CRAN Package Check Results for Package risk.assessr

Last updated on 2025-12-02 17:50:06 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	3.0.0	8.92	350.16	359.08	ERROR
r-devel-linux-x86_64-debian-gcc	3.0.0	6.77	247.73	254.50	ERROR
r-devel-linux-x86_64-fedora-clang	3.0.1	24.00	533.25	557.25	OK
r-devel-linux-x86_64-fedora-gcc	3.0.1	20.00	344.55	364.55	NOTE
r-devel-windows-x86_64	3.0.1	13.00	149.00	162.00	OK
r-patched-linux-x86_64	2.0.1	7.77	92.13	99.90	OK
r-release-linux-x86_64	3.0.0	9.55	330.93	340.48	ERROR
r-release-macos-arm64	3.0.1	2.00	330.00	332.00	OK
r-release-macos-x86_64	3.0.1	9.00	561.00	570.00	OK
r-release-windows-x86_64	2.0.1	10.00	146.00	156.00	OK
r-oldrel-macos-arm64	3.0.1	2.00	240.00	242.00	OK
r-oldrel-macos-x86_64	3.0.1	9.00	571.00	580.00	OK
r-oldrel-windows-x86_64	3.0.0	19.00	500.00	519.00	ERROR

Check Details

Version: 3.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [56s/92s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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 8.17.0 with GnuTLS/3.8.10 > 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 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 file382522da8d835.tar.gz locally unpacked file382522da8d835.tar.gz locally Checking for License in test.package.0001 unpacking file38252225b403ae.tar.gz locally unpacked file38252225b403ae.tar.gz 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 file3825224eeb6cd5.tar.gz locally unpacked file3825224eeb6cd5.tar.gz 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 file3825225a9ba128.tar.gz locally unpacked file3825225a9ba128.tar.gz 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 file3825226280d218.tar.gz locally unpacked file3825226280d218.tar.gz locally unpacking here locally unpacked here locally here has examples unpacking file3825221c912fc7.tar.gz locally unpacked file3825221c912fc7.tar.gz 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 file3825221845c7ce.tar.gz locally unpacked file3825221845c7ce.tar.gz 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 file3825227c3cbeef.tar.gz locally unpacked file3825227c3cbeef.tar.gz locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking file3825224dea9479.tar.gz locally unpacked file3825224dea9479.tar.gz 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 file38252258161138.tar.gz locally unpacked file38252258161138.tar.gz locally test.package.0001 has no vignettes unpacking file382522453799be.tar.gz locally unpacked file382522453799be.tar.gz locally unpacking stringr locally unpacked stringr locally Using package's default risk definition. Using package's default risk definition. Rendering report for test.package.0001 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 `/' 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 file3825227f76b09 code coverage for file3825227f76b09 unsuccessful R coverage for file3825227f76b09 failed. Read in the covr output to see what went wrong: unpacking file3825221aa8bb12.tar.gz locally unpacked file3825221aa8bb12.tar.gz locally unpacking file3825227f2d323.tar.gz locally unpacked file3825227f2d323.tar.gz locally unpacking file38252274f984f8.tar.gz locally unpacked file38252274f984f8.tar.gz locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking file3825224f90dd3f.tar.gz locally unpacked file3825224f90dd3f.tar.gz 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 1 | WARN 1 | SKIP 42 | PASS 1153 ] ══ 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generate_html_report.R:471:3'): generate_html_report creates an HTML report ── Error in `file(con, "w")`: cannot open the connection Backtrace: ▆ 1. └─risk.assessr::generate_html_report(toy_assessment_results, tmp_dir) at test-generate_html_report.R:471:3 2. └─rmarkdown::render(...) 3. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 4. └─xfun::write_utf8(res, output) 5. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE) 6. └─base::file(con, "w") [ FAIL 1 | WARN 1 | SKIP 42 | PASS 1153 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 3.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [41s/66s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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 8.17.0 with OpenSSL/3.5.4 > 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 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 file27166395f8665.tar.gz locally unpacked file27166395f8665.tar.gz locally Checking for License in test.package.0001 unpacking file27166360aaa9e3.tar.gz locally unpacked file27166360aaa9e3.tar.gz 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 file2716634ccf0ff0.tar.gz locally unpacked file2716634ccf0ff0.tar.gz 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 file2716633bacc951.tar.gz locally unpacked file2716633bacc951.tar.gz 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 file27166349a36559.tar.gz locally unpacked file27166349a36559.tar.gz locally unpacking here locally unpacked here locally here has examples unpacking file2716633325e99a.tar.gz locally unpacked file2716633325e99a.tar.gz 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 file27166337c19a1f.tar.gz locally unpacked file27166337c19a1f.tar.gz 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 file2716635fac48b3.tar.gz locally unpacked file2716635fac48b3.tar.gz locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking file27166341e0b061.tar.gz locally unpacked file27166341e0b061.tar.gz 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 file2716638053977.tar.gz locally unpacked file2716638053977.tar.gz locally test.package.0001 has no vignettes unpacking file271663601a4d18.tar.gz locally unpacked file271663601a4d18.tar.gz locally unpacking stringr locally unpacked stringr locally Using package's default risk definition. Using package's default risk definition. Rendering report for test.package.0001 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 `/' 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 file2716633475d31d code coverage for file2716633475d31d unsuccessful R coverage for file2716633475d31d failed. Read in the covr output to see what went wrong: unpacking file271663514ebcc7.tar.gz locally unpacked file271663514ebcc7.tar.gz locally unpacking file27166333878ead.tar.gz locally unpacked file27166333878ead.tar.gz locally unpacking file27166351a3e458.tar.gz locally unpacked file27166351a3e458.tar.gz locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking file271663780fffb8.tar.gz locally unpacked file271663780fffb8.tar.gz 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 1 | WARN 1 | SKIP 42 | PASS 1153 ] ══ 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generate_html_report.R:471:3'): generate_html_report creates an HTML report ── Error in `file(con, "w")`: cannot open the connection Backtrace: ▆ 1. └─risk.assessr::generate_html_report(toy_assessment_results, tmp_dir) at test-generate_html_report.R:471:3 2. └─rmarkdown::render(...) 3. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 4. └─xfun::write_utf8(res, output) 5. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE) 6. └─base::file(con, "w") [ FAIL 1 | WARN 1 | SKIP 42 | PASS 1153 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 3.0.1
Check: for non-standard things in the check directory
Result: NOTE Found the following files/directories: ‘test.package.0001’ ‘test.package.0005’ ‘test.package.0006’ ‘test.package.0009’ ‘test.package.0010’ Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 3.0.0
Check: tests
Result: ERROR Running ‘testthat.R’ [54s/88s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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 8.17.0 with GnuTLS/3.8.10 > 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 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 file18a0c72b76ea26.tar.gz locally unpacked file18a0c72b76ea26.tar.gz locally Checking for License in test.package.0001 unpacking file18a0c730c1f697.tar.gz locally unpacked file18a0c730c1f697.tar.gz 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 file18a0c71f99744a.tar.gz locally unpacked file18a0c71f99744a.tar.gz 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 file18a0c79746a78.tar.gz locally unpacked file18a0c79746a78.tar.gz 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 file18a0c732950d7c.tar.gz locally unpacked file18a0c732950d7c.tar.gz locally unpacking here locally unpacked here locally here has examples unpacking file18a0c73a1b61d1.tar.gz locally unpacked file18a0c73a1b61d1.tar.gz 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 file18a0c71ffe129b.tar.gz locally unpacked file18a0c71ffe129b.tar.gz 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 file18a0c76d301f40.tar.gz locally unpacked file18a0c76d301f40.tar.gz locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking file18a0c73d0fec50.tar.gz locally unpacked file18a0c73d0fec50.tar.gz 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 file18a0c74c29c38f.tar.gz locally unpacked file18a0c74c29c38f.tar.gz locally test.package.0001 has no vignettes unpacking file18a0c776e37f9.tar.gz locally unpacked file18a0c776e37f9.tar.gz locally unpacking stringr locally unpacked stringr locally Using package's default risk definition. Using package's default risk definition. Rendering report for test.package.0001 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 `/' 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 file18a0c77b2318f5 code coverage for file18a0c77b2318f5 unsuccessful R coverage for file18a0c77b2318f5 failed. Read in the covr output to see what went wrong: unpacking file18a0c75a45fd53.tar.gz locally unpacked file18a0c75a45fd53.tar.gz locally unpacking file18a0c7417ee574.tar.gz locally unpacked file18a0c7417ee574.tar.gz locally unpacking file18a0c76425cb40.tar.gz locally unpacked file18a0c76425cb40.tar.gz locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking file18a0c74c76a526.tar.gz locally unpacked file18a0c74c76a526.tar.gz 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 1 | WARN 1 | SKIP 42 | PASS 1153 ] ══ 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generate_html_report.R:471:3'): generate_html_report creates an HTML report ── Error in `file(con, "w")`: cannot open the connection Backtrace: ▆ 1. └─risk.assessr::generate_html_report(toy_assessment_results, tmp_dir) at test-generate_html_report.R:471:3 2. └─rmarkdown::render(...) 3. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 4. └─xfun::write_utf8(res, output) 5. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE) 6. └─base::file(con, "w") [ FAIL 1 | WARN 1 | SKIP 42 | PASS 1153 ] Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64

Version: 3.0.0
Check: tests
Result: ERROR Running 'testthat.R' [104s] Running the tests in 'tests/testthat.R' failed. Complete output: > # 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_12_01_18_19_37_23003\\RtmpOE7bsC/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. Rendering report for test.package.0001 File not found in resource path 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 file3bf071524491 code coverage for file3bf071524491 unsuccessful R coverage for file3bf071524491 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 1 | WARN 0 | SKIP 42 | PASS 1153 ] ══ 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generate_html_report.R:471:3'): generate_html_report creates an HTML report ── Error: pandoc document conversion failed with error 99 Backtrace: ▆ 1. └─risk.assessr::generate_html_report(toy_assessment_results, tmp_dir) at test-generate_html_report.R:471:3 2. └─rmarkdown::render(...) 3. └─rmarkdown (local) convert(output_file, run_citeproc) 4. └─rmarkdown (local) convert_it(pandoc_output_tmp) 5. └─rmarkdown (local) convert_fun(...) 6. └─rmarkdown:::stop2(...) [ FAIL 1 | WARN 0 | SKIP 42 | PASS 1153 ] Error: ! Test failures. Execution halted Flavor: r-oldrel-windows-x86_64

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