Back to Rapid builds (Linux only) of a subset of BioC 3.22
Report updated every 6 hours

This page was generated on 2025-06-17 22:14 -0400 (Tue, 17 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 886
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 28/221HostnameOS / ArchINSTALLBUILDCHECK
BiocCheck 1.45.7  (landing page)
Marcel Ramos
Snapshot Date: 2025-06-17 18:00 -0400 (Tue, 17 Jun 2025)
git_url: https://git.bioconductor.org/packages/BiocCheck
git_branch: devel
git_last_commit: d57c0ff
git_last_commit_date: 2025-05-15 22:16:42 -0400 (Thu, 15 May 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  

CHECK results for BiocCheck on teran2

To the developers/maintainers of the BiocCheck package:
- 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: 1.45.7
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings BiocCheck_1.45.7.tar.gz
StartedAt: 2025-06-17 20:01:14 -0400 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 20:04:00 -0400 (Tue, 17 Jun 2025)
EllapsedTime: 165.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocCheck.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings BiocCheck_1.45.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/BiocCheck.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.45.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocCheck’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘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 13.188  5.411  29.676
* 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
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/BiocCheck.Rcheck/00check.log’
for details.

Installation output

BiocCheck.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL BiocCheck
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘BiocCheck’ ...
** this is package ‘BiocCheck’ version ‘1.45.7’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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#181: tinytest::expect_match
 > test_BiocCheck.R#680: tinytest::expect_match
 > test_BiocCheck.R#711: tinytest::expect_match 
 Remove the 'tinytest::' prefix to register the test results.FALSE

test_BiocCheck.R..............    0 tests    Loading required package: usethis

test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    0 tests    ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html

test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    0 tests    ✖ ERROR: Invalid package Version, see
https://contributions.bioconductor.org/versionnum.html

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    ! WARNING: y of x.y.z version should be even in release

test_BiocCheck.R..............    0 tests    
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK ! 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..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK ✖ ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3

test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK ✖ ERROR: Remove 'file32ed9c6779d14d.BiocCheck' from the package directory

test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    6 tests OK 
test_BiocCheck.R..............    6 tests OK ✖ ERROR: Remove 'inst/doc' folder from the package source

test_BiocCheck.R..............    6 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK * Checking that biocViews are present...
✖ ERROR: No biocViews terms found.

test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK * 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..............    7 tests OK 
test_BiocCheck.R..............    8 tests OK 
test_BiocCheck.R..............    8 tests OK 
test_BiocCheck.R..............    8 tests OK * 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..............    8 tests OK 
test_BiocCheck.R..............    9 tests OK 
test_BiocCheck.R..............    9 tests OK 
test_BiocCheck.R..............    9 tests OK * 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..............    9 tests OK 
test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   10 tests OK ✖ ERROR: System files found that should not be Git tracked.
• something.Rproj

test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   12 tests OK 
test_BiocCheck.R..............   13 tests OK 
test_BiocCheck.R..............   13 tests OK * 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..............   13 tests OK 
test_BiocCheck.R..............   13 tests OK 
test_BiocCheck.R..............   13 tests OK * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0' restricts use

test_BiocCheck.R..............   13 tests OK 
test_BiocCheck.R..............   14 tests OK 
test_BiocCheck.R..............   14 tests OK * Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use

test_BiocCheck.R..............   14 tests OK 
test_BiocCheck.R..............   15 tests OK 
test_BiocCheck.R..............   15 tests OK * 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..............   15 tests OK 
test_BiocCheck.R..............   16 tests OK 
test_BiocCheck.R..............   16 tests OK * Checking License: for restrictive use...
ℹ NOTE: malformed 'License:' field 'NA'

test_BiocCheck.R..............   16 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   18 tests OK * 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..............   18 tests OK 
test_BiocCheck.R..............   19 tests OK 
test_BiocCheck.R..............   19 tests OK 
test_BiocCheck.R..............   19 tests OK 
test_BiocCheck.R..............   20 tests OK * Checking License: for restrictive use...

test_BiocCheck.R..............   20 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   21 tests OK ! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• fileA.rda
• fileB.rds

test_BiocCheck.R..............   21 tests OK 
test_BiocCheck.R..............   22 tests OK 
test_BiocCheck.R..............   22 tests OK ! WARNING: Data files exceed the 5MB size limit.
Use 'ExperimentHub' or 'AnnotationHub' for the files:
• fileA.rda
• fileB.rds

test_BiocCheck.R..............   22 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK * 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..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK ! WARNING: Description field in the DESCRIPTION file is too concise

test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK 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..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK * 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 'file32ed9c7450051' must match Package: field (got
'Foo').

test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK * 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..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK * 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..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK * 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..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK 
test_BiocCheck.R..............   25 tests OK * 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..............   25 tests OK 
test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK * 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..............   26 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   28 tests OK 
test_BiocCheck.R..............   28 tests OK 
test_BiocCheck.R..............   28 tests OK * 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..............   28 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK * 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..............   29 tests OK 
test_BiocCheck.R..............   30 tests OK 
test_BiocCheck.R..............   31 tests OK 
test_BiocCheck.R..............   31 tests OK 
test_BiocCheck.R..............   31 tests OK * 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..............   31 tests OK 
test_BiocCheck.R..............   32 tests OK 
test_BiocCheck.R..............   32 tests OK 
test_BiocCheck.R..............   32 tests OK * 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..............   32 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK * Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'

test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html

test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   36 tests OK 
test_BiocCheck.R..............   36 tests OK ℹ NOTE: skip_on_bioc() found in testthat files: a_test.R

test_BiocCheck.R..............   36 tests OK 
test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   39 tests OK 
test_BiocCheck.R..............   39 tests OK 
test_BiocCheck.R..............   40 tests OK 
test_BiocCheck.R..............   40 tests OK 
test_BiocCheck.R..............   41 tests OK 
test_BiocCheck.R..............   41 tests OK 
test_BiocCheck.R..............   41 tests OK 
test_BiocCheck.R..............   41 tests OK 
test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   43 tests OK 
test_BiocCheck.R..............   43 tests OK 
test_BiocCheck.R..............   43 tests OK 
test_BiocCheck.R..............   44 tests OK 
test_BiocCheck.R..............   44 tests OK 
test_BiocCheck.R..............   44 tests OK 
test_BiocCheck.R..............   44 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   46 tests OK 
test_BiocCheck.R..............   47 tests OK 
test_BiocCheck.R..............   47 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 tests OK ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAwlT7D/file32ed9c7fccd9ed/file32ed9c710fbac5/DESCRIPTION’ ... OK
* preparing ‘file32ed9c710fbac5’:
* 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 ‘file32ed9c710fbac5/R’
* building ‘file32ed9c710fbac5_0.99.0.tar.gz’


test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK ✖ ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated
and does not work on Windows.

test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   50 tests OK 
test_BiocCheck.R..............   50 tests OK 
test_BiocCheck.R..............   50 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   52 tests OK 
test_BiocCheck.R..............   53 tests OK 
test_BiocCheck.R..............   53 tests OK 
test_BiocCheck.R..............   53 tests OK 
test_BiocCheck.R..............   53 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   55 tests OK ✖ ERROR: Package installation calls found in vignette(s)
Found in files:
• vignettes/testpkg0.Rmd (chunk no. 3, line 18, column 18)
• vignettes/testpkg0.Rmd (chunk no. 4, line 26, column 20)
! WARNING: Potential package installation calls found in vignette(s)
Found in files:
• vignettes/testpkg0.Rmd (chunk no. 3, line 20, column 1)

test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   56 tests OK 
test_BiocCheck.R..............   56 tests OK 
test_BiocCheck.R..............   56 tests OK 
test_BiocCheck.R..............   56 tests OK ✖ ERROR: Vignette(s) found with duplicate chunk labels
Found in files:
• dupChunks.Rmd

test_BiocCheck.R..............   56 tests OK 
test_BiocCheck.R..............   57 tests OK 
test_BiocCheck.R..............   57 tests OK 
test_BiocCheck.R..............   57 tests OK ! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/testpkg0.Rmd (chunk no. 9, line 49, column 5)

test_BiocCheck.R..............   57 tests OK 
test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   58 tests OK ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/dupChunks.Rmd
• ...
• vignettes/testpkg0_child.Rmd

test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   59 tests OK ℹ Found install() in R/bad_coding.R (line 41, column 18)
ℹ Found install() in vignettes/testpkg0.Rmd

test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   60 tests OK 
test_BiocCheck.R..............   60 tests OK ! WARNING: BiocInstaller code found in vignette(s)
Found in files:
vignettes/testpkg0.Rmd (chunk no. 4, line 26, column 20)

test_BiocCheck.R..............   60 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   62 tests OK * Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION

test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   63 tests OK 
test_BiocCheck.R..............   63 tests OK 
test_BiocCheck.R..............   63 tests OK * Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION

test_BiocCheck.R..............   63 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   64 tests OK * Checking for recommended DESCRIPTION fields...

test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   65 tests OK 
test_BiocCheck.R..............   65 tests OK 
test_BiocCheck.R..............   65 tests OK * 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..............   65 tests OK 
test_BiocCheck.R..............   66 tests OK 
test_BiocCheck.R..............   66 tests OK 
test_BiocCheck.R..............   66 tests OK * Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (100%).

test_BiocCheck.R..............   66 tests OK 
test_BiocCheck.R..............   67 tests OK 
test_BiocCheck.R..............   67 tests OK 
test_BiocCheck.R..............   67 tests OK * Checking for pinned package versions in DESCRIPTION...
✖ ERROR: Dependencies in the DESCRIPTION file contain '=='

test_BiocCheck.R..............   67 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   68 tests OK ✖ ERROR: Package dependencies must be on CRAN or Bioconductor. Remove
'Remotes:' from DESCRIPTION

test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   69 tests OK 
test_BiocCheck.R..............   70 tests OK 
test_BiocCheck.R..............   70 tests OK 
test_BiocCheck.R..............   70 tests OK 
test_BiocCheck.R..............   70 tests OK 
test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   71 tests OK ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed

test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   72 tests OK 
test_BiocCheck.R..............   72 tests OK 
test_BiocCheck.R..............   72 tests OK ! 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..............   72 tests OK 
test_BiocCheck.R..............   73 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   74 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 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..............   75 tests OK 
test_BiocCheck.R..............   76 tests OK 
test_BiocCheck.R..............   77 tests OK 
test_BiocCheck.R..............   77 tests OK 
test_BiocCheck.R..............   77 tests OK 
test_BiocCheck.R..............   77 tests OK ✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• baddep.Rd

test_BiocCheck.R..............   77 tests OK 
test_BiocCheck.R..............   78 tests OK 
test_BiocCheck.R..............   78 tests OK 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..............   78 tests OK 
test_BiocCheck.R..............   79 tests OK 
test_BiocCheck.R..............   79 tests OK ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.

test_BiocCheck.R..............   79 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   80 tests OK ! WARNING: news(package='unitTestTempDir') failed with news file: inst/NEWS.Rd.
Refer to https://contributions.bioconductor.org/news.html to be included in
Bioconductor release announcements.

test_BiocCheck.R..............   80 tests OK 
test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   81 tests OK ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
Please remove one of the following:
• unitTestTempDir/NEWS.md
• inst/NEWS.Rd
! WARNING: news(package='unitTestTempDir') failed with news file:
unitTestTempDir/NEWS.md. Refer to
https://contributions.bioconductor.org/news.html to be included in Bioconductor
release announcements.WARNING: news(package='unitTestTempDir') failed with news
file: inst/NEWS.Rd. Refer to https://contributions.bioconductor.org/news.html
to be included in Bioconductor release announcements.

test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   82 tests OK 
test_BiocCheck.R..............   83 tests OK 
test_BiocCheck.R..............   83 tests OK 
test_BiocCheck.R..............   83 tests OK 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 (8%) 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..............   83 tests OK 
test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   84 tests OK ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
• man/a.Rd
• man/baddep.Rd

test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   85 tests OK 
test_BiocCheck.R..............   85 tests OK 
test_BiocCheck.R..............   85 tests OK 
test_BiocCheck.R..............   85 tests OK 
test_BiocCheck.R..............   86 tests OK 
test_BiocCheck.R..............   86 tests OK 
test_BiocCheck.R..............   87 tests OK 
test_BiocCheck.R..............   87 tests OK 
test_BiocCheck.R..............   88 tests OK 
test_BiocCheck.R..............   88 tests OK 
test_BiocCheck.R..............   89 tests OK 
test_BiocCheck.R..............   89 tests OK 
test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   91 tests OK 
test_BiocCheck.R..............   91 tests OK 
test_BiocCheck.R..............   91 tests OK 
test_BiocCheck.R..............   91 tests OK 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..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpAwlT7D/file32ed9c2015e068/file32ed9c71b6635d/DESCRIPTION’ ... OK
* preparing ‘file32ed9c71b6635d’:
* 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 ‘file32ed9c71b6635d/R’
* building ‘file32ed9c71b6635d_0.0.1.tar.gz’


test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK ✖ ERROR: Version number in tarball filename must match Version field in
DESCRIPTION. (Tip: create tarball with R CMD build)

test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK ℹ Found @ in ./FooBar
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.

test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............  100 tests OK 
test_BiocCheck.R..............  100 tests OK 
test_BiocCheck.R..............  100 tests OK 
test_BiocCheck.R..............  100 tests OK 
test_BiocCheck.R..............  101 tests OK 
test_BiocCheck.R..............  101 tests OK 
test_BiocCheck.R..............  101 tests OK 
test_BiocCheck.R..............  101 tests OK 
test_BiocCheck.R..............  101 tests OK ℹ NOTE: Update R version dependency from 1.0.0 to 4.5.0

test_BiocCheck.R..............  101 tests OK 
test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  104 tests OK 
test_BiocCheck.R..............  104 tests OK 
test_BiocCheck.R..............  104 tests OK 
test_BiocCheck.R..............  104 tests OK 
test_BiocCheck.R..............  105 tests OK 
test_BiocCheck.R..............  105 tests OK 
test_BiocCheck.R..............  105 tests OK 
test_BiocCheck.R..............  105 tests OK 
test_BiocCheck.R..............  105 tests OK 
test_BiocCheck.R..............  106 tests OK 
test_BiocCheck.R..............  107 tests OK 
test_BiocCheck.R..............  107 tests OK 
test_BiocCheck.R..............  107 tests OK 
test_BiocCheck.R..............  107 tests OK 
test_BiocCheck.R..............  108 tests OK 
test_BiocCheck.R..............  109 tests OK 
test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  113 tests OK ! WARNING: The package already exists on CRAN. Packages submitted to
Bioconductor must be removed from CRAN before the next Bioconductor release.

test_BiocCheck.R..............  113 tests OK 
test_BiocCheck.R..............  114 tests OK ✖ ERROR: 'GenomicRanges' already exists in Bioconductor.

test_BiocCheck.R..............  114 tests OK 
test_BiocCheck.R..............  114 tests OK 
test_BiocCheck.R..............  115 tests OK ✖ ERROR: 'gwascatData' already exists in Bioconductor.

test_BiocCheck.R..............  115 tests OK 
test_BiocCheck.R..............  115 tests OK 
test_BiocCheck.R..............  116 tests OK ✖ ERROR: 'TENxBrainData' already exists in Bioconductor.

test_BiocCheck.R..............  116 tests OK 
test_BiocCheck.R..............  116 tests OK 
test_BiocCheck.R..............  117 tests OK ✖ ERROR: 'annotation' already exists in Bioconductor.

test_BiocCheck.R..............  117 tests OK 
test_BiocCheck.R..............  117 tests OK 
test_BiocCheck.R..............  118 tests OK 
test_BiocCheck.R..............  118 tests OK 
test_BiocCheck.R..............  119 tests OK 
test_BiocCheck.R..............  119 tests OK 
test_BiocCheck.R..............  120 tests OK 
test_BiocCheck.R..............  120 tests OK 
test_BiocCheck.R..............  121 tests OK 
test_BiocCheck.R..............  121 tests OK 
test_BiocCheck.R..............  122 tests OK 
test_BiocCheck.R..............  122 tests OK 
test_BiocCheck.R..............  123 tests OK 
test_BiocCheck.R..............  123 tests OK 
test_BiocCheck.R..............  124 tests OK 
test_BiocCheck.R..............  124 tests OK 
test_BiocCheck.R..............  125 tests OK 
test_BiocCheck.R..............  125 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  126 tests OK 
test_BiocCheck.R..............  127 tests OK 
test_BiocCheck.R..............  128 tests OK 
test_BiocCheck.R..............  128 tests OK 
test_BiocCheck.R..............  128 tests OK 
test_BiocCheck.R..............  128 tests OK $undefined
$undefined$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 'file32ed9c6779d14d.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] "Package 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 (chunk no. 3, line 18, column 18)"
[2] "vignettes/testpkg0.Rmd (chunk no. 4, line 26, column 20)"


$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]]
$`Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[1]]$checkVigInstalls
[1] "Potential package 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 (chunk no. 3, line 20, 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 (chunk no. 9, line 49, 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.qmd 
      "vignettes/testpkg0.Rnw"       "vignettes/testpkg0.qmd" 
  vignettes/testpkg0_child.Rmd 
"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 (chunk no. 4, line 26, 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] "news(package='unitTestTempDir') failed with news file: inst/NEWS.Rd.\nRefer to https://contributions.bioconductor.org/news.html to 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 one 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] "unitTestTempDir/NEWS.md" "inst/NEWS.Rd"           


$`Checking for pinned package versions in DESCRIPTION...`$`3`
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]
$`Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]$`3`
[1] "news(package='unitTestTempDir') failed with news file: unitTestTempDir/NEWS.md.\nRefer to https://contributions.bioconductor.org/news.html to be included in Bioconductor release announcements."
[2] "news(package='unitTestTempDir') failed with news file: inst/NEWS.Rd.\nRefer to https://contributions.bioconductor.org/news.html to 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 (8%) 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 4.5.0"



$`Checking for pinned package versions in DESCRIPTION...`$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..............  128 tests OK 
test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  131 tests OK 
test_BiocCheck.R..............  131 tests OK 
test_BiocCheck.R..............  131 tests OK 
test_BiocCheck.R..............  131 tests OK 
test_BiocCheck.R..............  132 tests OK 
test_BiocCheck.R..............  132 tests OK 
test_BiocCheck.R..............  133 tests OK 
test_BiocCheck.R..............  134 tests OK 
test_BiocCheck.R..............  134 tests OK 
test_BiocCheck.R..............  134 tests OK 
test_BiocCheck.R..............  135 tests OK 
test_BiocCheck.R..............  136 tests OK 1.2s

test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    * Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.

test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    0 tests    
test_checkDESCRIPTION.R.......    1 tests OK * Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.

test_checkDESCRIPTION.R.......    1 tests OK 
test_checkDESCRIPTION.R.......    1 tests OK 
test_checkDESCRIPTION.R.......    1 tests OK 
test_checkDESCRIPTION.R.......    1 tests OK * Checking for 'fnd' role in Authors@R...

test_checkDESCRIPTION.R.......    1 tests OK 
test_checkDESCRIPTION.R.......    2 tests OK 
test_checkDESCRIPTION.R.......    2 tests OK 1.0s

test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    ✖ ERROR: No vignette sources in vignettes/ directory.

test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    0 tests    ! 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
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
Update the following files:
• test.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• test.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.Rnw

test_checkVignettes.R.........    0 tests    
test_checkVignettes.R.........    1 tests OK 
test_checkVignettes.R.........    2 tests OK 
test_checkVignettes.R.........    3 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.

test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK ! WARNING: Remove vignette sources from inst/doc; they belong in vignettes/.

test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    4 tests OK ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• testpkg0.Rnw

test_checkVignettes.R.........    4 tests OK 
test_checkVignettes.R.........    5 tests OK 
test_checkVignettes.R.........    5 tests OK ✖ ERROR: Vignette(s) found with duplicate chunk labels
Found in files:
• dupChunks.Rmd

test_checkVignettes.R.........    5 tests OK 
test_checkVignettes.R.........    6 tests OK 
test_checkVignettes.R.........    6 tests OK ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• testpkg0.Rmd

test_checkVignettes.R.........    6 tests OK 
test_checkVignettes.R.........    7 tests OK 
test_checkVignettes.R.........    7 tests OK ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• testpkg0.qmd

test_checkVignettes.R.........    7 tests OK 
test_checkVignettes.R.........    8 tests OK 
test_checkVignettes.R.........    8 tests OK ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• testpkg0.Rnw

test_checkVignettes.R.........    8 tests OK 
test_checkVignettes.R.........    9 tests OK 
test_checkVignettes.R.........    9 tests OK 
test_checkVignettes.R.........    9 tests OK 
test_checkVignettes.R.........   10 tests OK ! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• test.Rnw

test_checkVignettes.R.........   10 tests OK 
test_checkVignettes.R.........   11 tests OK 
test_checkVignettes.R.........   11 tests OK 
test_checkVignettes.R.........   11 tests OK ! WARNING: Quarto vignette found but 'SystemRequirements' field not in
DESCRIPTION.

test_checkVignettes.R.........   11 tests OK 
test_checkVignettes.R.........   12 tests OK 
test_checkVignettes.R.........   12 tests OK 
test_checkVignettes.R.........   12 tests OK ! WARNING: Quarto vignette found but 'SystemRequirements' does not list
'quarto'.

test_checkVignettes.R.........   12 tests OK 
test_checkVignettes.R.........   13 tests OK ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/test.qmd

test_checkVignettes.R.........   13 tests OK 
test_checkVignettes.R.........   14 tests OK 
test_checkVignettes.R.........   14 tests OK 
test_checkVignettes.R.........   14 tests OK ! WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette Title}'
The following files use template defaults:
• testpkg0.Rmd

test_checkVignettes.R.........   14 tests OK 
test_checkVignettes.R.........   15 tests OK 
test_checkVignettes.R.........   15 tests OK ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/evalfalse.Rmd

test_checkVignettes.R.........   15 tests OK 
test_checkVignettes.R.........   16 tests OK 
test_checkVignettes.R.........   16 tests OK 
test_checkVignettes.R.........   16 tests OK ! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• ThisWillFail
• FailBuilder

test_checkVignettes.R.........   16 tests OK 
test_checkVignettes.R.........   17 tests OK 
test_checkVignettes.R.........   17 tests OK ✖ ERROR: More than one VignetteEngine specified.
Found in files:
• vignettes/testpkg0.Rmd

test_checkVignettes.R.........   17 tests OK 
test_checkVignettes.R.........   18 tests OK 
test_checkVignettes.R.........   18 tests OK ! WARNING: Vignette(s) missing Vignette metadata. See
http://r-pkgs.had.co.nz/vignettes.html
Update the following files:
• testpkg0.Rmd

test_checkVignettes.R.........   18 tests OK 
test_checkVignettes.R.........   19 tests OK 
test_checkVignettes.R.........   19 tests OK ! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
Add the following to Suggests in DESCRIPTION:
• ThisWillFail
• FailBuilder

test_checkVignettes.R.........   19 tests OK 
test_checkVignettes.R.........   20 tests OK 
test_checkVignettes.R.........   20 tests OK ! WARNING: Evaluate more vignette chunks.
ℹ 3 out of 5 code chunks = 60% unevaluated
ℹ 1 non-exec code chunk(s) (e.g., '```r')

test_checkVignettes.R.........   20 tests OK 
test_checkVignettes.R.........   21 tests OK 
test_checkVignettes.R.........   21 tests OK 
test_checkVignettes.R.........   21 tests OK ℹ NOTE: Potential intermediate files found:
• vignettes/testpkg0.html

test_checkVignettes.R.........   21 tests OK 
test_checkVignettes.R.........   22 tests OK 
test_checkVignettes.R.........   22 tests OK ! WARNING: Vignette set global option 'eval=FALSE'
Found in files:
• vignettes/testpkg0.Rmd

test_checkVignettes.R.........   22 tests OK 
test_checkVignettes.R.........   23 tests OK 
test_checkVignettes.R.........   23 tests OK 
test_checkVignettes.R.........   23 tests OK 7.5s
All ok, 161 results (1m 18.3s)
Warning messages:
1: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  Invalid ORCID iD: '0000-000-0000-0000'.
2: In person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  Invalid ORCID iD: '0000-0000-000-0000'.
> 
> proc.time()
   user  system elapsed 
 53.762   9.025  80.533

Example timings

BiocCheck.Rcheck/BiocCheck-Ex.timings

nameusersystemelapsed
BiocCheck-class0.0000.0000.001
BiocCheck13.188 5.41129.676
BiocCheckGitClone0.3580.0110.485
BiocPackage-class000