Multiple platform build/check report for BioC 3.20 - CHECK results for BiocCheck on nebbiolo2

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"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
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*

CHECK results for BiocCheck on nebbiolo2

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.

raw results

Summary

Package: BiocCheck

Version: 1.42.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiocCheck_1.42.0.tar.gz

StartedAt: 2024-11-28 20:35:40 -0500 (Thu, 28 Nov 2024)

EndedAt: 2024-11-28 20:42:21 -0500 (Thu, 28 Nov 2024)

EllapsedTime: 401.3 seconds

RetCode: 0

Status: OK

CheckDir: BiocCheck.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiocCheck_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocCheck’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘knitr:::detect_pattern’
  ‘tools:::.build_news_db_from_package_NEWS_Rd’
  ‘tools:::.build_news_db_from_package_NEWS_md’
  ‘tools:::.news_reader_default’ ‘tools:::RdTags’
  ‘tools:::analyze_licenses’ ‘tools:::str_parse_logic’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘BiocCheckRun’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
BiocCheck 15.17  3.563  21.204
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.

Installation output

BiocCheck.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BiocCheck
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

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: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("BiocCheck")
 You are using 'tinytest::' to express test expectations.
 The results from these tests are not collected. Found the following occurrences:
 > test_BiocCheck.R#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 'file59d98572526f.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 'file59d98a0f9fee' 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 ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpndlcb3/file59d98c083217/file59d9862dfdab6/DESCRIPTION’ ... OK
* preparing ‘file59d9862dfdab6’:
* 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 ‘file59d9862dfdab6/R’
* building ‘file59d9862dfdab6_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 ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpndlcb3/file59d983471ceab/file59d984c5a1223/DESCRIPTION’ ... OK
* preparing ‘file59d984c5a1223’:
* 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 ‘file59d984c5a1223/R’
* building ‘file59d984c5a1223_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 'file59d98572526f.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;34m1.6s[0m
All ok, 175 results (1m 36.5s)
Warning message:
In file.remove(newname) :
  cannot remove file '/home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpndlcb3/file59d983471ceab/file59d984c5a1223_9.9.9.tar.gz', reason 'No such file or directory'
> 
> proc.time()
   user  system elapsed 
 80.844  11.862  98.491

Example timings

BiocCheck.Rcheck/BiocCheck-Ex.timings

name	user	system	elapsed
BiocCheck-class	0.001	0.000	0.000
BiocCheck	15.170	3.563	21.204
BiocCheckGitClone	0.437	0.019	0.455
BiocPackage-class	0.001	0.000	0.000