Last updated on 2026-06-05 18:49:41 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1.1 | 9.92 | 235.57 | 245.49 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 3.1.1 | 8.14 | 159.57 | 167.71 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 3.1.1 | 21.00 | 363.48 | 384.48 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 3.1.1 | 20.00 | 476.32 | 496.32 | ERROR | |
| r-devel-windows-x86_64 | 3.1.1 | 18.00 | 401.00 | 419.00 | OK | |
| r-patched-linux-x86_64 | 3.1.1 | 13.14 | 222.72 | 235.86 | OK | |
| r-release-linux-x86_64 | 3.1.1 | 10.72 | 223.32 | 234.04 | OK | |
| r-release-macos-arm64 | 3.1.1 | 3.00 | 399.00 | 402.00 | OK | |
| r-release-macos-x86_64 | 3.1.1 | 8.00 | 955.00 | 963.00 | OK | |
| r-release-windows-x86_64 | 3.1.1 | 16.00 | 404.00 | 420.00 | OK | |
| r-oldrel-macos-arm64 | 3.1.1 | 3.00 | 350.00 | 353.00 | OK | |
| r-oldrel-macos-x86_64 | 3.1.1 | 8.00 | 637.00 | 645.00 | OK | |
| r-oldrel-windows-x86_64 | 3.1.1 | 22.00 | 2051.00 | 2073.00 | OK |
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [73s/125s]
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 8.20.0 with GnuTLS/3.8.13
> library(xml2)
>
> test_check("risk.assessr")
checking package test config
An error occurred in checking suggested functions: Simulated error in inner handler
Checking for author 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 package test config
No recognised standard or non-standard testing configuration
Checking for author 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.
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 file335eb96dbd1e8b.tar.gz locally
unpacked file335eb96dbd1e8b.tar.gz 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 file335eb97efb3cf0.tar.gz locally
unpacked file335eb97efb3cf0.tar.gz 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 file335eb970d36a1a.tar.gz locally
unpacked file335eb970d36a1a.tar.gz 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 file335eb94bde3134.tar.gz locally
unpacked file335eb94bde3134.tar.gz 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 file335eb960157f6.tar.gz locally
unpacked file335eb960157f6.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-check_suggested_exp_funcs-367.R
No Suggested packages in the DESCRIPTION file
No Imports or Suggested packages in the DESCRIPTION file
No exported functions from source package mockpkg
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
Failed to download or parse testpkg - DESCRIPTION file not found for testpkg
Failed to download or parse testpkg -
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
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgD package
Finished building for pkgB
Dependency tree in progress for pkgC package
Finished building for pkgC
Finished building for pkgA
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgC package
Finished building for pkgA
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
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Finished building for pkgB
Finished building for pkgA
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg
├── dep1
└── dep2 (base)
Dependency tree in progress for testpkg package
Finished building for testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for 123 package
Dependency tree in progress for pkg1pkg2 package
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgA package
Finished building for pkgB
Finished building for pkgA
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 source control
stringr has vignettes
stringr: 92.00% of exported functions have examples
stringr: 94.00% of exported functions have documentation
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
unpacking file335eb97ecf68e8.tar.gz locally
unpacked file335eb97ecf68e8.tar.gz locally
unpacking file335eb957cdaf5d.tar.gz locally
unpacked file335eb957cdaf5d.tar.gz locally
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg has a source control
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg source control detected via BugReports URL
testpkg has a source control
unpacking stringr locally
unpacked stringr locally
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 bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file335eb9616d77ce.tar.gz locally
unpacked file335eb9616d77ce.tar.gz locally
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 bug reports URL
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 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
mockpkg has bug reports URL
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 source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file335eb95ecc5178.tar.gz locally
unpacked file335eb95ecc5178.tar.gz locally
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 bug reports URL
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 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
Checking for author in limma
Checking for author in limma
unpacking here locally
unpacked here locally
unpacking file335eb9ab57f2.tar.gz locally
unpacked file335eb9ab57f2.tar.gz locally
unpacking here locally
unpacked here locally
here: 75.00% of exported functions have examples
mockpkg: 0.00% of exported functions have examples
unpacking file335eb9b2754ee.tar.gz locally
unpacked file335eb9b2754ee.tar.gz locally
test.package.0001: 0.00% of exported functions have examples
unpacking file335eb9783e6570.tar.gz locally
unpacked file335eb9783e6570.tar.gz locally
test.package.0005: no exported functions found; example score = 0.00%
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 file335eb96e2fe7e1.tar.gz locally
unpacked file335eb96e2fe7e1.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-documentation_metrics-1671.R
unpacking here locally
unpacked here locally
here has news
unpacking file335eb96ebdfabb.tar.gz locally
unpacked file335eb96ebdfabb.tar.gz locally
test.package.0001 has no news
unpacking here locally
unpacked here locally
here has current news
unpacking file335eb9a2b3d1a.tar.gz locally
unpacked file335eb9a2b3d1a.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 file335eb91d150b59.tar.gz locally
unpacked file335eb91d150b59.tar.gz locally
test.package.0001 has no vignettes
unpacking file335eb967667e10.tar.gz locally
unpacked file335eb967667e10.tar.gz locally
unpacking stringr locally
unpacked stringr locally
Using package's default risk definition.
Checking stringr in configured repositories...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb96683ed1f
No testthat or testit configuration
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
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
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb92943284c.tar.gz
Checking VersionedPkg in configured repositories...
Download from configured repos failed: couldn't find package 'VersionedPkg'
Checking VersionedPkg on CRAN...
Checking VersionedPkg on Bioconductor...
No VersionedPkg package found on Bioconductor
Attempting internal fallback download for VersionedPkg
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb935aabf6b.tar.gz
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Checking test.package.0001 on Bioconductor...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb9794f9cf6.tar.gz
Checking BiocPkg in configured repositories...
Download from configured repos failed: couldn't find package 'BiocPkg'
Checking BiocPkg on CRAN...
Checking BiocPkg on Bioconductor...
Attempting internal fallback download for BiocPkg
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb9462a0acc.tar.gz
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.
tools::Rd_db() failed for 'pkgB': there is no package called 'pkgB'
unpacking file335eb94c75c888.tar.gz locally
unpacked file335eb94c75c888.tar.gz locally
installing test.package.0001 locally
test.package.0001 is already installed
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
getting package dependencies for testpkg
package dependencies successful for testpkg
package
1 bar
getting package dependencies for pkgname
package dependencies successful for pkgname
Starting lock file processing
Starting lock file processing
Finishing lock file processing
Starting lock file processing
Finishing lock file processing
running code coverage for test.pkg
running code coverage for empty.pkg
code coverage for empty.pkg successful
running code coverage for failing.pkg
R coverage for failing.pkg failed. Read in the covr output to see what went wrong:
running code coverage for weird.pkg
code coverage for weird.pkg unsuccessful
R coverage for weird.pkg failed. Read in the covr output to see what went wrong:
running standard testing framework
running skip testing with non-standard testing framework
Package fakepkg is not installed.
Project root not found.
running standard testing framework
running standard testing framework
running skip testing with standard testing framework
running non-standard testing framework
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
No recognised standard or non-standard testing configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
Total Coverage for mockpkg is: 80 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: 100 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
No test coverrage for this configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: NA %
performing source test mapping for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
No test coverrage for this configuration
Creating Default test reporter for RtmpPQY4jo
Mapping package test structure for RtmpPQY4jo
Creating test results for no skipped tests for RtmpPQY4jo
Error running coverage for mockpkg: Simulated error
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
Creating package coverage for mockpkg
Creating package coverage for mockpkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
rcmdcheck for test.pkg failed. Read in the rcmdcheck output to see what went wrong:
unpacking file335eb94715e1fb.tar.gz locally
unpacked file335eb94715e1fb.tar.gz locally
unpacking file335eb99e27b82.tar.gz locally
unpacked file335eb99e27b82.tar.gz locally
unpacking test.package.0001 locally
unpacked test.package.0001 locally
unpacking file335eb93a0f81df.tar.gz locally
unpacked file335eb93a0f81df.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
Output created: /home/hornik/tmp/scratch/RtmpPQY4jo/summary_report_mockpkg_0.1.0.html
Report will be written to: /home/hornik/tmp/scratch/RtmpPQY4jo/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp
Output created: /tmp/my-report.html
No output directory specified. Setting output to /tmp/render_root
Output created: /tmp/render_root/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp/render_root_md
Output created: /tmp/render_root_md/summary_report_mockpkg_0.1.0.md
Report will be written to: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb9421eba71/summary_report_pkgA_0.1.0.html
Output created: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb9421eba71/summary_report_pkgA_0.1.0.html
Report will be written to: x/out/summary_report_pkgB_0.2.0.md
Output created: x/out/summary_report_pkgB_0.2.0.md
No output directory specified. Setting output to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/risk.assessr.Rcheck/tests/testthat
Output created: reports/summary_report_pkgC_0.3.0.html
Output created: base/out/report.html
Output created: base/report.md
Output created: base/something.html
Checking SomePkg in configured repositories...
Download from configured repos failed: couldn't find package 'SomePkg'
Checking SomePkg on CRAN...
CRAN download failed: CRAN download failed due to timeout
Checking SomePkg on Bioconductor...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb95bc8db39.tar.gz
Checking Biobase in configured repositories...
Download from configured repos failed: couldn't find package 'Biobase'
Checking Biobase on CRAN...
Checking Biobase on Bioconductor...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb91cea433e.tar.gz
Checking InternalPkg in configured repositories...
Download from configured repos failed: couldn't find package 'InternalPkg'
Checking InternalPkg on CRAN...
Checking InternalPkg on Bioconductor...
No InternalPkg package found on Bioconductor
Attempting internal fallback download for InternalPkg
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb965b84318.tar.gz
Checking GhostPkg in configured repositories...
Download from configured repos failed: couldn't find package 'GhostPkg'
Checking GhostPkg on CRAN...
Checking GhostPkg on Bioconductor...
No GhostPkg package found on Bioconductor
Attempting internal fallback download for GhostPkg
Checking ggplot2 in configured repositories...
Package tarball saved at: /home/hornik/tmp/scratch/RtmpPQY4jo/file335eb948c7f4ca
Checking nonexistentpkg in configured repositories...
Download from configured repos failed: couldn't find package 'nonexistentpkg'
Checking nonexistentpkg on CRAN...
Checking nonexistentpkg on Bioconductor...
No nonexistentpkg package found on Bioconductor
Attempting internal fallback download for nonexistentpkg
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
══ Skipped tests (46) ══════════════════════════════════════════════════════════
• On CRAN (45): 'test-assess_pkg.R:6:5', 'test-assess_pkg.R:275:3',
'test-assess_pkg.R:431:3', 'test-assess_pkg.R:511:3',
'test-assess_pkg.R:655:3', 'test-assess_pkg.R:924:3',
'test-assess_pkg.R:1001:3', 'test-badges.R:44:3',
'test-check_suggested_exp_funcs.R:3:3',
'test-check_suggested_exp_funcs.R:218:3', '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:210:3', 'test-dependency_tree.R:539:1',
'test-dependency_tree.R:543:1', 'test-dependency_tree.R:607:1',
'test-dependency_tree.R:611:1', 'test-dependency_tree.R:1053:1',
'test-generate_html_report.R:788:3', 'test-get_exports.R:2:3',
'test-get_exports.R:52:3', 'test-get_exports.R:141:3',
'test-get_exports.R:223:3', 'test-get_exports.R:276:3',
'test-get_exports.R:327:3', 'test-get_exports.R:906:3',
'test-get_exports.R:956:3', 'test-get_exports.R:1045:3',
'test-get_exports.R:1127:3', 'test-get_exports.R:1180:3',
'test-get_exports.R:1231:3', 'test-parse_dcf_dependencies.R:10:3',
'test-parse_dcf_dependencies.R:53:3', 'test-reverse_dependencies.R:2:3',
'test-risk_assess_pkg.R:12:3', 'test-risk_assess_pkg.R:140:3',
'test-risk_assess_pkg.R:164:3', 'test-risk_assess_pkg.R:212:3',
'test-risk_assess_pkg.R:237:3', 'test-risk_assess_pkg.R:275:3',
'test-risk_assess_pkg.R:337:3', 'test-run_covr_skip_stf.R:2:3'
• Skipping test because CRAN is available (1):
'test-parse_dcf_dependencies.R:140:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_suggested_exp_funcs.R:366:3'): check_suggested_exp_funcs returns No R folder found in the package source path message ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-check_suggested_exp_funcs.R:366:3
── Error ('test-documentation_metrics.R:1670:3'): assess exports for no help files works correctly ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-documentation_metrics.R:1670:3
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [48s/83s]
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 8.20.0 with OpenSSL/3.6.2
> library(xml2)
>
> test_check("risk.assessr")
checking package test config
An error occurred in checking suggested functions: Simulated error in inner handler
Checking for author 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 package test config
No recognised standard or non-standard testing configuration
Checking for author 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.
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 file3a2a366956a5c2.tar.gz locally
unpacked file3a2a366956a5c2.tar.gz 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 file3a2a3632fa554.tar.gz locally
unpacked file3a2a3632fa554.tar.gz 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 file3a2a3651d33147.tar.gz locally
unpacked file3a2a3651d33147.tar.gz 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 file3a2a365355a476.tar.gz locally
unpacked file3a2a365355a476.tar.gz 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 file3a2a3610e4e5ea.tar.gz locally
unpacked file3a2a3610e4e5ea.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-check_suggested_exp_funcs-367.R
No Suggested packages in the DESCRIPTION file
No Imports or Suggested packages in the DESCRIPTION file
No exported functions from source package mockpkg
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
Failed to download or parse testpkg - DESCRIPTION file not found for testpkg
Failed to download or parse testpkg -
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
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgD package
Finished building for pkgB
Dependency tree in progress for pkgC package
Finished building for pkgC
Finished building for pkgA
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgC package
Finished building for pkgA
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
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Finished building for pkgB
Finished building for pkgA
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg
├── dep1
└── dep2 (base)
Dependency tree in progress for testpkg package
Finished building for testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for 123 package
Dependency tree in progress for pkg1pkg2 package
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgA package
Finished building for pkgB
Finished building for pkgA
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 source control
stringr has vignettes
stringr: 92.00% of exported functions have examples
stringr: 94.00% of exported functions have documentation
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
unpacking file3a2a366586ee1f.tar.gz locally
unpacked file3a2a366586ee1f.tar.gz locally
unpacking file3a2a36189e0282.tar.gz locally
unpacked file3a2a36189e0282.tar.gz locally
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg has a source control
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg source control detected via BugReports URL
testpkg has a source control
unpacking stringr locally
unpacked stringr locally
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 bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file3a2a3670b12910.tar.gz locally
unpacked file3a2a3670b12910.tar.gz locally
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 bug reports URL
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 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
mockpkg has bug reports URL
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 source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file3a2a36bfa1ce0.tar.gz locally
unpacked file3a2a36bfa1ce0.tar.gz locally
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 bug reports URL
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 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
Checking for author in limma
Checking for author in limma
unpacking here locally
unpacked here locally
unpacking file3a2a364a2bb1d9.tar.gz locally
unpacked file3a2a364a2bb1d9.tar.gz locally
unpacking here locally
unpacked here locally
here: 75.00% of exported functions have examples
mockpkg: 0.00% of exported functions have examples
unpacking file3a2a3659cf8d7c.tar.gz locally
unpacked file3a2a3659cf8d7c.tar.gz locally
test.package.0001: 0.00% of exported functions have examples
unpacking file3a2a361303bf.tar.gz locally
unpacked file3a2a361303bf.tar.gz locally
test.package.0005: no exported functions found; example score = 0.00%
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 file3a2a363fa246d1.tar.gz locally
unpacked file3a2a363fa246d1.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-documentation_metrics-1671.R
unpacking here locally
unpacked here locally
here has news
unpacking file3a2a3661edf495.tar.gz locally
unpacked file3a2a3661edf495.tar.gz locally
test.package.0001 has no news
unpacking here locally
unpacked here locally
here has current news
unpacking file3a2a364f279e25.tar.gz locally
unpacked file3a2a364f279e25.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 file3a2a365319f838.tar.gz locally
unpacked file3a2a365319f838.tar.gz locally
test.package.0001 has no vignettes
unpacking file3a2a362e2ca1fc.tar.gz locally
unpacked file3a2a362e2ca1fc.tar.gz locally
unpacking stringr locally
unpacked stringr locally
Using package's default risk definition.
Checking stringr in configured repositories...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a3639f4efa4
No testthat or testit configuration
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
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
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a361ab16b80.tar.gz
Checking VersionedPkg in configured repositories...
Download from configured repos failed: couldn't find package 'VersionedPkg'
Checking VersionedPkg on CRAN...
Checking VersionedPkg on Bioconductor...
No VersionedPkg package found on Bioconductor
Attempting internal fallback download for VersionedPkg
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a364705fdf6.tar.gz
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Checking test.package.0001 on Bioconductor...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a363752530a.tar.gz
Checking BiocPkg in configured repositories...
Download from configured repos failed: couldn't find package 'BiocPkg'
Checking BiocPkg on CRAN...
Checking BiocPkg on Bioconductor...
Attempting internal fallback download for BiocPkg
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a361eaca090.tar.gz
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.
tools::Rd_db() failed for 'pkgB': there is no package called 'pkgB'
unpacking file3a2a36decd0f.tar.gz locally
unpacked file3a2a36decd0f.tar.gz locally
installing test.package.0001 locally
test.package.0001 is already installed
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
getting package dependencies for testpkg
package dependencies successful for testpkg
package
1 bar
getting package dependencies for pkgname
package dependencies successful for pkgname
Starting lock file processing
Starting lock file processing
Finishing lock file processing
Starting lock file processing
Finishing lock file processing
running code coverage for test.pkg
running code coverage for empty.pkg
code coverage for empty.pkg successful
running code coverage for failing.pkg
R coverage for failing.pkg failed. Read in the covr output to see what went wrong:
running code coverage for weird.pkg
code coverage for weird.pkg unsuccessful
R coverage for weird.pkg failed. Read in the covr output to see what went wrong:
running standard testing framework
running skip testing with non-standard testing framework
Package fakepkg is not installed.
Project root not found.
running standard testing framework
running standard testing framework
running skip testing with standard testing framework
running non-standard testing framework
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
No recognised standard or non-standard testing configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
Total Coverage for mockpkg is: 80 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: 100 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
No test coverrage for this configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: NA %
performing source test mapping for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
No test coverrage for this configuration
Creating Default test reporter for RtmpRDmfIY
Mapping package test structure for RtmpRDmfIY
Creating test results for no skipped tests for RtmpRDmfIY
Error running coverage for mockpkg: Simulated error
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
Creating package coverage for mockpkg
Creating package coverage for mockpkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
rcmdcheck for test.pkg failed. Read in the rcmdcheck output to see what went wrong:
unpacking file3a2a3666774038.tar.gz locally
unpacked file3a2a3666774038.tar.gz locally
unpacking file3a2a3660f01a3.tar.gz locally
unpacked file3a2a3660f01a3.tar.gz locally
unpacking test.package.0001 locally
unpacked test.package.0001 locally
unpacking file3a2a365fe4dd6d.tar.gz locally
unpacked file3a2a365fe4dd6d.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
Output created: /tmp/RtmpRDmfIY/summary_report_mockpkg_0.1.0.html
Report will be written to: /tmp/RtmpRDmfIY/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp
Output created: /tmp/my-report.html
No output directory specified. Setting output to /tmp/render_root
Output created: /tmp/render_root/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp/render_root_md
Output created: /tmp/render_root_md/summary_report_mockpkg_0.1.0.md
Report will be written to: /tmp/RtmpRDmfIY/file3a2a363a8b3d70/summary_report_pkgA_0.1.0.html
Output created: /tmp/RtmpRDmfIY/file3a2a363a8b3d70/summary_report_pkgA_0.1.0.html
Report will be written to: x/out/summary_report_pkgB_0.2.0.md
Output created: x/out/summary_report_pkgB_0.2.0.md
No output directory specified. Setting output to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/risk.assessr.Rcheck/tests/testthat
Output created: reports/summary_report_pkgC_0.3.0.html
Output created: base/out/report.html
Output created: base/report.md
Output created: base/something.html
Checking SomePkg in configured repositories...
Download from configured repos failed: couldn't find package 'SomePkg'
Checking SomePkg on CRAN...
CRAN download failed: CRAN download failed due to timeout
Checking SomePkg on Bioconductor...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a362dbdc776.tar.gz
Checking Biobase in configured repositories...
Download from configured repos failed: couldn't find package 'Biobase'
Checking Biobase on CRAN...
Checking Biobase on Bioconductor...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a3613b0683d.tar.gz
Checking InternalPkg in configured repositories...
Download from configured repos failed: couldn't find package 'InternalPkg'
Checking InternalPkg on CRAN...
Checking InternalPkg on Bioconductor...
No InternalPkg package found on Bioconductor
Attempting internal fallback download for InternalPkg
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a3662e129ed.tar.gz
Checking GhostPkg in configured repositories...
Download from configured repos failed: couldn't find package 'GhostPkg'
Checking GhostPkg on CRAN...
Checking GhostPkg on Bioconductor...
No GhostPkg package found on Bioconductor
Attempting internal fallback download for GhostPkg
Checking ggplot2 in configured repositories...
Package tarball saved at: /tmp/RtmpRDmfIY/file3a2a3639b10287
Checking nonexistentpkg in configured repositories...
Download from configured repos failed: couldn't find package 'nonexistentpkg'
Checking nonexistentpkg on CRAN...
Checking nonexistentpkg on Bioconductor...
No nonexistentpkg package found on Bioconductor
Attempting internal fallback download for nonexistentpkg
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
══ Skipped tests (46) ══════════════════════════════════════════════════════════
• On CRAN (45): 'test-assess_pkg.R:6:5', 'test-assess_pkg.R:275:3',
'test-assess_pkg.R:431:3', 'test-assess_pkg.R:511:3',
'test-assess_pkg.R:655:3', 'test-assess_pkg.R:924:3',
'test-assess_pkg.R:1001:3', 'test-badges.R:44:3',
'test-check_suggested_exp_funcs.R:3:3',
'test-check_suggested_exp_funcs.R:218:3', '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:210:3', 'test-dependency_tree.R:539:1',
'test-dependency_tree.R:543:1', 'test-dependency_tree.R:607:1',
'test-dependency_tree.R:611:1', 'test-dependency_tree.R:1053:1',
'test-generate_html_report.R:788:3', 'test-get_exports.R:2:3',
'test-get_exports.R:52:3', 'test-get_exports.R:141:3',
'test-get_exports.R:223:3', 'test-get_exports.R:276:3',
'test-get_exports.R:327:3', 'test-get_exports.R:906:3',
'test-get_exports.R:956:3', 'test-get_exports.R:1045:3',
'test-get_exports.R:1127:3', 'test-get_exports.R:1180:3',
'test-get_exports.R:1231:3', 'test-parse_dcf_dependencies.R:10:3',
'test-parse_dcf_dependencies.R:53:3', 'test-reverse_dependencies.R:2:3',
'test-risk_assess_pkg.R:12:3', 'test-risk_assess_pkg.R:140:3',
'test-risk_assess_pkg.R:164:3', 'test-risk_assess_pkg.R:212:3',
'test-risk_assess_pkg.R:237:3', 'test-risk_assess_pkg.R:275:3',
'test-risk_assess_pkg.R:337:3', 'test-run_covr_skip_stf.R:2:3'
• Skipping test because CRAN is available (1):
'test-parse_dcf_dependencies.R:140:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_suggested_exp_funcs.R:366:3'): check_suggested_exp_funcs returns No R folder found in the package source path message ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-check_suggested_exp_funcs.R:366:3
── Error ('test-documentation_metrics.R:1670:3'): assess exports for no help files works correctly ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-documentation_metrics.R:1670:3
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [154s/384s]
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 8.11.1 with OpenSSL/3.2.6
> library(xml2)
>
> test_check("risk.assessr")
checking package test config
An error occurred in checking suggested functions: Simulated error in inner handler
Checking for author 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 package test config
No recognised standard or non-standard testing configuration
Checking for author 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.
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 file2ce95011a2d73d.tar.gz locally
unpacked file2ce95011a2d73d.tar.gz 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 file2ce950716ad158.tar.gz locally
unpacked file2ce950716ad158.tar.gz 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 file2ce95069c1878.tar.gz locally
unpacked file2ce95069c1878.tar.gz 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 file2ce9503c200fa8.tar.gz locally
unpacked file2ce9503c200fa8.tar.gz 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 file2ce9504d9c8e5f.tar.gz locally
unpacked file2ce9504d9c8e5f.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-check_suggested_exp_funcs-367.R
No Suggested packages in the DESCRIPTION file
No Imports or Suggested packages in the DESCRIPTION file
No exported functions from source package mockpkg
gzip: stdin: not in gzip format
/usr/bin/gtar: Child returned status 1
/usr/bin/gtar: 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
Failed to download or parse testpkg - DESCRIPTION file not found for testpkg
Failed to download or parse testpkg -
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
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgD package
Finished building for pkgB
Dependency tree in progress for pkgC package
Finished building for pkgC
Finished building for pkgA
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgC package
Finished building for pkgA
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
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Finished building for pkgB
Finished building for pkgA
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
└── pkg (v1.0.0)
└── dep (v2.0.0)
Dependency tree in progress for testpkg package
Finished building for testpkg
└── pkg
├── dep1
└── dep2 (base)
Dependency tree in progress for testpkg package
Finished building for testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for 123 package
Dependency tree in progress for pkg1pkg2 package
Building dependency tree for: testpkg
Building dependency tree for: testpkg
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for testpkg package
Dependency tree in progress for package
Dependency tree in progress for NA package
Dependency tree in progress for package
Dependency tree in progress for testpkg package
Finished building for testpkg
Dependency tree in progress for pkgA package
Dependency tree in progress for pkgB package
Dependency tree in progress for pkgA package
Finished building for pkgB
Finished building for pkgA
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 source control
stringr has vignettes
stringr: 92.00% of exported functions have examples
stringr: 94.00% of exported functions have documentation
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
unpacking file2ce9501b02282a.tar.gz locally
unpacked file2ce9501b02282a.tar.gz locally
unpacking file2ce9506382b7d.tar.gz locally
unpacked file2ce9506382b7d.tar.gz locally
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg has a source control
testpkg has bug reports URL
testpkg does not have a maintainer
testpkg has a website
testpkg source control detected via BugReports URL
testpkg has a source control
unpacking stringr locally
unpacked stringr locally
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 bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file2ce9508e248a0.tar.gz locally
unpacked file2ce9508e248a0.tar.gz locally
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 bug reports URL
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 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
mockpkg has bug reports URL
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 source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has bug reports URL
stringr has a website
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a source control
stringr has bug reports URL
stringr has a maintainer
stringr has a website
stringr has a source control
unpacking file2ce95055dae78c.tar.gz locally
unpacked file2ce95055dae78c.tar.gz locally
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 bug reports URL
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 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
Checking for author in limma
Checking for author in limma
unpacking here locally
unpacked here locally
unpacking file2ce9507ab7a6f7.tar.gz locally
unpacked file2ce9507ab7a6f7.tar.gz locally
unpacking here locally
unpacked here locally
here: 75.00% of exported functions have examples
mockpkg: 0.00% of exported functions have examples
unpacking file2ce95034257d9b.tar.gz locally
unpacked file2ce95034257d9b.tar.gz locally
test.package.0001: 0.00% of exported functions have examples
unpacking file2ce9504069eb4.tar.gz locally
unpacked file2ce9504069eb4.tar.gz locally
test.package.0005: no exported functions found; example score = 0.00%
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 file2ce9507fddb3e2.tar.gz locally
unpacked file2ce9507fddb3e2.tar.gz locally
installing test.package.0006 locally
Local installation issue is: Error: Failed to install 'test.package.0006' from local:
! System command 'R' failed
test.package.0006 not installed locally
Saving _problems/test-documentation_metrics-1671.R
unpacking here locally
unpacked here locally
here has news
unpacking file2ce9503768b9a4.tar.gz locally
unpacked file2ce9503768b9a4.tar.gz locally
test.package.0001 has no news
unpacking here locally
unpacked here locally
here has current news
unpacking file2ce9502eecca11.tar.gz locally
unpacked file2ce9502eecca11.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 file2ce9503330d491.tar.gz locally
unpacked file2ce9503330d491.tar.gz locally
test.package.0001 has no vignettes
unpacking file2ce950f6f7ae5.tar.gz locally
unpacked file2ce950f6f7ae5.tar.gz locally
unpacking stringr locally
unpacked stringr locally
Using package's default risk definition.
Checking stringr in configured repositories...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9501274fe74
No testthat or testit configuration
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
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
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce950f8a7020.tar.gz
Checking VersionedPkg in configured repositories...
Download from configured repos failed: couldn't find package 'VersionedPkg'
Checking VersionedPkg on CRAN...
Checking VersionedPkg on Bioconductor...
No VersionedPkg package found on Bioconductor
Attempting internal fallback download for VersionedPkg
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9503b3acceb.tar.gz
Checking test.package.0001 in configured repositories...
Download from configured repos failed: couldn't find package 'test.package.0001'
Checking test.package.0001 on CRAN...
Checking test.package.0001 on Bioconductor...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9502893745b.tar.gz
Checking BiocPkg in configured repositories...
Download from configured repos failed: couldn't find package 'BiocPkg'
Checking BiocPkg on CRAN...
Checking BiocPkg on Bioconductor...
Attempting internal fallback download for BiocPkg
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9504f0405e8.tar.gz
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.
tools::Rd_db() failed for 'pkgB': there is no package called 'pkgB'
unpacking file2ce950398e9ce3.tar.gz locally
unpacked file2ce950398e9ce3.tar.gz locally
installing test.package.0001 locally
test.package.0001 is already installed
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/gtar: Removing leading `/' from member names
getting package dependencies for testpkg
package dependencies successful for testpkg
package
1 bar
getting package dependencies for pkgname
package dependencies successful for pkgname
Starting lock file processing
Starting lock file processing
Finishing lock file processing
Starting lock file processing
Finishing lock file processing
running code coverage for test.pkg
running code coverage for empty.pkg
code coverage for empty.pkg successful
running code coverage for failing.pkg
R coverage for failing.pkg failed. Read in the covr output to see what went wrong:
running code coverage for weird.pkg
code coverage for weird.pkg unsuccessful
R coverage for weird.pkg failed. Read in the covr output to see what went wrong:
running standard testing framework
running skip testing with non-standard testing framework
Package fakepkg is not installed.
Project root not found.
running standard testing framework
running standard testing framework
running skip testing with standard testing framework
running non-standard testing framework
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
No recognised standard or non-standard testing configuration
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
No recognised standard or non-standard testing configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
Total Coverage for mockpkg is: 80 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: 100 %
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
No test coverrage for this configuration
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded:
running coverage manually for mockpkg
Total Coverage for mockpkg is: NA %
performing source test mapping for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
performing source test mapping for mockpkg
identifying problem tests for mockpkg
loading package and datasets for mockpkg
Datasets loaded: dataset1
running coverage manually for mockpkg
No test coverrage for this configuration
Creating Default test reporter for Rtmp1td5uI
Mapping package test structure for Rtmp1td5uI
Creating test results for no skipped tests for Rtmp1td5uI
Error running coverage for mockpkg: Simulated error
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Mock unloadNamespace called for mockpkg
Creating package coverage for mockpkg
Unloading mockpkg package to avoid coverage conflict...
Warning: Failed to unload mockpkg package. Proceeding anyway.
Details: Simulated unload failure
Creating package coverage for mockpkg
Creating package coverage for mockpkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
running rcmdcheck for test.pkg
rcmdcheck for test.pkg failed. Read in the rcmdcheck output to see what went wrong:
unpacking file2ce95062d9bf7a.tar.gz locally
unpacked file2ce95062d9bf7a.tar.gz locally
unpacking file2ce95048f178e1.tar.gz locally
unpacked file2ce95048f178e1.tar.gz locally
unpacking test.package.0001 locally
unpacked test.package.0001 locally
unpacking file2ce95067dfeb11.tar.gz locally
unpacked file2ce95067dfeb11.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
Output created: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/summary_report_mockpkg_0.1.0.html
Report will be written to: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp
Output created: /tmp/my-report.html
No output directory specified. Setting output to /tmp/render_root
Output created: /tmp/render_root/summary_report_mockpkg_0.1.0.html
No output directory specified. Setting output to /tmp/render_root_md
Output created: /tmp/render_root_md/summary_report_mockpkg_0.1.0.md
Report will be written to: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce95012919aa/summary_report_pkgA_0.1.0.html
Output created: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce95012919aa/summary_report_pkgA_0.1.0.html
Report will be written to: x/out/summary_report_pkgB_0.2.0.md
Output created: x/out/summary_report_pkgB_0.2.0.md
No output directory specified. Setting output to /data/gannet/ripley/R/packages/tests-devel/risk.assessr.Rcheck/tests/testthat
Output created: reports/summary_report_pkgC_0.3.0.html
Output created: base/out/report.html
Output created: base/report.md
Output created: base/something.html
Checking SomePkg in configured repositories...
Download from configured repos failed: couldn't find package 'SomePkg'
Checking SomePkg on CRAN...
CRAN download failed: CRAN download failed due to timeout
Checking SomePkg on Bioconductor...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9506e4c79e5.tar.gz
Checking Biobase in configured repositories...
Download from configured repos failed: couldn't find package 'Biobase'
Checking Biobase on CRAN...
Checking Biobase on Bioconductor...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9507c6b34a8.tar.gz
Checking InternalPkg in configured repositories...
Download from configured repos failed: couldn't find package 'InternalPkg'
Checking InternalPkg on CRAN...
Checking InternalPkg on Bioconductor...
No InternalPkg package found on Bioconductor
Attempting internal fallback download for InternalPkg
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce95062b052be.tar.gz
Checking GhostPkg in configured repositories...
Download from configured repos failed: couldn't find package 'GhostPkg'
Checking GhostPkg on CRAN...
Checking GhostPkg on Bioconductor...
No GhostPkg package found on Bioconductor
Attempting internal fallback download for GhostPkg
Checking ggplot2 in configured repositories...
Package tarball saved at: /tmp/Rtmpi66mKz/working_dir/Rtmp1td5uI/file2ce9505de4769d
Checking nonexistentpkg in configured repositories...
Download from configured repos failed: couldn't find package 'nonexistentpkg'
Checking nonexistentpkg on CRAN...
Checking nonexistentpkg on Bioconductor...
No nonexistentpkg package found on Bioconductor
Attempting internal fallback download for nonexistentpkg
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
══ Skipped tests (46) ══════════════════════════════════════════════════════════
• On CRAN (45): 'test-assess_pkg.R:6:5', 'test-assess_pkg.R:275:3',
'test-assess_pkg.R:431:3', 'test-assess_pkg.R:511:3',
'test-assess_pkg.R:655:3', 'test-assess_pkg.R:924:3',
'test-assess_pkg.R:1001:3', 'test-badges.R:44:3',
'test-check_suggested_exp_funcs.R:3:3',
'test-check_suggested_exp_funcs.R:218:3', '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:210:3', 'test-dependency_tree.R:539:1',
'test-dependency_tree.R:543:1', 'test-dependency_tree.R:607:1',
'test-dependency_tree.R:611:1', 'test-dependency_tree.R:1053:1',
'test-generate_html_report.R:788:3', 'test-get_exports.R:2:3',
'test-get_exports.R:52:3', 'test-get_exports.R:141:3',
'test-get_exports.R:223:3', 'test-get_exports.R:276:3',
'test-get_exports.R:327:3', 'test-get_exports.R:906:3',
'test-get_exports.R:956:3', 'test-get_exports.R:1045:3',
'test-get_exports.R:1127:3', 'test-get_exports.R:1180:3',
'test-get_exports.R:1231:3', 'test-parse_dcf_dependencies.R:10:3',
'test-parse_dcf_dependencies.R:53:3', 'test-reverse_dependencies.R:2:3',
'test-risk_assess_pkg.R:12:3', 'test-risk_assess_pkg.R:140:3',
'test-risk_assess_pkg.R:164:3', 'test-risk_assess_pkg.R:212:3',
'test-risk_assess_pkg.R:237:3', 'test-risk_assess_pkg.R:275:3',
'test-risk_assess_pkg.R:337:3', 'test-run_covr_skip_stf.R:2:3'
• Skipping test because CRAN is available (1):
'test-parse_dcf_dependencies.R:140:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_suggested_exp_funcs.R:366:3'): check_suggested_exp_funcs returns No R folder found in the package source path message ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-check_suggested_exp_funcs.R:366:3
── Error ('test-documentation_metrics.R:1670:3'): assess exports for no help files works correctly ──
<objectNotFoundError/error/condition>
Error in `install_package_local(pkg_source_path)`: object 'package_installed' not found
Backtrace:
▆
1. └─risk.assessr::install_package_local(pkg_source_path) at test-documentation_metrics.R:1670:3
[ FAIL 2 | WARN 1 | SKIP 46 | PASS 1899 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 3.1.1
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘test.package.0005’ ‘test.package.0009’ ‘test.package.0010’
Flavor: r-devel-linux-x86_64-fedora-gcc