Marcel Ramos
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BiocCheck |
| git_branch: RELEASE_3_20 |
| git_last_commit: 1684cf6 |
| git_last_commit_date: 2024-10-29 09:51:26 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 179/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocCheck 1.42.0 (landing page) Marcel Ramos
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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 | | ||||||||
|
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. |
| Package: BiocCheck |
| Version: 1.42.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocCheck_1.42.0.tar.gz |
| StartedAt: 2024-12-20 12:28:22 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 12:31:59 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 216.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocCheck.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocCheck_1.42.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.42.0’
* 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 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 18.459 5.02 28.299
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’
OK
* 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 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.
BiocCheck.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocCheck ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BiocCheck’ ... ** 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
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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#492: tinytest::expect_match
Remove the 'tinytest::' prefix to register the test results.FALSE
test_BiocCheck.R.............. 0 tests
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
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.............. 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
! 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.............. 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: 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.............. 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 ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.
test_BiocCheck.R.............. 3 tests [0;32mOK[0m
test_BiocCheck.R.............. 4 tests [0;32mOK[0m
test_BiocCheck.R.............. 4 tests [0;32mOK[0m
test_BiocCheck.R.............. 4 tests [0;32mOK[0m ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.
test_BiocCheck.R.............. 4 tests [0;32mOK[0m
test_BiocCheck.R.............. 5 tests [0;32mOK[0m
test_BiocCheck.R.............. 5 tests [0;32mOK[0m
test_BiocCheck.R.............. 5 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• testpkg0.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
test_BiocCheck.R.............. 7 tests [0;32mOK[0m ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• 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 ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw
test_BiocCheck.R.............. 8 tests [0;32mOK[0m
test_BiocCheck.R.............. 9 tests [0;32mOK[0m
test_BiocCheck.R.............. 9 tests [0;32mOK[0m
test_BiocCheck.R.............. 9 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.............. 9 tests [0;32mOK[0m
test_BiocCheck.R.............. 10 tests [0;32mOK[0m
test_BiocCheck.R.............. 10 tests [0;32mOK[0m
test_BiocCheck.R.............. 10 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.............. 10 tests [0;32mOK[0m
test_BiocCheck.R.............. 11 tests [0;32mOK[0m
test_BiocCheck.R.............. 11 tests [0;32mOK[0m
test_BiocCheck.R.............. 11 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.............. 11 tests [0;32mOK[0m
test_BiocCheck.R.............. 12 tests [0;32mOK[0m
test_BiocCheck.R.............. 13 tests [0;32mOK[0m
test_BiocCheck.R.............. 13 tests [0;32mOK[0m ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/evalfalse.Rmd
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.............. 15 tests [0;32mOK[0m
test_BiocCheck.R.............. 15 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.............. 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.............. 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 ℹ NOTE: Potential intermediate files found:
• vignettes/testpkg0.html
test_BiocCheck.R.............. 21 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m
test_BiocCheck.R.............. 22 tests [0;32mOK[0m ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/testpkg0.Rmd
test_BiocCheck.R.............. 22 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.............. 24 tests [0;32mOK[0m ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html
test_BiocCheck.R.............. 24 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m
test_BiocCheck.R.............. 25 tests [0;32mOK[0m ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html
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 ! WARNING: y of x.y.z version should be even in release
test_BiocCheck.R.............. 26 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 tests [0;32mOK[0m
test_BiocCheck.R.............. 27 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.............. 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.............. 29 tests [0;32mOK[0m
test_BiocCheck.R.............. 29 tests [0;32mOK[0m ✖ ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3
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
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.............. 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 ✖ ERROR: Remove 'file3ca625740312.BiocCheck' from the package directory
test_BiocCheck.R.............. 32 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 tests [0;32mOK[0m
test_BiocCheck.R.............. 33 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 ✖ ERROR: Remove 'inst/doc' folder from the package source
test_BiocCheck.R.............. 34 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m
test_BiocCheck.R.............. 35 tests [0;32mOK[0m * Checking that biocViews are present...
✖ ERROR: No biocViews terms found.
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 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.............. 36 tests [0;32mOK[0m
test_BiocCheck.R.............. 37 tests [0;32mOK[0m
test_BiocCheck.R.............. 37 tests [0;32mOK[0m
test_BiocCheck.R.............. 37 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.............. 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 * 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.............. 38 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m
test_BiocCheck.R.............. 39 tests [0;32mOK[0m ✖ ERROR: System files found that should not be Git tracked.
• something.Rproj
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.............. 40 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.............. 40 tests [0;32mOK[0m
test_BiocCheck.R.............. 41 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 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.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 42 tests [0;32mOK[0m * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0' restricts use
test_BiocCheck.R.............. 42 tests [0;32mOK[0m
test_BiocCheck.R.............. 43 tests [0;32mOK[0m
test_BiocCheck.R.............. 43 tests [0;32mOK[0m * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use
test_BiocCheck.R.............. 43 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 44 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.............. 44 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m
test_BiocCheck.R.............. 45 tests [0;32mOK[0m * Checking License: for restrictive use...
ℹ NOTE: malformed 'License:' field 'NA'
test_BiocCheck.R.............. 45 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.............. 47 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.............. 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
test_BiocCheck.R.............. 49 tests [0;32mOK[0m * Checking License: for restrictive use...
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
test_BiocCheck.R.............. 50 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 ! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• fileA.rda
• fileB.rds
test_BiocCheck.R.............. 50 tests [0;32mOK[0m
test_BiocCheck.R.............. 51 tests [0;32mOK[0m
test_BiocCheck.R.............. 51 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.............. 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
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 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.............. 52 tests [0;32mOK[0m
test_BiocCheck.R.............. 53 tests [0;32mOK[0m
test_BiocCheck.R.............. 53 tests [0;32mOK[0m
test_BiocCheck.R.............. 54 tests [0;32mOK[0m
test_BiocCheck.R.............. 54 tests [0;32mOK[0m ! WARNING: Description field in the DESCRIPTION file is too concise
test_BiocCheck.R.............. 54 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 55 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.............. 55 tests [0;32mOK[0m
test_BiocCheck.R.............. 56 tests [0;32mOK[0m
test_BiocCheck.R.............. 56 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 'file3ca66599507c' must match Package: field (got
'Foo').
test_BiocCheck.R.............. 56 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 * 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.............. 58 tests [0;32mOK[0m
test_BiocCheck.R.............. 59 tests [0;32mOK[0m
test_BiocCheck.R.............. 59 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.............. 59 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 60 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.............. 60 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 tests [0;32mOK[0m
test_BiocCheck.R.............. 61 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.............. 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 * 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.............. 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 * 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.............. 63 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 * 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.............. 65 tests [0;32mOK[0m
test_BiocCheck.R.............. 66 tests [0;32mOK[0m
test_BiocCheck.R.............. 66 tests [0;32mOK[0m
test_BiocCheck.R.............. 66 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.............. 66 tests [0;32mOK[0m
test_BiocCheck.R.............. 67 tests [0;32mOK[0m
test_BiocCheck.R.............. 67 tests [0;32mOK[0m
test_BiocCheck.R.............. 67 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.............. 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 * Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
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 ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
test_BiocCheck.R.............. 69 tests [0;32mOK[0m
test_BiocCheck.R.............. 70 tests [0;32mOK[0m
test_BiocCheck.R.............. 70 tests [0;32mOK[0m
test_BiocCheck.R.............. 70 tests [0;32mOK[0m
test_BiocCheck.R.............. 70 tests [0;32mOK[0m
test_BiocCheck.R.............. 71 tests [0;32mOK[0m
test_BiocCheck.R.............. 71 tests [0;32mOK[0m ℹ NOTE: skip_on_bioc() found in testthat files: a_test.R
test_BiocCheck.R.............. 71 tests [0;32mOK[0m
test_BiocCheck.R.............. 72 tests [0;32mOK[0m
test_BiocCheck.R.............. 72 tests [0;32mOK[0m
test_BiocCheck.R.............. 72 tests [0;32mOK[0m
test_BiocCheck.R.............. 72 tests [0;32mOK[0m
test_BiocCheck.R.............. 73 tests [0;32mOK[0m
test_BiocCheck.R.............. 73 tests [0;32mOK[0m
test_BiocCheck.R.............. 74 tests [0;32mOK[0m
test_BiocCheck.R.............. 74 tests [0;32mOK[0m
test_BiocCheck.R.............. 75 tests [0;32mOK[0m
test_BiocCheck.R.............. 75 tests [0;32mOK[0m
test_BiocCheck.R.............. 76 tests [0;32mOK[0m
test_BiocCheck.R.............. 76 tests [0;32mOK[0m
test_BiocCheck.R.............. 76 tests [0;32mOK[0m
test_BiocCheck.R.............. 76 tests [0;32mOK[0m
test_BiocCheck.R.............. 77 tests [0;32mOK[0m
test_BiocCheck.R.............. 77 tests [0;32mOK[0m
test_BiocCheck.R.............. 77 tests [0;32mOK[0m
test_BiocCheck.R.............. 78 tests [0;32mOK[0m
test_BiocCheck.R.............. 78 tests [0;32mOK[0m
test_BiocCheck.R.............. 78 tests [0;32mOK[0m
test_BiocCheck.R.............. 79 tests [0;32mOK[0m
test_BiocCheck.R.............. 79 tests [0;32mOK[0m
test_BiocCheck.R.............. 79 tests [0;32mOK[0m
test_BiocCheck.R.............. 79 tests [0;32mOK[0m
test_BiocCheck.R.............. 80 tests [0;32mOK[0m
test_BiocCheck.R.............. 80 tests [0;32mOK[0m
test_BiocCheck.R.............. 80 tests [0;32mOK[0m
test_BiocCheck.R.............. 80 tests [0;32mOK[0m
test_BiocCheck.R.............. 81 tests [0;32mOK[0m
test_BiocCheck.R.............. 82 tests [0;32mOK[0m
test_BiocCheck.R.............. 82 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/tmp/RtmpxHoKJo/file3ca666da5488/file3ca67e3e179/DESCRIPTION’ ... OK
* preparing ‘file3ca67e3e179’:
* 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 ‘file3ca67e3e179/R’
* building ‘file3ca67e3e179_0.99.0.tar.gz’
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 83 tests [0;32mOK[0m
test_BiocCheck.R.............. 84 tests [0;32mOK[0m
test_BiocCheck.R.............. 84 tests [0;32mOK[0m
test_BiocCheck.R.............. 84 tests [0;32mOK[0m
test_BiocCheck.R.............. 84 tests [0;32mOK[0m ✖ ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated
and does not work on Windows.
test_BiocCheck.R.............. 84 tests [0;32mOK[0m
test_BiocCheck.R.............. 85 tests [0;32mOK[0m
test_BiocCheck.R.............. 85 tests [0;32mOK[0m
test_BiocCheck.R.............. 85 tests [0;32mOK[0m
test_BiocCheck.R.............. 85 tests [0;32mOK[0m
test_BiocCheck.R.............. 85 tests [0;32mOK[0m
test_BiocCheck.R.............. 86 tests [0;32mOK[0m
test_BiocCheck.R.............. 86 tests [0;32mOK[0m
test_BiocCheck.R.............. 86 tests [0;32mOK[0m
test_BiocCheck.R.............. 87 tests [0;32mOK[0m
test_BiocCheck.R.............. 87 tests [0;32mOK[0m
test_BiocCheck.R.............. 87 tests [0;32mOK[0m
test_BiocCheck.R.............. 87 tests [0;32mOK[0m
test_BiocCheck.R.............. 87 tests [0;32mOK[0m
test_BiocCheck.R.............. 88 tests [0;32mOK[0m
test_BiocCheck.R.............. 88 tests [0;32mOK[0m
test_BiocCheck.R.............. 88 tests [0;32mOK[0m
test_BiocCheck.R.............. 88 tests [0;32mOK[0m
test_BiocCheck.R.............. 89 tests [0;32mOK[0m
test_BiocCheck.R.............. 89 tests [0;32mOK[0m
test_BiocCheck.R.............. 89 tests [0;32mOK[0m
test_BiocCheck.R.............. 89 tests [0;32mOK[0m
test_BiocCheck.R.............. 90 tests [0;32mOK[0m
test_BiocCheck.R.............. 90 tests [0;32mOK[0m
test_BiocCheck.R.............. 90 tests [0;32mOK[0m
test_BiocCheck.R.............. 90 tests [0;32mOK[0m
test_BiocCheck.R.............. 91 tests [0;32mOK[0m
test_BiocCheck.R.............. 91 tests [0;32mOK[0m
test_BiocCheck.R.............. 91 tests [0;32mOK[0m
test_BiocCheck.R.............. 91 tests [0;32mOK[0m
test_BiocCheck.R.............. 92 tests [0;32mOK[0m
test_BiocCheck.R.............. 92 tests [0;32mOK[0m
test_BiocCheck.R.............. 92 tests [0;32mOK[0m ✖ 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)
test_BiocCheck.R.............. 92 tests [0;32mOK[0m
test_BiocCheck.R.............. 93 tests [0;32mOK[0m
test_BiocCheck.R.............. 94 tests [0;32mOK[0m
test_BiocCheck.R.............. 94 tests [0;32mOK[0m
test_BiocCheck.R.............. 94 tests [0;32mOK[0m ✖ ERROR: Vignette(s) found with duplicate chunk labels
Found in files:
• dupChunks.Rmd
test_BiocCheck.R.............. 94 tests [0;32mOK[0m
test_BiocCheck.R.............. 95 tests [0;32mOK[0m
test_BiocCheck.R.............. 96 tests [0;32mOK[0m
test_BiocCheck.R.............. 96 tests [0;32mOK[0m ! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/testpkg0.Rmd (code line 47, column 5)
test_BiocCheck.R.............. 96 tests [0;32mOK[0m
test_BiocCheck.R.............. 97 tests [0;32mOK[0m
test_BiocCheck.R.............. 97 tests [0;32mOK[0m
test_BiocCheck.R.............. 97 tests [0;32mOK[0m ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/dupChunks.Rmd
• ...
• vignettes/testpkg0_child.Rmd
test_BiocCheck.R.............. 97 tests [0;32mOK[0m
test_BiocCheck.R.............. 98 tests [0;32mOK[0m
test_BiocCheck.R.............. 98 tests [0;32mOK[0m
test_BiocCheck.R.............. 98 tests [0;32mOK[0m
test_BiocCheck.R.............. 98 tests [0;32mOK[0m ℹ Found install() in R/bad_coding.R (line 41, column 18)
ℹ Found install() in vignettes/testpkg0.Rmd
test_BiocCheck.R.............. 98 tests [0;32mOK[0m
test_BiocCheck.R.............. 99 tests [0;32mOK[0m
test_BiocCheck.R.............. 99 tests [0;32mOK[0m ! WARNING: BiocInstaller code found in vignette(s)
Found in files:
vignettes/testpkg0.Rmd (code line 24, column 20)
test_BiocCheck.R.............. 99 tests [0;32mOK[0m
test_BiocCheck.R.............. 100 tests [0;32mOK[0m
test_BiocCheck.R.............. 100 tests [0;32mOK[0m
test_BiocCheck.R.............. 100 tests [0;32mOK[0m
test_BiocCheck.R.............. 100 tests [0;32mOK[0m
test_BiocCheck.R.............. 100 tests [0;32mOK[0m
test_BiocCheck.R.............. 101 tests [0;32mOK[0m
test_BiocCheck.R.............. 101 tests [0;32mOK[0m
test_BiocCheck.R.............. 101 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
test_BiocCheck.R.............. 101 tests [0;32mOK[0m
test_BiocCheck.R.............. 102 tests [0;32mOK[0m
test_BiocCheck.R.............. 102 tests [0;32mOK[0m
test_BiocCheck.R.............. 102 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
test_BiocCheck.R.............. 102 tests [0;32mOK[0m
test_BiocCheck.R.............. 103 tests [0;32mOK[0m
test_BiocCheck.R.............. 103 tests [0;32mOK[0m
test_BiocCheck.R.............. 103 tests [0;32mOK[0m * Checking for recommended DESCRIPTION fields...
test_BiocCheck.R.............. 103 tests [0;32mOK[0m
test_BiocCheck.R.............. 104 tests [0;32mOK[0m
test_BiocCheck.R.............. 104 tests [0;32mOK[0m
test_BiocCheck.R.............. 104 tests [0;32mOK[0m * Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
test_BiocCheck.R.............. 104 tests [0;32mOK[0m
test_BiocCheck.R.............. 105 tests [0;32mOK[0m
test_BiocCheck.R.............. 105 tests [0;32mOK[0m
test_BiocCheck.R.............. 105 tests [0;32mOK[0m * Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (100%).
test_BiocCheck.R.............. 105 tests [0;32mOK[0m
test_BiocCheck.R.............. 106 tests [0;32mOK[0m
test_BiocCheck.R.............. 106 tests [0;32mOK[0m
test_BiocCheck.R.............. 106 tests [0;32mOK[0m * Checking for pinned package versions in DESCRIPTION...
✖ ERROR: Dependencies in the DESCRIPTION file contain '=='
test_BiocCheck.R.............. 106 tests [0;32mOK[0m
test_BiocCheck.R.............. 107 tests [0;32mOK[0m
test_BiocCheck.R.............. 107 tests [0;32mOK[0m
test_BiocCheck.R.............. 107 tests [0;32mOK[0m ✖ ERROR: Package dependencies must be on CRAN or Bioconductor. Remove
'Remotes:' from DESCRIPTION
test_BiocCheck.R.............. 107 tests [0;32mOK[0m
test_BiocCheck.R.............. 108 tests [0;32mOK[0m
test_BiocCheck.R.............. 109 tests [0;32mOK[0m
test_BiocCheck.R.............. 109 tests [0;32mOK[0m
test_BiocCheck.R.............. 109 tests [0;32mOK[0m
test_BiocCheck.R.............. 109 tests [0;32mOK[0m
test_BiocCheck.R.............. 110 tests [0;32mOK[0m
test_BiocCheck.R.............. 110 tests [0;32mOK[0m
test_BiocCheck.R.............. 110 tests [0;32mOK[0m ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
test_BiocCheck.R.............. 110 tests [0;32mOK[0m
test_BiocCheck.R.............. 111 tests [0;32mOK[0m
test_BiocCheck.R.............. 111 tests [0;32mOK[0m
test_BiocCheck.R.............. 111 tests [0;32mOK[0m ! WARNING: Avoid the use of 'library' or 'require' in R code
Found in files:
• library() in R/requireme.R (line 3, column 5)
• ...
• require() in R/requireme.R (line 18, column 5)
test_BiocCheck.R.............. 111 tests [0;32mOK[0m
test_BiocCheck.R.............. 112 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 113 tests [0;32mOK[0m
test_BiocCheck.R.............. 114 tests [0;32mOK[0m
test_BiocCheck.R.............. 114 tests [0;32mOK[0m
test_BiocCheck.R.............. 114 tests [0;32mOK[0m ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• really_long_function() (R/bad_coding.R): 53 lines
test_BiocCheck.R.............. 114 tests [0;32mOK[0m
test_BiocCheck.R.............. 115 tests [0;32mOK[0m
test_BiocCheck.R.............. 116 tests [0;32mOK[0m
test_BiocCheck.R.............. 116 tests [0;32mOK[0m
test_BiocCheck.R.............. 116 tests [0;32mOK[0m
test_BiocCheck.R.............. 116 tests [0;32mOK[0m ✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• baddep.Rd
test_BiocCheck.R.............. 116 tests [0;32mOK[0m
test_BiocCheck.R.............. 117 tests [0;32mOK[0m
test_BiocCheck.R.............. 117 tests [0;32mOK[0m ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
Found in files:
• a.Rd
• baddep.Rd
ℹ NOTE: Use donttest instead of dontrun.
Found in files:
• baddep.Rd
test_BiocCheck.R.............. 117 tests [0;32mOK[0m
test_BiocCheck.R.............. 118 tests [0;32mOK[0m
test_BiocCheck.R.............. 118 tests [0;32mOK[0m ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
test_BiocCheck.R.............. 118 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 119 tests [0;32mOK[0m ! WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be
included in Bioconductor release announcements.
test_BiocCheck.R.............. 119 tests [0;32mOK[0m
test_BiocCheck.R.............. 120 tests [0;32mOK[0m
test_BiocCheck.R.............. 120 tests [0;32mOK[0m
test_BiocCheck.R.............. 120 tests [0;32mOK[0m ℹ NOTE: More than 1 NEWS file found. See ?news for recognition ordering.
Please remove one of the following:
• /inst/NEWS.Rd
• /./NEWS.md
! WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be
included in Bioconductor release announcements.
test_BiocCheck.R.............. 120 tests [0;32mOK[0m
test_BiocCheck.R.............. 121 tests [0;32mOK[0m
test_BiocCheck.R.............. 122 tests [0;32mOK[0m
test_BiocCheck.R.............. 122 tests [0;32mOK[0m
test_BiocCheck.R.............. 122 tests [0;32mOK[0m ℹ NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long.
First few lines:
• R/morebadcode.R#L2 # this is a really long line with many c ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
First few lines:
• man/a.Rd#L48 ##-- or do help(data=index) for the st ...
• man/baddep.Rd#L41 ##-- or do help(data=index) for the st ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 52 lines (9%) are not.
First few lines:
• R/bad_coding.R#L86 ...
• ...
• R/morebadcode.R#L6 # something other than a multiple o ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
test_BiocCheck.R.............. 122 tests [0;32mOK[0m
test_BiocCheck.R.............. 123 tests [0;32mOK[0m
test_BiocCheck.R.............. 123 tests [0;32mOK[0m
test_BiocCheck.R.............. 123 tests [0;32mOK[0m ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
• man/a.Rd
• man/baddep.Rd
test_BiocCheck.R.............. 123 tests [0;32mOK[0m
test_BiocCheck.R.............. 124 tests [0;32mOK[0m
test_BiocCheck.R.............. 124 tests [0;32mOK[0m
test_BiocCheck.R.............. 124 tests [0;32mOK[0m
test_BiocCheck.R.............. 124 tests [0;32mOK[0m
test_BiocCheck.R.............. 125 tests [0;32mOK[0m
test_BiocCheck.R.............. 125 tests [0;32mOK[0m
test_BiocCheck.R.............. 126 tests [0;32mOK[0m
test_BiocCheck.R.............. 126 tests [0;32mOK[0m
test_BiocCheck.R.............. 127 tests [0;32mOK[0m
test_BiocCheck.R.............. 127 tests [0;32mOK[0m
test_BiocCheck.R.............. 128 tests [0;32mOK[0m
test_BiocCheck.R.............. 128 tests [0;32mOK[0m
test_BiocCheck.R.............. 129 tests [0;32mOK[0m
test_BiocCheck.R.............. 129 tests [0;32mOK[0m
test_BiocCheck.R.............. 130 tests [0;32mOK[0m
test_BiocCheck.R.............. 130 tests [0;32mOK[0m
test_BiocCheck.R.............. 130 tests [0;32mOK[0m
test_BiocCheck.R.............. 130 tests [0;32mOK[0m ℹ Maintainer is registered at support site.
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
ℹ Package is in the Support Site Watched Tags.
ℹ Package is in the Support Site Watched Tags.
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/tmp/RtmpxHoKJo/file3ca625f7fde3/file3ca63c3d558e/DESCRIPTION’ ... OK
* preparing ‘file3ca63c3d558e’:
* 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 ‘file3ca63c3d558e/R’
* building ‘file3ca63c3d558e_0.0.1.tar.gz’
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 137 tests [0;32mOK[0m ✖ ERROR: Version number in tarball filename must match Version field in
DESCRIPTION. (Tip: create tarball with R CMD build)
test_BiocCheck.R.............. 137 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 138 tests [0;32mOK[0m ℹ Found @ in ./FooBar
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
test_BiocCheck.R.............. 138 tests [0;32mOK[0m
test_BiocCheck.R.............. 139 tests [0;32mOK[0m
test_BiocCheck.R.............. 139 tests [0;32mOK[0m
test_BiocCheck.R.............. 139 tests [0;32mOK[0m
test_BiocCheck.R.............. 139 tests [0;32mOK[0m
test_BiocCheck.R.............. 140 tests [0;32mOK[0m
test_BiocCheck.R.............. 140 tests [0;32mOK[0m
test_BiocCheck.R.............. 140 tests [0;32mOK[0m
test_BiocCheck.R.............. 140 tests [0;32mOK[0m
test_BiocCheck.R.............. 140 tests [0;32mOK[0m ℹ NOTE: Update R version dependency from 1.0.0 to 4.4.0.
test_BiocCheck.R.............. 140 tests [0;32mOK[0m
test_BiocCheck.R.............. 141 tests [0;32mOK[0m
test_BiocCheck.R.............. 141 tests [0;32mOK[0m
test_BiocCheck.R.............. 141 tests [0;32mOK[0m
test_BiocCheck.R.............. 141 tests [0;32mOK[0m
test_BiocCheck.R.............. 142 tests [0;32mOK[0m
test_BiocCheck.R.............. 142 tests [0;32mOK[0m
test_BiocCheck.R.............. 142 tests [0;32mOK[0m
test_BiocCheck.R.............. 142 tests [0;32mOK[0m
test_BiocCheck.R.............. 143 tests [0;32mOK[0m
test_BiocCheck.R.............. 143 tests [0;32mOK[0m
test_BiocCheck.R.............. 143 tests [0;32mOK[0m
test_BiocCheck.R.............. 143 tests [0;32mOK[0m
test_BiocCheck.R.............. 144 tests [0;32mOK[0m
test_BiocCheck.R.............. 144 tests [0;32mOK[0m
test_BiocCheck.R.............. 144 tests [0;32mOK[0m
test_BiocCheck.R.............. 144 tests [0;32mOK[0m
test_BiocCheck.R.............. 144 tests [0;32mOK[0m
test_BiocCheck.R.............. 145 tests [0;32mOK[0m
test_BiocCheck.R.............. 146 tests [0;32mOK[0m
test_BiocCheck.R.............. 146 tests [0;32mOK[0m
test_BiocCheck.R.............. 146 tests [0;32mOK[0m
test_BiocCheck.R.............. 146 tests [0;32mOK[0m
test_BiocCheck.R.............. 147 tests [0;32mOK[0m
test_BiocCheck.R.............. 148 tests [0;32mOK[0m
test_BiocCheck.R.............. 149 tests [0;32mOK[0m
test_BiocCheck.R.............. 149 tests [0;32mOK[0m
test_BiocCheck.R.............. 149 tests [0;32mOK[0m
test_BiocCheck.R.............. 149 tests [0;32mOK[0m
test_BiocCheck.R.............. 150 tests [0;32mOK[0m
test_BiocCheck.R.............. 151 tests [0;32mOK[0m
test_BiocCheck.R.............. 151 tests [0;32mOK[0m
test_BiocCheck.R.............. 151 tests [0;32mOK[0m
test_BiocCheck.R.............. 151 tests [0;32mOK[0m
test_BiocCheck.R.............. 152 tests [0;32mOK[0m ! WARNING: The package already exists on CRAN. Packages submitted to
Bioconductor must be removed from CRAN before the next Bioconductor release.
test_BiocCheck.R.............. 152 tests [0;32mOK[0m
test_BiocCheck.R.............. 153 tests [0;32mOK[0m ✖ ERROR: 'GenomicRanges' already exists in Bioconductor.
test_BiocCheck.R.............. 153 tests [0;32mOK[0m
test_BiocCheck.R.............. 153 tests [0;32mOK[0m
test_BiocCheck.R.............. 154 tests [0;32mOK[0m ✖ ERROR: 'gwascatData' already exists in Bioconductor.
test_BiocCheck.R.............. 154 tests [0;32mOK[0m
test_BiocCheck.R.............. 154 tests [0;32mOK[0m
test_BiocCheck.R.............. 155 tests [0;32mOK[0m ✖ ERROR: 'TENxBrainData' already exists in Bioconductor.
test_BiocCheck.R.............. 155 tests [0;32mOK[0m
test_BiocCheck.R.............. 155 tests [0;32mOK[0m
test_BiocCheck.R.............. 156 tests [0;32mOK[0m ✖ ERROR: 'annotation' already exists in Bioconductor.
test_BiocCheck.R.............. 156 tests [0;32mOK[0m
test_BiocCheck.R.............. 156 tests [0;32mOK[0m
test_BiocCheck.R.............. 157 tests [0;32mOK[0m
test_BiocCheck.R.............. 157 tests [0;32mOK[0m
test_BiocCheck.R.............. 158 tests [0;32mOK[0m
test_BiocCheck.R.............. 158 tests [0;32mOK[0m
test_BiocCheck.R.............. 159 tests [0;32mOK[0m
test_BiocCheck.R.............. 159 tests [0;32mOK[0m
test_BiocCheck.R.............. 160 tests [0;32mOK[0m
test_BiocCheck.R.............. 160 tests [0;32mOK[0m
test_BiocCheck.R.............. 161 tests [0;32mOK[0m
test_BiocCheck.R.............. 161 tests [0;32mOK[0m
test_BiocCheck.R.............. 162 tests [0;32mOK[0m
test_BiocCheck.R.............. 162 tests [0;32mOK[0m
test_BiocCheck.R.............. 163 tests [0;32mOK[0m
test_BiocCheck.R.............. 163 tests [0;32mOK[0m
test_BiocCheck.R.............. 164 tests [0;32mOK[0m
test_BiocCheck.R.............. 164 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 165 tests [0;32mOK[0m
test_BiocCheck.R.............. 166 tests [0;32mOK[0m
test_BiocCheck.R.............. 167 tests [0;32mOK[0m
test_BiocCheck.R.............. 167 tests [0;32mOK[0m
test_BiocCheck.R.............. 167 tests [0;32mOK[0m
test_BiocCheck.R.............. 167 tests [0;32mOK[0m $undefined
$undefined$checkVignetteDir
$undefined$checkVignetteDir[[1]]
$undefined$checkVignetteDir[[1]]$checkVignetteDir
[1] "No vignette sources in vignettes/ directory."
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "test.Rnw"
$undefined$checkVigTemplate
$undefined$checkVigTemplate[[1]]
$undefined$checkVigTemplate[[1]]$checkVigTemplate
[1] "Vignette(s) missing '\\%VignetteIndexEntry{{Vignette Title}}'. "
$undefined$checkVigTemplate[[2]]
[1] "Update the following files:"
$undefined$checkVigTemplate[[3]]
[1] "test.Rnw"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/test.Rnw
"vignettes/test.Rnw"
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "test.Rnw"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/test.Rnw
"vignettes/test.Rnw"
$undefined$checkInstContents
$undefined$checkInstContents[[1]]
$undefined$checkInstContents[[1]]$checkInstContents
[1] "Remove vignette sources from inst/doc; they belong in vignettes/."
$undefined$checkInstContents
$undefined$checkInstContents[[1]]
$undefined$checkInstContents[[1]]$checkInstContents
[1] "Remove vignette sources from inst/doc; they belong in vignettes/."
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "testpkg0.Rnw"
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "test.Rnw"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/test.Rnw
"vignettes/test.Rnw"
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "test.Rnw"
$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
$undefined$checkVigSuggests[[1]]$checkVigSuggests
[1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. "
$undefined$checkVigSuggests[[2]]
[1] "Add the following to Suggests in DESCRIPTION:"
$undefined$checkVigSuggests[[3]]
[1] "knitr"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/test.Rnw
"vignettes/test.Rnw"
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "test.Rnw"
$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
$undefined$checkVigSuggests[[1]]$checkVigSuggests
[1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. "
$undefined$checkVigSuggests[[2]]
[1] "Add the following to Suggests in DESCRIPTION:"
$undefined$checkVigSuggests[[3]]
[1] "Sweave"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/test.Rnw
"vignettes/test.Rnw"
$undefined$checkVigBuilder
$undefined$checkVigBuilder[[1]]
$undefined$checkVigBuilder[[1]]$checkVigBuilder
[1] "'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"
$undefined$checkVigBuilder[[2]]
[1] "knitr"
$undefined$checkVigMetadata
$undefined$checkVigMetadata[[1]]
$undefined$checkVigMetadata[[1]]$checkVigMetadata
[1] "Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html"
$undefined$checkVigMetadata[[2]]
[1] "Update the following files:"
$undefined$checkVigMetadata[[3]]
[1] "dupChunks.Rmd" "evalfalse.Rmd" "testpkg0.Rmd"
[4] "testpkg0_child.Rmd"
$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
$undefined$checkVigTypeRNW[[1]]$checkVigTypeRNW
[1] "Use RMarkdown instead of Sweave 'Rnw' vignettes."
$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"
$undefined$checkVigTypeRNW[[3]]
[1] "testpkg0.Rnw"
$undefined$checkVigEngine
$undefined$checkVigEngine[[1]]
$undefined$checkVigEngine[[1]]$checkVigEngine
[1] "No 'VignetteEngine' specified in vignette."
$undefined$checkVigEngine[[2]]
[1] "Add 'VignetteEngine' to the following files:"
$undefined$checkVigEngine[[3]]
[1] "vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd"
[3] "vignettes/testpkg0.Rmd" "vignettes/testpkg0_child.Rmd"
$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
$undefined$checkVigSuggests[[1]]$checkVigSuggests
[1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. "
$undefined$checkVigSuggests[[2]]
[1] "Add the following to Suggests in DESCRIPTION:"
$undefined$checkVigSuggests[[3]]
[1] "knitr"
$undefined$checkVigTemplate
$undefined$checkVigTemplate[[1]]
$undefined$checkVigTemplate[[1]]$checkVigTemplate
[1] "Vignette(s) still using 'VignetteIndexEntry{{Vignette Title}}' "
$undefined$checkVigTemplate[[2]]
[1] "The following files use template defaults:"
$undefined$checkVigTemplate[[3]]
[1] "testpkg0.Rmd"
$undefined$checkVigTemplate
$undefined$checkVigTemplate[[1]]
$undefined$checkVigTemplate[[1]]$checkVigTemplate
[1] "Vignette(s) missing '\\%VignetteIndexEntry{{Vignette Title}}'. "
$undefined$checkVigTemplate[[2]]
[1] "Update the following files:"
$undefined$checkVigTemplate[[3]]
[1] "dupChunks.Rmd" "evalfalse.Rmd" "testpkg0_child.Rmd"
$undefined$checkDupChunkLabels
$undefined$checkDupChunkLabels[[1]]
$undefined$checkDupChunkLabels[[1]]$checkDupChunkLabels
[1] " Vignette(s) found with duplicate chunk labels"
$undefined$checkDupChunkLabels[[2]]
[1] "Found in files:"
$undefined$checkDupChunkLabels[[3]]
[1] "dupChunks.Rmd"
$undefined$checkVigBiocInst
$undefined$checkVigBiocInst[[1]]
$undefined$checkVigBiocInst[[1]]$checkVigBiocInst
[1] " BiocInstaller code found in vignette(s)"
$undefined$checkVigBiocInst[[2]]
[1] "Found in files:"
$undefined$checkVigBiocInst[[3]]
$undefined$checkVigBiocInst[[3]]$`vignettes/testpkg0.Rmd`
[1] "vignettes/testpkg0.Rmd (code line 24, column 20)"
$undefined$checkVigInstalls
$undefined$checkVigInstalls[[1]]
$undefined$checkVigInstalls[[1]]$checkVigInstalls
[1] "Installation calls found in vignette(s)"
$undefined$checkVigInstalls[[2]]
[1] "Found in files:"
$undefined$checkVigInstalls[[3]]
[1] "vignettes/testpkg0.Rmd (code line 16, column 18)"
[2] "vignettes/testpkg0.Rmd (code line 24, column 20)"
[3] "vignettes/testpkg0.Rmd (code line 18, column 1)"
$undefined$checkVigClassUsage
$undefined$checkVigClassUsage[[1]]
$undefined$checkVigClassUsage[[1]]$checkVigClassUsage
[1] " Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes"
$undefined$checkVigClassUsage[[2]]
[1] "Found in files:"
$undefined$checkVigClassUsage[[3]]
[1] "testpkg0.Rmd (code line 64, column 10)"
[2] "testpkg0_child.Rmd (code line 3, column 10)"
$undefined$checkTFSymbolUsage
$undefined$checkTFSymbolUsage[[1]]
$undefined$checkTFSymbolUsage[[1]]$checkTFSymbolUsage
[1] " Avoid T/F variables; If logical, use TRUE/FALSE"
$undefined$checkTFSymbolUsage[[2]]
[1] "Found in files:"
$undefined$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 47, column 5)"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/dupChunks.Rmd vignettes/evalfalse.Rmd
"vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd"
vignettes/testpkg0.Rnw vignettes/testpkg0_child.Rmd
"vignettes/testpkg0.Rnw" "vignettes/testpkg0_child.Rmd"
$undefined$checkVigEvalAllFalse
$undefined$checkVigEvalAllFalse[[1]]
$undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse
[1] " Vignette set global option 'eval=FALSE'"
$undefined$checkVigEvalAllFalse[[2]]
[1] "Found in files:"
$undefined$checkVigEvalAllFalse[[3]]
[1] "vignettes/evalfalse.Rmd"
$undefined$checkVigEvalAllFalse
$undefined$checkVigEvalAllFalse[[1]]
$undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse
[1] " Vignette set global option 'eval=FALSE'"
$undefined$checkVigEvalAllFalse[[2]]
[1] "Found in files:"
$undefined$checkVigEvalAllFalse[[3]]
[1] "vignettes/evalfalse.Rmd"
$undefined$checkVigFiles
$undefined$checkVigFiles[[1]]
$undefined$checkVigFiles[[1]]$checkVigFiles
[1] "Potential intermediate files found:"
$undefined$checkVigFiles[[2]]
[1] "vignettes/testpkg0.html"
$undefined$checkVigBuilder
$undefined$checkVigBuilder[[1]]
$undefined$checkVigBuilder[[1]]$checkVigBuilder
[1] "'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"
$undefined$checkVigBuilder[[2]]
[1] "FailBuilder"
$undefined$checkVigMetadata
$undefined$checkVigMetadata[[1]]
$undefined$checkVigMetadata[[1]]$checkVigMetadata
[1] "Vignette(s) missing Vignette metadata. See http://r-pkgs.had.co.nz/vignettes.html"
$undefined$checkVigMetadata[[2]]
[1] "Update the following files:"
$undefined$checkVigMetadata[[3]]
[1] "testpkg0.Rmd"
$undefined$checkVigEngine
$undefined$checkVigEngine[[1]]
$undefined$checkVigEngine[[1]]$checkVigEngine
[1] "More than one VignetteEngine specified."
$undefined$checkVigEngine[[2]]
[1] "Found in files:"
$undefined$checkVigEngine[[3]]
[1] "vignettes/testpkg0.Rmd"
$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
$undefined$checkVigSuggests[[1]]$checkVigSuggests
[1] "Package listed as VignetteEngine or VignetteBuilder but not currently Suggested. "
$undefined$checkVigSuggests[[2]]
[1] "Add the following to Suggests in DESCRIPTION:"
$undefined$checkVigSuggests[[3]]
[1] "ThisWillFail" "FailBuilder"
$undefined$checkVigChunkEval
$undefined$checkVigChunkEval[[1]]
$undefined$checkVigChunkEval[[1]]$checkVigChunkEval
[1] "Evaluate more vignette chunks."
$undefined$checkTFSymbolUsage
$undefined$checkTFSymbolUsage[[1]]
$undefined$checkTFSymbolUsage[[1]]$checkTFSymbolUsage
[1] " Avoid T/F variables; If logical, use TRUE/FALSE"
$undefined$checkTFSymbolUsage[[2]]
[1] "Found in files:"
$undefined$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 9, column 7)"
$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
$undefined$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$undefined$checkVigSessionInfo[[3]]
vignettes/testpkg0.Rmd
"vignettes/testpkg0.Rmd"
$undefined$checkVigEvalAllFalse
$undefined$checkVigEvalAllFalse[[1]]
$undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse
[1] " Vignette set global option 'eval=FALSE'"
$undefined$checkVigEvalAllFalse[[2]]
[1] "Found in files:"
$undefined$checkVigEvalAllFalse[[3]]
[1] "vignettes/testpkg0.Rmd"
$undefined$checkVigFiles
$undefined$checkVigFiles[[1]]
$undefined$checkVigFiles[[1]]$checkVigFiles
[1] "Potential intermediate files found:"
$undefined$checkVigFiles[[2]]
[1] "vignettes/testpkg0.html"
$undefined$checkVigEvalAllFalse
$undefined$checkVigEvalAllFalse[[1]]
$undefined$checkVigEvalAllFalse[[1]]$checkVigEvalAllFalse
[1] " Vignette set global option 'eval=FALSE'"
$undefined$checkVigEvalAllFalse[[2]]
[1] "Found in files:"
$undefined$checkVigEvalAllFalse[[3]]
[1] "vignettes/testpkg0.Rmd"
$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
$undefined$checkVersionNumber[[1]]$checkVersionNumber
[1] "Invalid package Version, see https://contributions.bioconductor.org/versionnum.html"
$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
$undefined$checkVersionNumber[[1]]$checkVersionNumber
[1] "Invalid package Version, see https://contributions.bioconductor.org/versionnum.html"
$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
$undefined$checkVersionNumber[[1]]$checkVersionNumber
[1] "y of x.y.z version should be even in release"
$undefined$checkNewPackageVersionNumber
$undefined$checkNewPackageVersionNumber[[1]]
$undefined$checkNewPackageVersionNumber[[1]]$checkNewPackageVersionNumber
[1] "New package x version starting with non-zero value (e.g., 1.y.z, 2.y.z); got '1.99.3'."
$undefined$checkNewPackageVersionNumber
$undefined$checkNewPackageVersionNumber[[1]]
$undefined$checkNewPackageVersionNumber[[1]]$checkNewPackageVersionNumber
[1] "New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3"
$undefined$checkBiocCheckOutputFolder
$undefined$checkBiocCheckOutputFolder[[1]]
$undefined$checkBiocCheckOutputFolder[[1]]$checkBiocCheckOutputFolder
[1] "Remove 'file3ca625740312.BiocCheck' from the package directory"
$undefined$checkInstDocFolder
$undefined$checkInstDocFolder[[1]]
$undefined$checkInstDocFolder[[1]]$checkInstDocFolder
[1] "Remove 'inst/doc' folder from the package source"
$`Checking that biocViews are present...`
list()
$`Checking package type based on biocViews...`
list()
$`Checking for non-trivial biocViews...`
list()
$`Checking that biocViews come from the same category...`
$`Checking that biocViews come from the same category...`$checkBiocViews
$`Checking that biocViews come from the same category...`$checkBiocViews[[1]]
$`Checking that biocViews come from the same category...`$checkBiocViews[[1]]$checkBiocViews
[1] "Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow)"
$`Checking that biocViews come from the same category...`$checkBadFiles
$`Checking that biocViews come from the same category...`$checkBadFiles[[1]]
$`Checking that biocViews come from the same category...`$checkBadFiles[[1]]$checkBadFiles
[1] "System files found that should not be Git tracked."
$`Checking that biocViews come from the same category...`$checkBadFiles[[2]]
[1] "something.Rproj"
$`Checking biocViews validity...`
list()
$`Checking for recommended biocViews...`
list()
$`Checking License: for restrictive use...`
$`Checking License: for restrictive use...`$checkIndivFileSizes
$`Checking License: for restrictive use...`$checkIndivFileSizes[[1]]
$`Checking License: for restrictive use...`$checkIndivFileSizes[[1]]$checkIndivFileSizes
[1] "Package files exceed the 5MB size limit."
$`Checking License: for restrictive use...`$checkIndivFileSizes[[2]]
[1] "Files over the limit: "
$`Checking License: for restrictive use...`$checkIndivFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"
$`Checking License: for restrictive use...`$checkDataFileSizes
$`Checking License: for restrictive use...`$checkDataFileSizes[[1]]
$`Checking License: for restrictive use...`$checkDataFileSizes[[1]]$checkDataFileSizes
[1] "Data files exceed the 5MB size limit."
$`Checking License: for restrictive use...`$checkDataFileSizes[[2]]
[1] "Use 'ExperimentHub' or 'AnnotationHub' for the files: "
$`Checking License: for restrictive use...`$checkDataFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"
$`Checking for proper Description: field...`
list()
$`Checking if DESCRIPTION is well formatted...`
list()
$`Checking for whitespace in DESCRIPTION field names...`
list()
$`Checking that Package field matches directory/tarball name...`
list()
$`Checking for Version: field...`
list()
$`Checking for valid maintainer...`
$`Checking for valid maintainer...`$validMaintainer
$`Checking for valid maintainer...`$validMaintainer[[1]]
$`Checking for valid maintainer...`$validMaintainer[[1]]$validMaintainer
[1] "Use Authors@R field not Author/Maintainer fields. Do not use both."
$`Checking for valid maintainer...`$checkBBScompatibility
$`Checking for valid maintainer...`$checkBBScompatibility[[1]]
$`Checking for valid maintainer...`$checkBBScompatibility[[1]]$checkBBScompatibility
[1] "Designate only one maintainer with Authors@R [cre]."
$`Checking for valid maintainer...`$checkBBScompatibility
$`Checking for valid maintainer...`$checkBBScompatibility[[1]]
$`Checking for valid maintainer...`$checkBBScompatibility[[1]]$checkBBScompatibility
[1] "Invalid ORCID iD for Bioconductor Package Maintainer "
$`Checking that provided CITATION file is correctly formatted...`
$`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile
$`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkForCitationFile[[1]]$checkForCitationFile
[1] "Unable to read CITATION file with 'utils::readCitationFile()'"
$`Checking that provided CITATION file is correctly formatted...`$checkUnitTests
$`Checking that provided CITATION file is correctly formatted...`$checkUnitTests[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkUnitTests[[1]]$checkUnitTests
[1] "Consider adding unit tests. We strongly encourage them. See\n https://contributions.bioconductor.org/tests.html"
$`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc
$`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkSkipOnBioc[[1]]$checkSkipOnBioc
[1] "skip_on_bioc() found in testthat files: a_test.R"
$`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages
$`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkDeprecatedPackages[[1]]$checkDeprecatedPackages
[1] "Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows."
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]]$checkVigInstalls
[1] "Installation calls found in vignette(s)"
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[2]]
[1] "Found in files:"
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[3]]
[1] "vignettes/testpkg0.Rmd (code line 16, column 18)"
[2] "vignettes/testpkg0.Rmd (code line 24, column 20)"
[3] "vignettes/testpkg0.Rmd (code line 18, column 1)"
$`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels
$`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[1]]$checkDupChunkLabels
[1] " Vignette(s) found with duplicate chunk labels"
$`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[2]]
[1] "Found in files:"
$`Checking that provided CITATION file is correctly formatted...`$checkDupChunkLabels[[3]]
[1] "dupChunks.Rmd"
$`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage
$`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[1]]$checkTFSymbolUsage
[1] " Avoid T/F variables; If logical, use TRUE/FALSE"
$`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[2]]
[1] "Found in files:"
$`Checking that provided CITATION file is correctly formatted...`$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 47, column 5)"
$`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo
$`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[1]]$checkVigSessionInfo
[1] " 'sessionInfo' not found in vignette(s)"
$`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"
$`Checking that provided CITATION file is correctly formatted...`$checkVigSessionInfo[[3]]
vignettes/dupChunks.Rmd vignettes/evalfalse.Rmd
"vignettes/dupChunks.Rmd" "vignettes/evalfalse.Rmd"
vignettes/testpkg0.Rnw vignettes/testpkg0_child.Rmd
"vignettes/testpkg0.Rnw" "vignettes/testpkg0_child.Rmd"
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[1]]$checkVigBiocInst
[1] " BiocInstaller code found in vignette(s)"
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[2]]
[1] "Found in files:"
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[3]]
$`Checking that provided CITATION file is correctly formatted...`$checkVigBiocInst[[3]]$`vignettes/testpkg0.Rmd`
[1] "vignettes/testpkg0.Rmd (code line 24, column 20)"
$`Checking for recommended DESCRIPTION fields...`
list()
$`Checking for Bioconductor software dependencies...`
list()
$`Checking for pinned package versions in DESCRIPTION...`
$`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps
$`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkPinnedDeps[[1]]$checkPinnedDeps
[1] "Dependencies in the DESCRIPTION file contain '=='"
$`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage
$`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage[[1]]$checkRemotesUsage
[1] "Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION"
$`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage
$`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkLazyDataUsage[[1]]$checkLazyDataUsage
[1] "'LazyData:' in the 'DESCRIPTION' should be set to false or removed"
$`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire
$`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[1]]$checkForLibraryRequire
[1] " Avoid the use of 'library' or 'require' in R code"
$`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[2]]
[1] "Found in files:"
$`Checking for pinned package versions in DESCRIPTION...`$checkForLibraryRequire[[3]]
[1] "library() in R/requireme.R (line 3, column 5)"
[2] "library() in R/requireme.R (line 5, column 5)"
[3] "library() in R/requireme.R (line 7, column 5)"
[4] "library() in R/requireme.R (line 8, column 5)"
[5] "library() in R/requireme.R (line 13, column 5)"
[6] "require() in R/requireme.R (line 4, column 5)"
[7] "require() in R/requireme.R (line 6, column 5)"
[8] "require() in R/requireme.R (line 9, column 5)"
[9] "require() in R/requireme.R (line 10, column 5)"
[10] "require() in R/requireme.R (line 11, column 5)"
[11] "require() in R/requireme.R (line 12, column 5)"
[12] "require() in R/requireme.R (line 14, column 5)"
[13] "require() in R/requireme.R (line 17, column 5)"
[14] "require() in R/requireme.R (line 18, column 5)"
$`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths
$`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[1]]$checkFunctionLengths
[1] "The recommended function length is 50 lines or less. There is 1 function greater than 50 lines."
$`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[2]]
[1] "The longest 5 functions are:"
$`Checking for pinned package versions in DESCRIPTION...`$checkFunctionLengths[[3]]
R/bad_coding.R.15
"really_long_function() (R/bad_coding.R): 53 lines"
$`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented
$`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[1]]$checkExportsAreDocumented
[1] "At least 80% of man pages documenting exported objects must have runnable examples."
$`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[2]]
[1] "The following pages do not:"
$`Checking for pinned package versions in DESCRIPTION...`$checkExportsAreDocumented[[3]]
[1] "baddep.Rd"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont
[1] "Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "a.Rd" "baddep.Rd"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont
[1] "Use donttest{} instead of dontrun{}."
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]$checkNEWS
[1] "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."
$`Checking for pinned package versions in DESCRIPTION...`$`3`
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]$`3`
[1] "Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[1]]$checkNEWS
[1] "More than 1 NEWS file found. See ?news for recognition ordering."
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[2]]
[1] "Please remove one of the following: "
$`Checking for pinned package versions in DESCRIPTION...`$checkNEWS[[3]]
[1] "/inst/NEWS.Rd" "/./NEWS.md"
$`Checking for pinned package versions in DESCRIPTION...`$`3`
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]$`3`
[1] "Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting
[1] "Consider shorter lines; 1 lines (0%) are > 80 characters long."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
[1] "R/morebadcode.R#L2 # this is a really long line with many c ..."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting
[1] "Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
[1] "man/a.Rd#L48 ##--\tor do help(data=index) for the st ..."
[2] "man/baddep.Rd#L41 ##--\tor do help(data=index) for the st ..."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[1]]$checkFormatting
[1] "Consider multiples of 4 spaces for line indents; 52 lines (9%) are not."
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[2]]
[1] "First few lines:"
$`Checking for pinned package versions in DESCRIPTION...`$checkFormatting[[3]]
[1] "R/bad_coding.R#L86 ..."
[2] "R/bad_coding.R#L87 ..."
[3] "R/bad_coding.R#L88 ..."
[4] "R/bad_coding.R#L89 ..."
[5] "R/bad_coding.R#L90 ..."
[6] "R/bad_coding.R#L91 ..."
[7] "R/bad_coding.R#L92 ..."
[8] "R/bad_coding.R#L93 ..."
[9] "R/bad_coding.R#L94 ..."
[10] "R/bad_coding.R#L95 ..."
[11] "R/bad_coding.R#L96 ..."
[12] "R/bad_coding.R#L97 ..."
[13] "R/bad_coding.R#L98 ..."
[14] "R/bad_coding.R#L99 ..."
[15] "R/bad_coding.R#L100 ..."
[16] "R/bad_coding.R#L101 ..."
[17] "R/bad_coding.R#L102 ..."
[18] "R/bad_coding.R#L103 ..."
[19] "R/bad_coding.R#L104 ..."
[20] "R/bad_coding.R#L105 ..."
[21] "R/bad_coding.R#L106 ..."
[22] "R/bad_coding.R#L107 ..."
[23] "R/bad_coding.R#L108 ..."
[24] "R/bad_coding.R#L109 ..."
[25] "R/bad_coding.R#L110 ..."
[26] "R/bad_coding.R#L111 ..."
[27] "R/bad_coding.R#L112 ..."
[28] "R/bad_coding.R#L113 ..."
[29] "R/bad_coding.R#L114 ..."
[30] "R/bad_coding.R#L115 ..."
[31] "R/bad_coding.R#L116 ..."
[32] "R/bad_coding.R#L117 ..."
[33] "R/bad_coding.R#L118 ..."
[34] "R/bad_coding.R#L119 ..."
[35] "R/bad_coding.R#L120 ..."
[36] "R/bad_coding.R#L121 ..."
[37] "R/bad_coding.R#L122 ..."
[38] "R/bad_coding.R#L123 ..."
[39] "R/bad_coding.R#L124 ..."
[40] "R/bad_coding.R#L125 ..."
[41] "R/bad_coding.R#L126 ..."
[42] "R/bad_coding.R#L127 ..."
[43] "R/bad_coding.R#L128 ..."
[44] "R/bad_coding.R#L129 ..."
[45] "R/bad_coding.R#L130 ..."
[46] "R/bad_coding.R#L131 ..."
[47] "R/bad_coding.R#L132 ..."
[48] "R/bad_coding.R#L133 ..."
[49] "R/bad_coding.R#L134 ..."
[50] "R/bad_coding.R#L135 ..."
[51] "R/bad_coding.R#L136 return(TRUE) ..."
[52] "R/morebadcode.R#L6 # something other than a multiple o ..."
$`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments
$`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[1]]$checkForPromptComments
[1] "Auto-generated '%% ~' comments found in Rd man pages."
$`Checking for pinned package versions in DESCRIPTION...`$checkForPromptComments[[2]]
[1] "man/a.Rd" "man/baddep.Rd"
$`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg
$`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkSupportReg[[1]]$checkSupportReg
[1] "Unable to find your email in the Support Site:\n HTTP 404 Not Found."
$`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag
$`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkWatchedTag[[1]]$checkWatchedTag
[1] "Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile"
$`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch
$`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkForVersionNumberMismatch[[1]]$checkForVersionNumberMismatch
[1] "Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build)"
$`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess
$`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess[[1]]$checkForDirectSlotAccess
[1] "Use accessors; don't access S4 class slots via '@' in examples/vignettes."
$`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency
$`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkRVersionDependency[[1]]$checkRVersionDependency
[1] "Update R version dependency from 1.0.0 to 4.4.0."
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse
[1] "The package already exists on CRAN. Packages submitted to Bioconductor must be removed from CRAN before the next Bioconductor release."
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse
[1] "'GenomicRanges' already exists in Bioconductor."
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse
[1] "'gwascatData' already exists in Bioconductor."
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse
[1] "'TENxBrainData' already exists in Bioconductor."
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]$checkIsPackageNameAlreadyInUse
[1] "'annotation' already exists in Bioconductor."
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont
[1] "Usage of dontrun{} / donttest{} tags found in man page examples. 67% of man pages use at least one of these tags."
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "a.Rd" "baddep.Rd"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]$checkUsageOfDont
[1] "Use donttest{} instead of dontrun{}."
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[2]]
[1] "Found in files:"
$`Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"
test_BiocCheck.R.............. 167 tests [0;32mOK[0m
test_BiocCheck.R.............. 168 tests [0;32mOK[0m
test_BiocCheck.R.............. 169 tests [0;32mOK[0m
test_BiocCheck.R.............. 169 tests [0;32mOK[0m
test_BiocCheck.R.............. 169 tests [0;32mOK[0m
test_BiocCheck.R.............. 169 tests [0;32mOK[0m
test_BiocCheck.R.............. 169 tests [0;32mOK[0m
test_BiocCheck.R.............. 170 tests [0;32mOK[0m
test_BiocCheck.R.............. 170 tests [0;32mOK[0m
test_BiocCheck.R.............. 170 tests [0;32mOK[0m
test_BiocCheck.R.............. 170 tests [0;32mOK[0m
test_BiocCheck.R.............. 171 tests [0;32mOK[0m
test_BiocCheck.R.............. 171 tests [0;32mOK[0m
test_BiocCheck.R.............. 172 tests [0;32mOK[0m
test_BiocCheck.R.............. 173 tests [0;32mOK[0m
test_BiocCheck.R.............. 173 tests [0;32mOK[0m
test_BiocCheck.R.............. 173 tests [0;32mOK[0m
test_BiocCheck.R.............. 174 tests [0;32mOK[0m
test_BiocCheck.R.............. 175 tests [0;32mOK[0m [0;34m2.0s[0m
All ok, 175 results (2m 1.7s)
Warning message:
In file.remove(newname) :
cannot remove file '/private/tmp/RtmpxHoKJo/file3ca625f7fde3/file3ca63c3d558e_9.9.9.tar.gz', reason 'No such file or directory'
>
> proc.time()
user system elapsed
96.613 16.034 123.965
BiocCheck.Rcheck/BiocCheck-Ex.timings
| name | user | system | elapsed | |
| BiocCheck-class | 0.001 | 0.000 | 0.001 | |
| BiocCheck | 18.459 | 5.020 | 28.299 | |
| BiocCheckGitClone | 0.523 | 0.015 | 0.538 | |
| BiocPackage-class | 0.000 | 0.001 | 0.000 | |