Marcel Ramos
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BiocCheck |
| git_branch: RELEASE_3_21 |
| git_last_commit: c9bf2e8 |
| git_last_commit_date: 2025-05-15 17:39:40 -0400 (Thu, 15 May 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:41 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 183/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocCheck 1.44.2 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the BiocCheck package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocCheck.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BiocCheck |
| Version: 1.44.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocCheck_1.44.2.tar.gz |
| StartedAt: 2025-09-23 07:27:04 -0000 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 07:42:21 -0000 (Tue, 23 Sep 2025) |
| EllapsedTime: 917.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BiocCheck.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocCheck_1.44.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocCheck.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.44.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocCheck’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘knitr:::detect_pattern’
‘tools:::.build_news_db_from_package_NEWS_Rd’
‘tools:::.build_news_db_from_package_NEWS_md’
‘tools:::.news_reader_default’ ‘tools:::RdTags’
‘tools:::analyze_licenses’ ‘tools:::str_parse_logic’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘BiocCheckRun’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BiocCheck 20.01 3.526 49.696
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
ERROR
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
In addition: Warning messages:
1: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
2: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
3: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
4: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
5: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
6: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.
BiocCheck.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BiocCheck ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘BiocCheck’ ... ** this is package ‘BiocCheck’ version ‘1.44.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocCheck)
BiocCheck.Rcheck/tests/tinytest.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (requireNamespace("tinytest", quietly = TRUE))
+ tinytest::test_package("BiocCheck")
You are using 'tinytest::' to express test expectations.
The results from these tests are not collected. Found the following occurrences:
> test_BiocCheck.R#427: tinytest::expect_match
Remove the 'tinytest::' prefix to register the test results.FALSE
test_BiocCheck.R.............. 0 tests Loading required package: usethis
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests ✖ ERROR: No vignette sources in vignettes/ directory.
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 0 tests ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
Update the following files:
• test.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 0 tests
test_BiocCheck.R.............. 1 tests [0;32mOK[0m
test_BiocCheck.R.............. 1 tests [0;32mOK[0m
test_BiocCheck.R.............. 1 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 1 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 2 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• testpkg0.Rnw
test_BiocCheck.R.............. 2 tests [0;32mOK[0m
test_BiocCheck.R.............. 3 tests [0;32mOK[0m
test_BiocCheck.R.............. 3 tests [0;32mOK[0m
test_BiocCheck.R.............. 3 tests [0;32mOK[0m
test_BiocCheck.R.............. 4 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw
test_BiocCheck.R.............. 4 tests [0;32mOK[0m
test_BiocCheck.R.............. 5 tests [0;32mOK[0m
test_BiocCheck.R.............. 5 tests [0;32mOK[0m ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 5 tests [0;32mOK[0m
test_BiocCheck.R.............. 6 tests [0;32mOK[0m
test_BiocCheck.R.............. 6 tests [0;32mOK[0m
test_BiocCheck.R.............. 6 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• knitr
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 6 tests [0;32mOK[0m
test_BiocCheck.R.............. 7 tests [0;32mOK[0m
test_BiocCheck.R.............. 7 tests [0;32mOK[0m
test_BiocCheck.R.............. 7 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• Sweave
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 7 tests [0;32mOK[0m
test_BiocCheck.R.............. 8 tests [0;32mOK[0m
test_BiocCheck.R.............. 8 tests [0;32mOK[0m
test_BiocCheck.R.............. 8 tests [0;32mOK[0m ✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
• knitr
! WARNING: Vignette(s) missing Vignette metadata. See
http://r-pkgs.had.co.nz/vignettes.html
Update the following files:
• dupChunks.Rmd
• ...
• testpkg0_child.Rmd
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• testpkg0.Rnw
✖ ERROR: No 'VignetteEngine' specified in vignette.
Add 'VignetteEngine' to the following files:
• vignettes/dupChunks.Rmd
• ...
• vignettes/testpkg0_child.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• knitr
! WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette Title}'
The following files use template defaults:
• testpkg0.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
Update the following files:
• dupChunks.Rmd
• evalfalse.Rmd
• testpkg0_child.Rmd
✖ ERROR: Vignette(s) found with duplicate chunk labels
Found in files:
• dupChunks.Rmd
! WARNING: BiocInstaller code found in vignette(s)
Found in files:
vignettes/testpkg0.Rmd (code line 24, column 20)
✖ ERROR: Installation calls found in vignette(s)
Found in files:
• vignettes/testpkg0.Rmd (code line 16, column 18)
• vignettes/testpkg0.Rmd (code line 24, column 20)
• vignettes/testpkg0.Rmd (code line 18, column 1)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• testpkg0.Rmd (code line 64, column 10)
• testpkg0_child.Rmd (code line 3, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/testpkg0.Rmd (code line 47, column 5)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/dupChunks.Rmd
• ...
• vignettes/testpkg0_child.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/evalfalse.Rmd
test_BiocCheck.R.............. 8 tests [0;32mOK[0m
test_BiocCheck.R.............. 9 tests [0;32mOK[0m
test_BiocCheck.R.............. 10 tests [0;32mOK[0m
test_BiocCheck.R.............. 10 tests [0;32mOK[0m ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/evalfalse.Rmd
test_BiocCheck.R.............. 10 tests [0;32mOK[0m
test_BiocCheck.R.............. 11 tests [0;32mOK[0m
test_BiocCheck.R.............. 12 tests [0;32mOK[0m
test_BiocCheck.R.............. 12 tests [0;32mOK[0m
test_BiocCheck.R.............. 12 tests [0;32mOK[0m ℹ NOTE: Potential intermediate files found:
• vignettes/testpkg0.html
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
• FailBuilder
! WARNING: Vignette(s) missing Vignette metadata. See
http://r-pkgs.had.co.nz/vignettes.html
Update the following files:
• testpkg0.Rmd
✖ ERROR: More than one VignetteEngine specified.
Found in files:
• vignettes/testpkg0.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• ThisWillFail
• FailBuilder
! WARNING: Evaluate more vignette chunks.
ℹ 3 out of 5 code chunks = 60% unevaluated
ℹ 1 non-exec code chunk(s) (e.g., '```r')
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/testpkg0.Rmd (code line 9, column 7)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/testpkg0.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/testpkg0.Rmd
test_BiocCheck.R.............. 12 tests [0;32mOK[0m
test_BiocCheck.R.............. 13 tests [0;32mOK[0m
test_BiocCheck.R.............. 14 tests [0;32mOK[0m
test_BiocCheck.R.............. 15 tests [0;32mOK[0m
test_BiocCheck.R.............. 16 tests [0;32mOK[0m
test_BiocCheck.R.............. 17 tests [0;32mOK[0m
test_BiocCheck.R.............. 18 tests [0;32mOK[0m
test_BiocCheck.R.............. 18 tests [0;32mOK[0m
test_BiocCheck.R.............. 18 tests [0;32mOK[0m ℹ NOTE: Potential intermediate files found:
• vignettes/testpkg0.html
test_BiocCheck.R.............. 18 tests [0;32mOK[0m
test_BiocCheck.R.............. 19 tests [0;32mOK[0m
test_BiocCheck.R.............. 19 tests [0;32mOK[0m ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/testpkg0.Rmd
test_BiocCheck.R.............. 19 tests [0;32mOK[0m
test_BiocCheck.R.............. 20 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 21 tests [0;32mOK[0m ! WARNING: y of x.y.z version should be even in release
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m ! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got '1.99.3'.
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 23 tests [0;32mOK[0m
test_BiocCheck.R.............. 23 tests [0;32mOK[0m ✖ ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3
test_BiocCheck.R.............. 23 tests [0;32mOK[0m
test_BiocCheck.R.............. 23 tests [0;32mOK[0m
test_BiocCheck.R.............. 23 tests [0;32mOK[0m
test_BiocCheck.R.............. 23 tests [0;32mOK[0m
test_BiocCheck.R.............. 24 tests [0;32mOK[0m
test_BiocCheck.R.............. 24 tests [0;32mOK[0m
test_BiocCheck.R.............. 24 tests [0;32mOK[0m
test_BiocCheck.R.............. 24 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m ✖ ERROR: Remove 'file1a748d7769f04c.BiocCheck' from the package directory
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m ✖ ERROR: Remove 'inst/doc' folder from the package source
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m * Checking that biocViews are present...
✖ ERROR: No biocViews terms found.
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 28 tests [0;32mOK[0m * Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
! WARNING: Invalid BiocViews term(s):
• 'foo'
• ...
• 'baz': Did you mean 'ag'?
* Checking for recommended biocViews...
No man pages found.
No vignettes found.
test_BiocCheck.R.............. 28 tests [0;32mOK[0m
test_BiocCheck.R.............. 29 tests [0;32mOK[0m
test_BiocCheck.R.............. 29 tests [0;32mOK[0m
test_BiocCheck.R.............. 29 tests [0;32mOK[0m * Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
No man pages found.
No vignettes found.
test_BiocCheck.R.............. 29 tests [0;32mOK[0m
test_BiocCheck.R.............. 30 tests [0;32mOK[0m
test_BiocCheck.R.............. 30 tests [0;32mOK[0m
test_BiocCheck.R.............. 30 tests [0;32mOK[0m * Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
test_BiocCheck.R.............. 30 tests [0;32mOK[0m
test_BiocCheck.R.............. 31 tests [0;32mOK[0m
test_BiocCheck.R.............. 31 tests [0;32mOK[0m
test_BiocCheck.R.............. 31 tests [0;32mOK[0m
test_BiocCheck.R.............. 31 tests [0;32mOK[0m
test_BiocCheck.R.............. 31 tests [0;32mOK[0m ✖ ERROR: System files found that should not be Git tracked.
• something.Rproj
test_BiocCheck.R.............. 31 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 34 tests [0;32mOK[0m
test_BiocCheck.R.............. 34 tests [0;32mOK[0m * Checking License: for restrictive use...
ℹ NOTE: License 'GPL-3.0' unknown; refer to $R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
test_BiocCheck.R.............. 34 tests [0;32mOK[0m
test_BiocCheck.R.............. 34 tests [0;32mOK[0m
test_BiocCheck.R.............. 34 tests [0;32mOK[0m * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0' restricts use
test_BiocCheck.R.............. 34 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 36 tests [0;32mOK[0m
test_BiocCheck.R.............. 36 tests [0;32mOK[0m * Checking License: for restrictive use...
ℹ NOTE: License 'UNKNOWN' unknown; refer to $R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
test_BiocCheck.R.............. 36 tests [0;32mOK[0m
test_BiocCheck.R.............. 37 tests [0;32mOK[0m
test_BiocCheck.R.............. 37 tests [0;32mOK[0m * Checking License: for restrictive use...
ℹ NOTE: malformed 'License:' field 'NA'
test_BiocCheck.R.............. 37 tests [0;32mOK[0m
test_BiocCheck.R.............. 38 tests [0;32mOK[0m
test_BiocCheck.R.............. 38 tests [0;32mOK[0m
test_BiocCheck.R.............. 38 tests [0;32mOK[0m
test_BiocCheck.R.............. 38 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m * Checking License: for restrictive use...
ℹ NOTE: License 'GPL-3.0' unknown; refer to $R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
test_BiocCheck.R.............. 39 tests [0;32mOK[0m
test_BiocCheck.R.............. 40 tests [0;32mOK[0m
test_BiocCheck.R.............. 40 tests [0;32mOK[0m
test_BiocCheck.R.............. 40 tests [0;32mOK[0m
test_BiocCheck.R.............. 41 tests [0;32mOK[0m * Checking License: for restrictive use...
test_BiocCheck.R.............. 41 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m ! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• fileA.rda
• fileB.rds
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 43 tests [0;32mOK[0m
test_BiocCheck.R.............. 43 tests [0;32mOK[0m ! WARNING: Data files exceed the 5MB size limit.
Use 'ExperimentHub' or 'AnnotationHub' for the files:
• fileA.rda
• fileB.rds
test_BiocCheck.R.............. 43 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
✖ ERROR: Remove whitespace from DESCRIPTION field names.
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m ! WARNING: Description field in the DESCRIPTION file is too concise
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m ℹ NOTE: The Description field in the DESCRIPTION is made up of less than 3
sentences. Provide a more detailed description of the package.
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
✖ ERROR: Package directory 'file1a748d1d3a9ad5' must match Package: field (got
'Foo').
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: Authors@R field must be valid 'person' object.
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: No Authors@R maintainer [cre] field in DESCRIPTION.
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: No Authors@R [cre] or Maintainer field in DESCRIPTION file.
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 46 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
✖ ERROR: No email address for Authors@R maintainer [cre] field.
test_BiocCheck.R.............. 46 tests [0;32mOK[0m
test_BiocCheck.R.............. 47 tests [0;32mOK[0m
test_BiocCheck.R.............. 47 tests [0;32mOK[0m
test_BiocCheck.R.............. 47 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
test_BiocCheck.R.............. 47 tests [0;32mOK[0m
test_BiocCheck.R.............. 48 tests [0;32mOK[0m
test_BiocCheck.R.............. 48 tests [0;32mOK[0m
test_BiocCheck.R.............. 48 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
ℹ NOTE: Invalid ORCID iD for Bioconductor Package Maintainer
test_BiocCheck.R.............. 48 tests [0;32mOK[0m
test_BiocCheck.R.............. 49 tests [0;32mOK[0m
test_BiocCheck.R.............. 50 tests [0;32mOK[0m
test_BiocCheck.R.............. 50 tests [0;32mOK[0m
test_BiocCheck.R.............. 50 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: Do not use Author/Maintainer fields. Use Authors@R.
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
test_BiocCheck.R.............. 50 tests [0;32mOK[0m
test_BiocCheck.R.............. 51 tests [0;32mOK[0m
test_BiocCheck.R.............. 51 tests [0;32mOK[0m
test_BiocCheck.R.............. 51 tests [0;32mOK[0m * Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
✖ ERROR: Designate only one maintainer with Authors@R [cre].
ℹ NOTE: Invalid ORCID iD for Bioconductor Package Maintainer
test_BiocCheck.R.............. 51 tests [0;32mOK[0m
test_BiocCheck.R.............. 52 tests [0;32mOK[0m
test_BiocCheck.R.............. 52 tests [0;32mOK[0m
test_BiocCheck.R.............. 52 tests [0;32mOK[0m * Checking that provided CITATION file is correctly formatted...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
test_BiocCheck.R.............. 52 tests [0;32mOK[0m
test_BiocCheck.R.............. 53 tests [0;32mOK[0m
test_BiocCheck.R.............. 53 tests [0;32mOK[0m
test_BiocCheck.R.............. 53 tests [0;32mOK[0m * Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
test_BiocCheck.R.............. 53 tests [0;32mOK[0m
test_BiocCheck.R.............. 54 tests [0;32mOK[0m
test_BiocCheck.R.............. 54 tests [0;32mOK[0m
test_BiocCheck.R.............. 54 tests [0;32mOK[0m ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
test_BiocCheck.R.............. 54 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 56 tests [0;32mOK[0m
test_BiocCheck.R.............. 56 tests [0;32mOK[0m ℹ NOTE: skip_on_bioc() found in testthat files: a_test.R
test_BiocCheck.R.............. 56 tests [0;32mOK[0m
test_BiocCheck.R.............. 57 tests [0;32mOK[0m
test_BiocCheck.R.............. 57 tests [0;32mOK[0m
test_BiocCheck.R.............. 57 tests [0;32mOK[0m
test_BiocCheck.R.............. 57 tests [0;32mOK[0m
test_BiocCheck.R.............. 58 tests [0;32mOK[0m
test_BiocCheck.R.............. 58 tests [0;32mOK[0m
test_BiocCheck.R.............. 59 tests [0;32mOK[0m
test_BiocCheck.R.............. 59 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 tests [0;32mOK[0m
test_BiocCheck.R.............. 62 tests [0;32mOK[0m
test_BiocCheck.R.............. 62 tests [0;32mOK[0m
test_BiocCheck.R.............. 62 tests [0;32mOK[0m
test_BiocCheck.R.............. 63 tests [0;32mOK[0m
test_BiocCheck.R.............. 63 tests [0;32mOK[0m
test_BiocCheck.R.............. 63 tests [0;32mOK[0m
test_BiocCheck.R.............. 64 tests [0;32mOK[0m
test_BiocCheck.R.............. 64 tests [0;32mOK[0m
test_BiocCheck.R.............. 64 tests [0;32mOK[0m
test_BiocCheck.R.............. 64 tests [0;32mOK[0m
test_BiocCheck.R.............. 65 tests [0;32mOK[0m
test_BiocCheck.R.............. 65 tests [0;32mOK[0m
test_BiocCheck.R.............. 65 tests [0;32mOK[0m
test_BiocCheck.R.............. 65 tests [0;32mOK[0m
test_BiocCheck.R.............. 66 tests [0;32mOK[0m
test_BiocCheck.R.............. 67 tests [0;32mOK[0m
test_BiocCheck.R.............. 67 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/home/biocbuild/tmp/Rtmp1fX5bd/file1a748d208a42f/file1a748d6cb05a9/DESCRIPTION’ ... OK
* preparing ‘file1a748d6cb05a9’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘file1a748d6cb05a9/R’
* building ‘file1a748d6cb05a9_0.99.0.tar.gz’
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 68 tests [0;32mOK[0m
test_BiocCheck.R.............. 69 tests [0;32mOK[0m
test_BiocCheck.R.............. 69 tests [0;32mOK[0m
test_BiocCheck.R.............. 69 tests [0;32mOK[0m
test_BiocCheck.R.............. 69 tests [0;32mOK[0m Error in curl::curl_fetch_memory(url, handle = handle) :
Server returned nothing (no headers, no data) [bioconductor.org]: Empty reply from server
Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
In addition: Warning messages:
1: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
2: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
3: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
4: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
5: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
6: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]], :
Invalid ORCID iD: '0000-0000-000-0000'.
Execution halted
BiocCheck.Rcheck/BiocCheck-Ex.timings
| name | user | system | elapsed | |
| BiocCheck-class | 0.001 | 0.000 | 0.001 | |
| BiocCheck | 20.010 | 3.526 | 49.696 | |
| BiocCheckGitClone | 0.745 | 0.008 | 0.755 | |
| BiocPackage-class | 0.000 | 0.000 | 0.001 | |