/4/packages/%s?bioc_version=%s",
+          package,
+          pkgcache::bioc_version()
+        )
         release_date <- as.POSIXct(jsonlite::fromJSON(readLines(url, warn = FALSE))$occurred)
         cran_current <- data.frame(
           type = "bioc",