chore: Update quarto, requirements.txt and software versions (#42)

csgillespie · web-flow · commit 609957391cbb · 2026-02-01T16:15:19.000Z
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,5 @@ rsconnect/
 ^\.commitlintrc\.yml$
 ^[.]?air[.]toml$
 ^\.vscode$
+\.venv
+\.husky
diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,4 @@ inst/doc
 *.swp
 .Rproj.user
 config-uat-rsc.yml
+.venv/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
diff --git a/.lintr b/.lintr
@@ -1,6 +1,7 @@
 linters: linters_with_defaults(
     assignment_linter = NULL,
     line_length_linter(100),
+	pipe_consistency_linter = NULL,
     undesirable_operator_linter(
       modify_defaults(
         default_undesirable_operators,
@@ -9,5 +10,6 @@ linters: linters_with_defaults(
     )
   )
 exclusions: list(
-    "^cache/"
+    "^cache/",
+    "inst/extdata/render_quarto/observable/"
   )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: audit.base
 Title: Base package for Posit Checks
-Version: 0.6.22
+Version: 0.6.23
 Authors@R:
     person("Jumping", "Rivers", , "info@jumpingrivers.com", role = c("aut", "cre"))
 Description: Base package for sharing classes between posit audit
@@ -32,4 +32,4 @@ Remotes:
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# audit.base 0.6.23 _2026-01-30_
+- chore: Update quarto, requirements.txt and software versions
+
 # audit.base 0.6.22 _2025-07-21_
 - chore: Use air for formatting
 - chore: Update requirements.txt for python example
diff --git a/R/check.R b/R/check.R
@@ -29,5 +29,5 @@ init_r6_check = function(export, dir, file, pkg_name) {
   } else {
     obj = NULL
   }
-  return(obj)
+  obj
 }
diff --git a/R/check_sys_deps.R b/R/check_sys_deps.R
@@ -12,9 +12,6 @@
 check_sys_deps = function(os_release, installed_libs, debug_level = 0:2) {
   debug_level = get_debug_level(debug_level)
   cli::cli_h2("Systems Libraries")
-  cli::cli_alert_info(
-    "This may take a few minutes as we are deploying a plumber API onto Connect"
-  )
   # Clean up response
   pkg_look_up = get_os_sys_deps(os_release)
 
@@ -28,7 +25,7 @@ check_sys_deps = function(os_release, installed_libs, debug_level = 0:2) {
     cli::cli_alert_info("Missing sys_libs: {sys_libs}")
     cli::cli_alert_info("Note: this is not necessarily a bad thing")
   }
-  return(missing_libs)
+  missing_libs
 }
 
 # Contents of /etc/os-release
diff --git a/R/config.R b/R/config.R
@@ -21,8 +21,7 @@ create_config = function(file, pkg_name) {
     yaml_file = file.path(dir, file)
     if (type == "error" && file.exists(yaml_file)) {
       cli::cli_abort(
-        "Config file already exists.
-                   Either delete or change the `type` argument."
+        "Config file already exists. Either delete or change the `type` argument."
       )
     }
 
@@ -32,7 +31,7 @@ create_config = function(file, pkg_name) {
       new_config = merge_configs(new_config, existing_config)
     }
     yaml::write_yaml(new_config, file = yaml_file)
-    return(invisible(new_config))
+    invisible(new_config)
   }
 }
 create_config_list = function(dir, file, default, pkg_name) {
diff --git a/R/get_latest_versions_remote.R b/R/get_latest_versions_remote.R
@@ -15,6 +15,7 @@ get_latest_versions_remote = function() {
     "1.4.557",
     "1.5.57",
     "1.6.43",
+    "1.7.34",
     stringr::str_remove(q$name, "^v")
   )
 
diff --git a/R/get_pkg_requirements.R b/R/get_pkg_requirements.R
@@ -11,6 +11,10 @@ get_pkg_requirements = function(
     "{repo_id}/sysreqs?all=true&distribution={distribution}&release={release}"
   ) # nolint
   url = glue::glue("{base_url}{config_url}")
+  cli::cli_alert_info(
+    "Connecting to {url} for system requirements"
+  )
+
   res = httr::GET(url)
   r = httr::content(res)
 
diff --git a/R/posit_versions.R b/R/posit_versions.R
@@ -32,7 +32,7 @@ get_posit_versions = function(
     versions = readr::read_csv(fname, comment = "#", col_types = c("c", "c"))
   }
   versions = dplyr::arrange(versions, dplyr::desc(.data$version))
-  return(versions)
+  versions
 }
 
 #' Audit Posit Server
@@ -67,10 +67,9 @@ audit_posit_version = function(
   } else {
     cli::cli_alert_info("Posit {type} is up to date")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }
 
-
 lookup_version = function(posit_version, type) {
   versions = get_posit_versions(type = type)
   version_as_date = version_to_date(posit_version)
@@ -92,7 +91,7 @@ lookup_version = function(posit_version, type) {
     )
     row_number = which(versions$version == posit_version)[1]
   }
-  return(row_number)
+  row_number
 }
 
 version_to_date = function(version) {
diff --git a/R/r6-base_check.R b/R/r6-base_check.R
@@ -66,7 +66,7 @@ base_check = R6::R6Class(
         return(FALSE)
       }
       group = config[[private$group]]
-      return(isFALSE(group[[private$short]]))
+      isFALSE(group[[private$short]])
     },
     checker = function(check) {
       self$start_logger()
@@ -77,7 +77,7 @@ base_check = R6::R6Class(
         has_passed = !inherits(res, "try-error") && isTRUE(res)
       }
       self$stop_logger(has_passed)
-      return(invisible(self))
+      invisible(self)
     }
   )
 )
diff --git a/R/r6-logger.R b/R/r6-logger.R
@@ -28,8 +28,7 @@ logger = R6::R6Class(
       )
 
       msg_function(passed)
-
-      return(invisible(self))
+      invisible(self)
     },
     #' @description Retrieve the log
     #' @return Check log
@@ -51,5 +50,5 @@ msg_function = function(has_passed) {
   } else {
     cli::cli_alert_danger("Check finished")
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }
diff --git a/R/software-versions.R b/R/software-versions.R
@@ -26,7 +26,7 @@ print_colour_versions = function(installed) {
     row = installed[i, ]
     print_colour_version(row)
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }
 
 print_colour_version = function(row) {
@@ -50,7 +50,7 @@ print_colour_version = function(row) {
       "{software_name}: Latest version installed v{row$installed_version}"
     )
   }
-  return(invisible(NULL))
+  invisible(NULL)
 }
 
 # Returns X.Y from X.Y.Z
diff --git a/inst/extdata/versions/connect.csv b/inst/extdata/versions/connect.csv
@@ -1,4 +1,17 @@
 version,cve
+2026.01.1,
+2026.01.0,
+2025.12.1,
+2025.12.0,
+2025.11.0,
+2025.10.0,
+2025.09.1,
+2025.09.0,CVE-2025-47906
+2025.09.0,CVE-2025-47907
+2025.09.0,CVE-2025-47906
+2025.09.0,CVE-2025-47907
+2025.07.0,CVE-2025-4674
+2025.07.0,CVE-2025-4674
 2025.06.0,CVE-2025-4673
 2025.06.0,CVE-2025-0913
 2025.06.0,CVE-2025-22874
diff --git a/inst/extdata/versions/drivers.csv b/inst/extdata/versions/drivers.csv
@@ -1,8 +1,10 @@
 # https://docs.posit.co/pro-drivers/documentation/
 version,cve
+2026.01.0
+2025.07.0
+2025.03.0,
 2024.03.0,
 2023.12.1,
 2023.05.0,
 2022.11.0,
 2021.10.0,
-
diff --git a/inst/extdata/versions/software.csv b/inst/extdata/versions/software.csv
@@ -1,18 +1,19 @@
 software,version
-python,3.13.5
-python,3.12.11
-python,3.11.13
-python,3.10.18
-python,3.9.23
-quarto,1.7.32
+python,3.13.9
+python,3.12.12
+python,3.11.14
+python,3.10.19
+python,3.9.25
+quarto,1.8.27
+quarto,1.7.34
 quarto,1.6.43
 quarto,1.5.57
 quarto,1.4.557
 quarto,1.3.450
 quarto,1.2.475
 quarto,1.1.189
 quarto,1.0.38
-r,4.5.1
+r,4.5.2
 r,4.4.3
 r,4.3.3
 r,4.2.3
diff --git a/inst/extdata/versions/workbench.csv b/inst/extdata/versions/workbench.csv
@@ -1,4 +1,8 @@
 version,cve
+2026.01.0,
+2025.09.2,
+2025.09.1,
+2025.09.0,
 2025.05.1,
 2025.05.0,
 2024.12.1,

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,7 @@`
`1`	`1`	`linters: linters_with_defaults(`
`2`	`2`	`assignment_linter = NULL,`
`3`	`3`	`line_length_linter(100),`
	`4`	`+ pipe_consistency_linter = NULL,`
`4`	`5`	`undesirable_operator_linter(`
`5`	`6`	`modify_defaults(`
`6`	`7`	`default_undesirable_operators,`
`@@ -9,5 +10,6 @@ linters: linters_with_defaults(`
`9`	`10`	`)`
`10`	`11`	`)`
`11`	`12`	`exclusions: list(`
`12`		`- "^cache/"`
	`13`	`+ "^cache/",`
	`14`	`+ "inst/extdata/render_quarto/observable/"`
`13`	`15`	`)`
Original file line number	Diff line number	Diff line change
`@@ -29,5 +29,5 @@ init_r6_check = function(export, dir, file, pkg_name) {`
`29`	`29`	`} else {`
`30`	`30`	`obj = NULL`
`31`	`31`	`}`
`32`		`- return(obj)`
	`32`	`+ obj`
`33`	`33`	`}`
Original file line number	Diff line number	Diff line change
`@@ -21,8 +21,7 @@ create_config = function(file, pkg_name) {`
`21`	`21`	`yaml_file = file.path(dir, file)`
`22`	`22`	`if (type == "error" && file.exists(yaml_file)) {`
`23`	`23`	`cli::cli_abort(`
`24`		`- "Config file already exists.`
`25`		- Either delete or change the `type` argument."
	`24`	+ "Config file already exists. Either delete or change the `type` argument."
`26`	`25`	`)`
`27`	`26`	`}`
`28`	`27`
`@@ -32,7 +31,7 @@ create_config = function(file, pkg_name) {`
`32`	`31`	`new_config = merge_configs(new_config, existing_config)`
`33`	`32`	`}`
`34`	`33`	`yaml::write_yaml(new_config, file = yaml_file)`
`35`		`- return(invisible(new_config))`
	`34`	`+ invisible(new_config)`
`36`	`35`	`}`
`37`	`36`	`}`
`38`	`37`	`create_config_list = function(dir, file, default, pkg_name) {`
Original file line number	Diff line number	Diff line change
`@@ -15,6 +15,7 @@ get_latest_versions_remote = function() {`
`15`	`15`	`"1.4.557",`
`16`	`16`	`"1.5.57",`
`17`	`17`	`"1.6.43",`
	`18`	`+ "1.7.34",`
`18`	`19`	`stringr::str_remove(q$name, "^v")`
`19`	`20`	`)`
`20`	`21`