R Under development (unstable) (2025-11-24 r89059 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # setting R_TESTS to empty string because of > # https://github.com/hadley/testthat/issues/144 > # and https://github.com/r-lib/testthat/issues/86 > # revert this when that issue in R is fixed. > Sys.setenv("R_TESTS" = "") > > library(testthat) > library(mockery) > library(risk.assessr) > library(withr) > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(jsonlite) > library(fs) > library(curl) Using libcurl 8.14.1 with Schannel > library(xml2) > > test_check("risk.assessr") An error occurred in checking suggested functions: no 'restart' 'muffleError' found Checking for author in mockpkg Checking for License in mockpkg Checking host package NO INTERNAL_RSPM FOUND Checking GitHub data for NA/mockpkg... Owner is NA or empty. Returning empty response. Using package's default risk definition. No testthat or testit configuration Checking for author in mockpkg Checking for License in mockpkg Checking host package NO INTERNAL_RSPM FOUND Checking GitHub data for NA/mockpkg... Owner is NA or empty. Returning empty response. Using package's default risk definition. Checking SomePkg on CRAN... Checking SomePkg on Bioconductor... unpacking fallback locally unpacked fallback locally Checking Biobase on CRAN... Checking Biobase on Bioconductor... unpacking fake locally unpacked fake locally Checking InternalPkg on CRAN... Checking InternalPkg on Bioconductor... No InternalPkg package found on Bioconductor Attempting internal fallback download for InternalPkg unpacking internal locally unpacked internal locally Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg NO INTERNAL_RSPM FOUND Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg NO INTERNAL_RSPM FOUND Failed to download the package from any source. Error: Failed to find the package URL from the internal repository.FALSE Checking ggplot2 on CRAN... unpacking cran locally unpacked cran locally Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg NO INTERNAL_RSPM FOUND Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg NO INTERNAL_RSPM FOUND Failed to download the package from any source. Error: Failed to find the package URL from the internal repository.FALSE Invalid 'which' value. Must be one or more of: Depends, Imports, LinkingTo, Suggests, Enhances or 'all'. No forbidden notes for mockpkg No forbidden notes for mockpkg unpacking test.package.0009 locally unpacked test.package.0009 locally installing test.package.0009 locally test.package.0009 installed locally Extracting exported function names for test.package.0009 Extracting exported function bodies for test.package.0009 unpacking test.package.0009 locally unpacked test.package.0009 locally installing test.package.0009 locally test.package.0009 is already installed Extracting exported function names for test.package.0009 Extracting exported function bodies for test.package.0009 unpacking test.package.0010 locally unpacked test.package.0010 locally installing test.package.0010 locally test.package.0010 installed locally Extracting exported function names for test.package.0010 Extracting exported function bodies for test.package.0010 unpacking test.package.0005 locally unpacked test.package.0005 locally installing test.package.0005 locally test.package.0005 installed locally Extracting exported function names for test.package.0005 No exported functions from source package test.package.0005 No exported functions from Suggested packages in the DESCRIPTION file unpacking test.package.0006 locally unpacked test.package.0006 locally installing test.package.0006 locally test.package.0006 installed locally No R folder found in the package source path No Suggested packages in the DESCRIPTION file No Imports or Suggested packages in the DESCRIPTION file /usr/bin/tar: Removing leading `D:' from member names /usr/bin/tar: D\:\temp\2025_11_25_11_25_17_18416\\RtmpyC2tyW/old_structure: Cannot stat: No such file or directory /usr/bin/tar: Exiting with failure status due to previous errors gzip: stdin: not in gzip format /usr/bin/tar: Child returned status 1 /usr/bin/tar: Error is not recoverable: exiting now traceability matrix for unsuccessful [1] "No sourceable R scripts were found in the R/ directory for package dummy_path. Make sure this was expected.\n" No top level assignments found in R folder for path The following exports were not found in R/ for path: function2 generic1 In package `path`, the R scripts (NA) are missing documentation for the following exports: function2 generic1 traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful high risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful medium risk coverage traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful defunct functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful imported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful rexported functions traceability matrix for testpkg not generated traceability matrix for testpkg unsuccessful experimental functions traceability matrix for testpkg not generated creating traceability matrix for mockpkg creating traceability matrices for mockpkg without test coverage creating traceability matrix for mockPkg the execute_coverage parameter = TRUE but the 'function_coverage' object for mockPkg is NULL or non compliant creating traceability matrices for mockPkg with test coverage traceability matrices for mockPkg successful creating traceability matrix for mockPkg the execute_coverage parameter = TRUE but the 'function_coverage' object for mockPkg is NULL or non compliant creating traceability matrices for mockPkg with test coverage traceability matrices for mockPkg successful Error: Dependency tree in progress for pkgA package Dependency tree in progress for pkgB package Dependency tree in progress for pkgD package Finished building for pkgD Finished building for pkgB Dependency tree in progress for pkgC package Finished building for pkgC Finished building for pkgA Finished building for testpkg Dependency tree in progress for testpkg package Dependency tree in progress for pkgA package Dependency tree in progress for pkgB package Dependency tree in progress for pkgD package Finished building for pkgD Finished building for pkgB Dependency tree in progress for pkgC package Finished building for pkgC Finished building for pkgA Dependency tree in progress for pkgC package Finished building for pkgC Dependency tree in progress for pkgE package Dependency tree in progress for pkgF package Dependency tree in progress for pkgG package Finished building for pkgG Finished building for pkgF Finished building for pkgE Dependency tree in progress for unknownPkg package Finished building for unknownPkg Dependency tree in progress for basePkg package Finished building for basePkg Building dependency tree for: ggplot2 unpacking stringr locally unpacked stringr locally Some exported functions are missing help files in stringr stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has vignettes stringr has examples stringr has news stringr has current news Checking for author in test Checking for author in test Checking for author in mockpkg Checking for author in test Checking for author in test unpacking here locally unpacked here locally Checking for License in here unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally Checking for License in test.package.0001 unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally Checking for License in test.package.0007 unpacking stringr locally unpacked stringr locally stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has bug reports URL stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have bug reports URL test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control mockpkg has bug reports URL mockpkg has a website mockpkg has a website mockpkg does not have a source control Checking for author in limma Checking for author in limma unpacking stringr locally unpacked stringr locally stringr has a maintainer stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has bug reports URL stringr has a website stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a maintainer stringr has a website stringr has a website stringr has a source control unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have bug reports URL test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a website test.package.0007 does not have a source control Checking for author in limma Checking for author in limma unpacking here locally unpacked here locally unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally unpacking here locally unpacked here locally here has examples unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0001 has no examples unpacking here locally unpacked here locally All exported functions have corresponding help files in here unpacking stringr locally unpacked stringr locally Some exported functions are missing help files in stringr unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally installing test.package.0006 locally test.package.0006 is already installed No exported functions in test.package.0006 unpacking here locally unpacked here locally here has news unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0001 has no news path test.package.0001 has no current news test.package.0001 has no news path test.package.0001 has no current news unpacking here locally unpacked here locally here has vignettes unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally test.package.0001 has no vignettes unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally unpacking stringr locally unpacked stringr locally Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Checking stringr on CRAN... Checking SomePkg on CRAN... CRAN download failed: CRAN download failed due to timeout Checking SomePkg on Bioconductor... Checking Biobase on CRAN... Checking Biobase on Bioconductor... Checking InternalPkg on CRAN... Checking InternalPkg on Bioconductor... No InternalPkg package found on Bioconductor Attempting internal fallback download for InternalPkg Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg Checking GhostPkg on CRAN... Checking GhostPkg on Bioconductor... No GhostPkg package found on Bioconductor Attempting internal fallback download for GhostPkg Failed to download the package from any source. Error: couldn't find package 'GhostPkg'FALSE Checking ggplot2 on CRAN... Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg Checking nonexistentpkg on CRAN... Checking nonexistentpkg on Bioconductor... No nonexistentpkg package found on Bioconductor Attempting internal fallback download for nonexistentpkg Failed to download the package from any source. Error: all fallback failedFALSE Checking mockpkg on CRAN... Checking mockpkg on CRAN... No testthat or testit configuration Checking mockpkg on CRAN... url_page: https://bioconductor.org/packages/3.20/bioc/html/limma.html url_page: https://bioconductor.org/packages/3.20/bioc/html/noarchive.html Failed to fetch page: https://bioconductor.org/packages/3.20/bioc/html/noarchive.html url_page: https://bioconductor.org/packages/3.20/bioc/html/archiveonly.html url_page: https://bioconductor.org/packages/3.20/bioc/html/doesnotexist.html Checking Bioconductor version: 3.17 Checking package version: 1.38.0 Date: 2005-10-14 Checking Bioconductor version: 3.18 Checking package version: 1.38.0 Date: 2006-10-04 Checking Bioconductor version: 3.19 Checking package version: 1.38.0 Date: 2007-10-08 Checking Bioconductor version: 3.17 Checking package version: 3.40.2 Date: 2005-10-14 Checking Bioconductor version: 3.18 Checking package version: 3.40.2 Date: 2006-10-04 Checking Bioconductor version: 3.19 Checking package version: 3.40.2 Date: 2007-10-08 Checking Bioconductor version: 3.17 Checking Bioconductor version: 3.18 Checking Bioconductor version: 3.19 Package URL not found on Bioconductor Checking Bioconductor version: 3.17 Skipping Bioconductor version 3.17 due to error: Simulated error Checking Bioconductor version: 3.18 Skipping Bioconductor version 3.18 due to error: Simulated error Checking Bioconductor version: 3.19 Skipping Bioconductor version 3.19 due to error: Simulated error Package URL not found on Bioconductor No download data found or invalid format for: ggplot2 Could not fetch CRAN download data for package: ggplot2 No download data found or invalid format for: ggplot2 Could not fetch CRAN download data for package: nonexistent8package No download data found or invalid format for: nonexistent8package could not fetch download data for package: FakePackage123 No download data found for package: FakePackage123 No download data found for package: FakePackage123 could not fetch download data for package: FakePackage123 No download data found for package: EmptyDataPkg No R folder found in the package source path for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Extracting exported function names for testpkg Checking GitHub data for tidyverse/ggplot2... Checking GitHub data for /ggplot2... Owner is NA or empty. Returning empty response. Checking GitHub data for tidyverse/non_existent_repo... Failed to fetch repository details: Mocked API call failure Checking GitHub data for tidyverse/ggplot2... Failed to fetch commits: Mocked commits API failure Checking GitHub data for tidyverse/non_existent_repo... Failed to fetch repository details: Mocked API call failure Repository not found: Not Found NO INTERNAL_RSPM FOUND NO INTERNAL_RSPM FOUND NO INTERNAL_RSPM FOUND Checking host package Checking host package Checking host package Checking host package Checking host package No articles found on pubmed for ggplot2 No articles found on pubmed for ggplot2 No articles found on pubmed for ggplot2 Using custom risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using custom risk definition. Using package's default risk definition. Using package's default risk definition. Using package's default risk definition. unpacking test.package.0001 locally unpacked test.package.0001 locally installing test.package.0001 locally test.package.0001 installed locally installing invalidPackage locally installing mock_package locally mock_package installed locally mock_package installed locally installing non_existent_directory locally No such file or directory: non_existent_directory installing mock_package locally mock_package is already installed /usr/bin/tar: Removing leading `D:\' from member names Starting lock file processing Starting lock file processing Finishing lock file processing Starting lock file processing Finishing lock file processing running code coverage for filed8e066af6a12 code coverage for filed8e066af6a12 unsuccessful R coverage for filed8e066af6a12 failed. Read in the covr output to see what went wrong: unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking D:\temp\2025 locally unpacked D:\temp\2025 locally checking package test config checking package test config checking package test config checking package test config checking package test config checking package test config checking package test config unpacking here locally unpacked here locally unpacking empty.tar.gz locally not able to unpack empty.tar.gz locally unpacking here locally unpacked here locally [ FAIL 0 | WARN 0 | SKIP 42 | PASS 1159 ] ══ Skipped tests (42) ══════════════════════════════════════════════════════════ • On CRAN (41): 'test-assess_pkg.R:2:3', 'test-assess_pkg.R:216:3', 'test-assess_pkg.R:372:3', 'test-assess_pkg.R:451:3', 'test-assess_pkg.R:546:3', 'test-assess_pkg.R:731:3', 'test-assess_pkg.R:808:3', 'test-badges.R:44:3', 'test-check_suggested_exp_funcs.R:3:3', 'test-check_suggested_exp_funcs.R:185:3', 'test-cran_packages.R:3:3', 'test-cran_packages.R:12:3', 'test-create_traceability_matrix.R:2:3', 'test-create_traceability_matrix.R:65:3', 'test-create_traceability_matrix.R:138:3', 'test-create_traceability_matrix.R:207:3', 'test-dependency_tree.R:462:1', 'test-dependency_tree.R:466:1', 'test-dependency_tree.R:530:1', 'test-dependency_tree.R:534:1', 'test-get_exports.R:2:3', 'test-get_exports.R:41:3', 'test-get_exports.R:119:3', 'test-get_exports.R:190:3', 'test-get_exports.R:232:3', 'test-get_exports.R:272:3', 'test-parse_dcf_dependencies.R:2:3', 'test-parse_dcf_dependencies.R:43:3', 'test-reverse_dependencies.R:2:3', 'test-risk_assess_pkg.R:10:3', 'test-risk_assess_pkg.R:130:3', 'test-risk_assess_pkg.R:154:3', 'test-run_coverage.R:2:3', 'test-run_coverage.R:49:3', 'test-run_coverage.R:93:3', 'test-run_coverage.R:137:3', 'test-run_coverage.R:182:3', 'test-run_rcmdcheck.R:2:3', 'test-run_rcmdcheck.R:61:3', 'test-run_rcmdcheck.R:136:3', 'test-run_rcmdcheck.R:206:3' • Skipping test because CRAN is available (1): 'test-parse_dcf_dependencies.R:126:3' [ FAIL 0 | WARN 0 | SKIP 42 | PASS 1159 ] > > proc.time() user system elapsed 21.48 4.48 61.32