* using log directory ‘/srv/hornik/tmp/CRAN_pretest/risk.assessr.Rcheck’ * using R Under development (unstable) (2025-06-02 r88257) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘risk.assessr/DESCRIPTION’ ... OK * this is package ‘risk.assessr’ version ‘2.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Edward Gillian ’ New submission * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘risk.assessr’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s/5s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [21s/26s] ERROR Running ‘testthat.R’ [21s/26s] 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 object is masked from 'package:testthat': matches 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) > > test_check("risk.assessr") unpacking stringr locally unpacked stringr locally stringr has a license Checking for creator in stringr stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a license Checking for creator in stringr stringr has a maintainer stringr has a website stringr has bug reports URL Checking for creator in stringr stringr has a maintainer stringr has a website stringr has a source control stringr has bug reports URL stringr has a license Checking for creator in stringr stringr has a website stringr has a source control stringr has bug reports URL stringr has a license Checking for creator in stringr stringr has a maintainer stringr has a source control stringr has bug reports URL stringr has a license Checking for creator in stringr stringr has a maintainer stringr has a website stringr has a source control unpacking test.package.0007 locally unpacked test.package.0007 locally test.package.0007 does not have a license Checking for creator in test.package.0007 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 does not have a license Checking for creator in test.package.0007 test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have bug reports URL Checking for creator in test.package.0007 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 does not have a license Checking for creator in test.package.0007 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 does not have a license Checking for creator in test.package.0007 test.package.0007 has a maintainer test.package.0007 does not have a source control test.package.0007 does not have bug reports URL test.package.0007 does not have a license Checking for creator in test.package.0007 test.package.0007 has a maintainer test.package.0007 does not have a website test.package.0007 does not have a source control testpkg has a maintainer testpkg has a maintainer testpkg has a maintainer testpkg has a maintainer testpkg does not have a maintainer testpkg does not have a maintainer Checking for author in limma Checking for author in limma unpacking here locally unpacked here locally here has examples unpacking test.package.0001 locally unpacked test.package.0001 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 test.package.0006 locally unpacked test.package.0006 locally installing test.package.0006 locally test.package.0006 installed locally No exported functions in test.package.0006 unpacking here locally unpacked here locally unpacking test.package.0006 locally unpacked test.package.0006 locally unpacking here locally unpacked here locally here has news unpacking test.package.0001 locally unpacked test.package.0001 locally test.package.0001 has no news unpacking here locally unpacked here locally here has current news unpacking test.package.0001 locally unpacked test.package.0001 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 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 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 unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking stringr locally unpacked stringr locally unpacking here locally unpacked here locally here has vignettes unpacking test.package.0001 locally unpacked test.package.0001 locally test.package.0001 has no vignettes unpacking test.package.0009 locally unpacked test.package.0009 locally installing test.package.0009 locally test.package.0009 installed locally Loading required package: test.package.0009 unpacking test.package.0009 locally unpacked test.package.0009 locally installing test.package.0009 locally test.package.0009 is already installed unpacking test.package.0010 locally unpacked test.package.0010 locally installing test.package.0010 locally test.package.0010 installed locally Loading required package: test.package.0010 unpacking test.package.0005 locally unpacked test.package.0005 locally installing test.package.0005 locally test.package.0005 installed locally Loading required package: test.package.0005 No exported functions from source package test.package.0005 unpacking test.package.0006 locally unpacked test.package.0006 locally installing test.package.0006 locally test.package.0006 is already installed 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 unpacking stringr locally unpacked stringr locally Some exported functions are missing help files in stringr stringr has bug reports URL stringr has a license Checking for creator in stringr stringr has a maintainer stringr has a website stringr has a source control stringr has vignettes stringr has examples stringr has news stringr has current news Failed to fetch page: https://bioconductor.org/packages/3.20/bioc/html/noarchive.html Checking Bioconductor version: 3.17 Checking package version: 1.38.0 Checking Bioconductor version: 3.18 Checking package version: 1.38.0 Checking Bioconductor version: 3.19 Checking package version: 1.38.0 Checking Bioconductor version: 3.16 Checking package version: 3.40.2 Checking Bioconductor version: 3.17 Checking package version: 3.40.2 Checking Bioconductor version: 3.18 Checking package version: 3.40.2 Checking Bioconductor version: 3.17 Checking Bioconductor version: 3.18 Checking Bioconductor version: 3.19 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 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 [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.class1 In package `path`, the R scripts (NA) are missing documentation for the following exports: function2 generic1.class1 Checking github data Checking github data Owner is NA or empty. Returning empty response object. Checking github data Failed to fetch repository details: Mocked API call failure Checking github data Failed to fetch commits: Mocked commits API failure Checking github data Failed to fetch repository details: Simulated API failure Failed to parse JSON response:parse error: premature EOF (right here) ------^ Failed to parse JSON response:lexical error: invalid char in json text. Invalid JSON (right here) ------^ Checking host package Checking host package Checking host package Checking host package Checking host package unpacking here locally unpacked here locally unpacking here locally unpacked here locally Checking for License in here unpacking test.package.0001 locally unpacked test.package.0001 locally Checking for License in test.package.0001 unpacking test.package.0007 locally unpacked test.package.0007 locally Checking for License in test.package.0007 [1] "No sourceable R scripts were found in the R/ directory for package dummy_path. Make sure this was expected.\n" 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 unpacking here locally unpacked here locally Checking for author in test $maintainer [1] "Kirill Müller [aut, cre] (ORCID: )" $funder [1] "No package foundation found" $authors [1] "Kirill Müller [aut, cre] (ORCID: )" [2] "Jennifer Bryan [ctb] (ORCID: )" unpacking stringr locally unpacked stringr locally Checking for author in test User defined weights used User defined weights used Risk profile calculated Risk profile calculated Starting lock file processing Starting lock file processing Finishing lock file processing Starting lock file processing Finishing lock file processing running code coverage for file5f31a29531679 code coverage for file5f31a29531679 unsuccessful R coverage for file5f31a29531679 failed. Read in the covr output to see what went wrong: unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking test.package.0001 locally unpacked test.package.0001 locally unpacking here locally unpacked here locally unpacking empty.tar.gz locally not able to unpack empty.tar.gz locally Default weights used User defined weights used Risk profile calculated Risk profile calculated Risk profile calculated [ FAIL 1 | WARN 0 | SKIP 27 | PASS 610 ] ══ Skipped tests (27) ══════════════════════════════════════════════════════════ • On CRAN (27): 'test-assess_pkg.R:2:3', 'test-assess_pkg.R:132:3', 'test-assess_pkg.R:264:3', 'test-assess_pkg.R:316:3', 'test-assess_pkg.R:374:3', 'test-calc_dependencies.R:2:3', 'test-calc_reverse_dependencies.R:2:3', 'test-check_suggested_exp_funcs.R:3:3', 'test-check_suggested_exp_funcs.R:38:3', 'test-create_traceability_matrix.R:2:3', 'test-create_traceability_matrix.R:60:3', 'test-create_traceability_matrix.R:121:3', 'test-create_traceability_matrix.R:181:3', 'test-parse_dcf_dependencies.R:2:3', 'test-parse_dcf_dependencies.R:38:3', 'test-risk_assess_pkg.R:10:3', 'test-risk_assess_pkg.R:119:3', 'test-risk_assess_pkg.R:143:3', 'test-run_coverage.R:2:3', 'test-run_coverage.R:36:3', 'test-run_coverage.R:68:3', 'test-run_coverage.R:100:3', 'test-run_coverage.R:133:3', 'test-run_rcmdcheck.R:2:3', 'test-run_rcmdcheck.R:39:3', 'test-run_rcmdcheck.R:83:3', 'test-run_rcmdcheck.R:121:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_bioconductor_data.R:190:3'): fetch_bioconductor_package_info returns only main version when no archive exists ── `result` has length 1, not length 2. [ FAIL 1 | WARN 0 | SKIP 27 | PASS 610 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE