Merge pull request #84 from Genentech/dev

0.5.0 checked refactor

Author: maksymiuks

.Rbuildignore

@@ -11,3 +11,4 @@
 ^codecov\.yml$
 ^README\.html$
 ^README_cache$
+^\.lintr

.github/workflows/R-CMD-check.yaml

@@ -24,11 +24,12 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_FORCE_SUGGESTS_: false
       NOT_CRAN: "true"
 
     steps:

.lintr

@@ -0,0 +1,14 @@
+linters:
+	linters_with_defaults(
+	  defaults = default_linters,
+		object_length_linter = NULL,
+		object_name_linter = NULL,
+		cyclocomp_linter = NULL
+	)
+exclusions:
+  list(
+      "tests/testthat/testing_pkgs",
+      "tests/testthat/fixtures",
+      "inst/"
+  )
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: checked
 Title: Systematically Run R CMD Checks
-Version: 0.2.9
+Version: 0.5.1
 Authors@R:
     c(
       person(
@@ -11,8 +11,8 @@ Authors@R:
         comment = c(ORCID = "0000-0002-3120-1601")
       ),
       person(
-        "Doug", "Kelkhoff", , 
-        "doug.kelkhoff@gmail.com", 
+        "Doug", "Kelkhoff",
+        email = "doug.kelkhoff@gmail.com", 
         role = c("aut"),
         comment = c(ORCID = "0009-0003-7845-4061")
       ),
@@ -31,20 +31,27 @@ URL:
 BugReports: https://github.com/Genentech/checked/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
+Depends:
+    R (>= 3.6.2)
 Imports:
     callr,
     cli,
+    glue,
     igraph,
     jsonlite,
+    memoise,
     options,
     R6,
     rcmdcheck,
+    rlang,
     utils (>= 3.6.2),
     tools
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-Suggests: 
+RoxygenNote: 7.3.3
+Suggests:
+    remotes,
     testthat (>= 3.0.0),
+    visNetwork,
     withr
 Config/Needs/website:
     r-lib/asciicast

NAMESPACE

@@ -1,87 +1,165 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("[",checked_results)
-S3method(check_path,package_spec)
-S3method(check_path,package_spec_archive_source)
-S3method(check_path,package_spec_source)
+S3method("$",enum)
+S3method(Ops,enum)
+S3method(as_vertex_name,default)
+S3method(as_vertex_name,local_check_meta_task)
+S3method(as_vertex_name,task)
+S3method(check_path,pkg_origin)
+S3method(check_path,pkg_origin_archive)
+S3method(check_path,pkg_origin_local)
+S3method(check_path,pkg_origin_remote)
+S3method(check_path,pkg_origin_repo)
 S3method(count,default)
 S3method(count,issues)
 S3method(count,potential_issues)
-S3method(format,list_of_task_spec)
-S3method(format,task_spec)
+S3method(format,lib_path)
+S3method(format,local_check_meta_task)
+S3method(format,pkg_origin)
+S3method(format,pkg_origin_base)
+S3method(format,pkg_origin_local)
+S3method(format,pkg_origin_remote)
+S3method(format,pkg_origin_source)
+S3method(format,reporter_cell)
+S3method(format,reporter_line)
+S3method(format,task)
 S3method(format_status_line_ansi,check_process)
 S3method(format_status_line_ansi,default)
-S3method(get_package_spec_dependencies,default)
-S3method(get_package_spec_dependencies,package_spec)
-S3method(get_package_spec_dependencies,package_spec_archive_source)
-S3method(get_package_spec_dependencies,package_spec_source)
-S3method(install_parameters,package_spec)
-S3method(install_parameters,package_spec_archive_source)
-S3method(install_parameters,package_spec_source)
-S3method(print,check_design)
+S3method(format_task_name,check_task)
+S3method(format_task_name,default)
+S3method(format_task_name,install_task)
+S3method(format_task_name,rev_dep_check_meta_task)
+S3method(format_task_name,rev_dep_dep_meta_task)
+S3method(format_task_name,task)
+S3method(format_task_type,local_check_meta_task)
+S3method(format_task_type,rev_dep_check_meta_task)
+S3method(format_task_type,rev_dep_dep_meta_task)
+S3method(format_task_type,task)
+S3method(get_remote_tasks,default)
+S3method(get_remote_tasks,pkg_origin_local)
+S3method(get_remote_tasks,pkg_origin_remote)
+S3method(get_remote_tasks,task)
+S3method(install_params,pkg_origin)
+S3method(install_params,pkg_origin_archive)
+S3method(install_params,pkg_origin_base)
+S3method(install_params,pkg_origin_local)
+S3method(install_params,pkg_origin_remote)
+S3method(install_params,pkg_origin_repo)
+S3method(install_params,pkg_origin_unknown)
+S3method(is_type,default)
+S3method(is_type,list)
+S3method(is_type,process)
+S3method(is_type,task)
+S3method(lib,"NULL")
+S3method(lib,character)
+S3method(lib,check_task)
+S3method(lib,install_task)
+S3method(lib,lib_path_default)
+S3method(lib,lib_path_isolated)
+S3method(lib,task)
+S3method(lib_path,default)
+S3method(lib_path,pkg_origin_local)
+S3method(lib_path,pkg_origin_remote)
+S3method(lib_path,pkg_origin_repo)
+S3method(package,"NULL")
+S3method(package,default)
+S3method(package,pkg_origin)
+S3method(package,task)
+S3method(package_install_type,pkg_origin)
+S3method(package_install_type,pkg_origin_local)
+S3method(pkg_deps,default)
+S3method(pkg_deps,pkg_origin)
+S3method(pkg_deps,pkg_origin_archive)
+S3method(pkg_deps,pkg_origin_local)
+S3method(pkg_deps,pkg_origin_remote)
+S3method(plot,task_graph)
 S3method(print,checked_results)
-S3method(print,checked_results_check_task_spec)
-S3method(print,checked_results_revdep_check_task_spec)
+S3method(print,checker)
 S3method(print,issues)
+S3method(print,local_check_results)
 S3method(print,potential_issues)
-S3method(print,rcmdcheck_diff)
-S3method(print,task_spec)
+S3method(print,rcmdcheck_check_results)
+S3method(print,rcmdcheck_results)
+S3method(print,rcmdcheck_rev_dep_results)
+S3method(print,rev_dep_dep_results)
+S3method(print,task)
+S3method(remotes_graph,check_task)
+S3method(remotes_graph,igraph.vs)
+S3method(remotes_graph,install_task)
+S3method(remotes_graph,integer)
+S3method(remotes_graph,task)
+S3method(remotes_graph,task_graph)
 S3method(report_finalize,"NULL")
 S3method(report_finalize,reporter_ansi_tty)
 S3method(report_finalize,reporter_basic_tty)
-S3method(report_initialize,"NULL")
-S3method(report_initialize,reporter_ansi_tty)
-S3method(report_initialize,reporter_basic_tty)
+S3method(report_sleep,"NULL")
 S3method(report_sleep,default)
 S3method(report_sleep,reporter_ansi_tty)
+S3method(report_sleep,reporter_basic_tty)
+S3method(report_start_checks,"NULL")
+S3method(report_start_checks,reporter_ansi_tty)
+S3method(report_start_setup,"NULL")
+S3method(report_start_setup,reporter_ansi_tty)
+S3method(report_start_setup,reporter_basic_tty)
 S3method(report_status,"NULL")
 S3method(report_status,reporter_ansi_tty)
 S3method(report_status,reporter_basic_tty)
-S3method(results,check_design)
-S3method(results,check_task_spec)
-S3method(results,list_check_task_spec)
-S3method(results,list_revdep_check_task_spec)
-S3method(results,revdep_check_task_spec)
+S3method(report_step,"NULL")
+S3method(report_step,reporter_ansi_tty)
+S3method(report_step,reporter_basic_tty)
+S3method(report_task,reporter_ansi_tty)
+S3method(report_task_ansi_tty,check_task)
+S3method(report_task_ansi_tty,default)
+S3method(report_task_ansi_tty,rev_dep_check_meta_task)
+S3method(results,checker)
+S3method(results,igraph.vs)
+S3method(results,integer)
+S3method(results,local_check_meta_task)
+S3method(results,rev_dep_check_meta_task)
+S3method(results,rev_dep_dep_meta_task)
+S3method(results_to_df,checked_results)
+S3method(results_to_df,default)
 S3method(run,character)
-S3method(run,check_design)
-S3method(start_task,check_task_spec)
-S3method(start_task,custom_install_task_spec)
-S3method(start_task,install_task_spec)
-S3method(summary,check_design)
-S3method(summary,checked_results)
-S3method(summary,checked_results_check_task_spec)
-S3method(summary,checked_results_revdep_check_task_spec)
-export(check_design)
-export(check_dev_rev_deps)
-export(check_dir)
+S3method(run,checker)
+S3method(start_task,check_task)
+S3method(start_task,igraph.vs)
+S3method(start_task,install_task)
+S3method(task_graph,task)
+S3method(task_graph,task_graph)
+export(STATUS)
 export(check_pkgs)
 export(check_rev_deps)
-export(check_task_spec)
-export(custom_install_task_spec)
-export(install_task_spec)
-export(new_check_design)
-export(new_rev_dep_check_design)
-export(package_spec)
-export(package_spec_archive_source)
-export(package_spec_source)
+export(check_task)
+export(checker)
+export(install_task)
+export(meta_task)
+export(new_checker)
+export(new_rev_dep_checker)
+export(pkg_origin)
+export(pkg_origin_archive)
+export(pkg_origin_base)
+export(pkg_origin_is_base)
+export(pkg_origin_local)
+export(pkg_origin_remote)
+export(pkg_origin_repo)
+export(pkg_origin_unknown)
+export(plan_local_checks)
+export(plan_rev_dep_checks)
 export(reporter_ansi_tty)
+export(reporter_ansi_tty2)
 export(reporter_basic_tty)
 export(reporter_default)
 export(results)
-export(results_to_file)
-export(rev_dep_check_tasks_df)
-export(revdep_check_task_spec)
+export(results_to_df)
 export(run)
-export(source_check_tasks_df)
-export(task_spec)
+export(task)
 import(cli)
 import(options)
 importFrom(R6,R6Class)
 importFrom(callr,r_process)
 importFrom(cli,make_spinner)
 importFrom(igraph,"E<-")
 importFrom(igraph,"V<-")
-importFrom(igraph,.env)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,incident_edges)
@@ -91,6 +169,8 @@ importFrom(igraph,subgraph.edges)
 importFrom(igraph,tail_of)
 importFrom(igraph,topo_sort)
 importFrom(igraph,vertex_attr)
+importFrom(memoise,memoise)
 importFrom(rcmdcheck,rcmdcheck_process)
+importFrom(rlang,hash)
 importFrom(utils,install.packages)
 importFrom(utils,packageName)

NEWS.md

@@ -1,35 +1,16 @@
-# checked (0.2.9)
+# checked 0.5.1
 
-* Add `igraph_subgraph_from_edges` wrapper to used work around deprecation
-  messages and alternate between `igraph::subgraph.edges` and 
-  `igraph::subgraph_from_edges` depending on the `igraph` version.
-  
-* Address CRAN results issues
-
-* In `install_packages_process` use `withCallingHandlers` instead
-  of the `tryCatch` to prevent accidental interruptions if `install.packages()`
-  triggers a benign warning.
+* Export STATUS vector to make external statuses analysis easier.
 
-# checked 0.2.8
+* Allow obtaining partial results for uncompleted checks.
 
-* Unify notes, warnings and errors are internally stored when generating
-  results (R4.5 compatibility)
-  
-# checked 0.2.7
-
-* Fix a bug where wrong lib.loc was used to derive whether a package has already
-  been satisfied.
-  
-# checked 0.2.6
+* Export `results_to_df()` and make it a generic.
 
-* Save minimal version required by each edge and use them to properly identify
-  whether dependecy is satisfied when calling `task_graph_update_done`
+# checked 0.5.0
 
-# checked 0.2.5
+* Entire package refactor
 
-* Refine reverse suggested dependecy strategy.
-
-# checked 0.2.4
+# checked 0.2.3
 
 * Fix check processes hanging forever in some system configurations.
 
@@ -46,16 +27,12 @@
 
 * Add tests for the reverse dependency check use case.
 
-* Make `install_packages_process` capture session's `available_packages_filters`
+* Make `install_process` capture session's `available_packages_filters`
   and reuse them when installing packages to ensure consistency with the main
   session filtering.
 
 * Prettify output by stripping excessive new lines.
 
-* `checked` now depends on `options`
-
-* Expose `...` allowing customization of check subprocesses when creating checks df.
-
 * Force garbage collection before scheduling task, to make sure any already
   finished processes are removed from the memory.
 
@@ -110,4 +87,4 @@
 
 # checked 0.1.0
 
-* Package released to CRAN
+* Package released to CRAN