Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 174/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocCheck 1.41.4  (landing page)
Marcel Ramos
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/BiocCheck
git_branch: devel
git_last_commit: 4767b0d
git_last_commit_date: 2024-07-11 18:03:17 -0400 (Thu, 11 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for BiocCheck on palomino6

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: 1.41.4
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocCheck.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocCheck_1.41.4.tar.gz
StartedAt: 2024-07-15 22:05:15 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:09:28 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 253.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocCheck.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocCheck.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocCheck_1.41.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocCheck/DESCRIPTION' ... OK
* this is package 'BiocCheck' version '1.41.4'
* 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 whether package 'BiocCheck' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'knitr:::detect_pattern'
  'tools:::.build_news_db_from_package_NEWS_Rd'
  'tools:::.build_news_db_from_package_NEWS_md'
  'tools:::.news_reader_default' 'tools:::RdTags'
  'tools:::analyze_licenses' 'tools:::str_parse_logic'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'BiocCheckRun'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
BiocCheck 4.13   1.47   25.79
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck/00check.log'
for details.


Installation output

BiocCheck.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BiocCheck
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")

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 OK 
test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    1 tests OK     * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............    1 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    2 tests OK     * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............    2 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    3 tests OK     * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.

test_BiocCheck.R..............    3 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    4 tests OK     * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.

test_BiocCheck.R..............    4 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    5 tests OK     * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.

test_BiocCheck.R..............    5 tests OK 
test_BiocCheck.R..............    6 tests OK 
test_BiocCheck.R..............    6 tests OK 
test_BiocCheck.R..............    6 tests OK     * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............    6 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    7 tests OK     * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............    7 tests OK 
test_BiocCheck.R..............    8 tests OK 
test_BiocCheck.R..............    8 tests OK 
test_BiocCheck.R..............    8 tests OK     * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............    8 tests OK 
test_BiocCheck.R..............    9 tests OK 
test_BiocCheck.R..............    9 tests OK 
test_BiocCheck.R..............    9 tests OK     * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Vignette(s) missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * WARNING: Vignette(s) still using 'VignetteIndexEntry{Vignette
      Title}'
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * ERROR: Vignette(s) found with duplicate chunk labels
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Vignette set global option 'eval=FALSE'

test_BiocCheck.R..............    9 tests OK 
test_BiocCheck.R..............   10 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   11 tests OK     * NOTE: Potential intermediate files found:
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Vignette(s) missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html
    * ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * WARNING: Evaluate more vignette chunks.
        1 out of 2 code chunks = 50% unevaluated
        1 non-exec code chunk(s) (e.g., '```r')
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............   11 tests OK 
test_BiocCheck.R..............   12 tests OK 
test_BiocCheck.R..............   13 tests OK 
test_BiocCheck.R..............   14 tests OK 
test_BiocCheck.R..............   15 tests OK 
test_BiocCheck.R..............   16 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   17 tests OK     * NOTE: Potential intermediate files found:

test_BiocCheck.R..............   17 tests OK 
test_BiocCheck.R..............   18 tests OK 
test_BiocCheck.R..............   18 tests OK 
test_BiocCheck.R..............   18 tests OK 
test_BiocCheck.R..............   18 tests OK 
test_BiocCheck.R..............   18 tests OK     * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html

test_BiocCheck.R..............   18 tests OK 
test_BiocCheck.R..............   19 tests OK 
test_BiocCheck.R..............   19 tests OK     * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html

test_BiocCheck.R..............   19 tests OK 
test_BiocCheck.R..............   20 tests OK 
test_BiocCheck.R..............   20 tests OK 
test_BiocCheck.R..............   20 tests OK 
test_BiocCheck.R..............   20 tests OK     * WARNING: y of x.y.z version should be odd in devel

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     * 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..............   21 tests OK 
test_BiocCheck.R..............   22 tests OK 
test_BiocCheck.R..............   22 tests OK 
test_BiocCheck.R..............   22 tests OK 
test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   23 tests OK     * ERROR: New package 'y' version not 99 (i.e., x.99.z); Package
      version: 0.2.3

test_BiocCheck.R..............   23 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 tests OK 
test_BiocCheck.R..............   24 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..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   26 tests OK     * ERROR: Remove 'file2e328416879b9.BiocCheck' from the package
      directory

test_BiocCheck.R..............   26 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   27 tests OK 
test_BiocCheck.R..............   28 tests OK 
test_BiocCheck.R..............   28 tests OK     * ERROR: Remove 'inst/doc' folder from the package source

test_BiocCheck.R..............   28 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   29 tests OK * Checking that biocViews are present...
    * ERROR: No biocViews terms found.

test_BiocCheck.R..............   29 tests OK 
test_BiocCheck.R..............   30 tests OK 
test_BiocCheck.R..............   30 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):
* Checking for recommended biocViews...
No man pages found.
No vignettes found.

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 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..............   31 tests OK 
test_BiocCheck.R..............   32 tests OK 
test_BiocCheck.R..............   32 tests OK 
test_BiocCheck.R..............   32 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..............   32 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   33 tests OK     * ERROR: System files found that should not be Git tracked.

test_BiocCheck.R..............   33 tests OK 
test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK * Checking License: for restrictive use...
    * NOTE: License 'GPL-3.0' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.

test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   34 tests OK * Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0' restricts use

test_BiocCheck.R..............   34 tests OK 
test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   35 tests OK * Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use

test_BiocCheck.R..............   35 tests OK 
test_BiocCheck.R..............   36 tests OK 
test_BiocCheck.R..............   36 tests OK * Checking License: for restrictive use...
    * NOTE: License 'UNKNOWN' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.

test_BiocCheck.R..............   36 tests OK 
test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   37 tests OK * Checking License: for restrictive use...
    * NOTE: malformed 'License:' field 'NA'

test_BiocCheck.R..............   37 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   38 tests OK 
test_BiocCheck.R..............   39 tests OK * Checking License: for restrictive use...
    * NOTE: License 'GPL-3.0' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.

test_BiocCheck.R..............   39 tests OK 
test_BiocCheck.R..............   40 tests OK 
test_BiocCheck.R..............   40 tests OK 
test_BiocCheck.R..............   40 tests OK 
test_BiocCheck.R..............   41 tests OK * Checking License: for restrictive use...

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..............   42 tests OK 
test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   42 tests OK     * WARNING: Package files exceed the 5MB size limit.

test_BiocCheck.R..............   42 tests OK 
test_BiocCheck.R..............   43 tests OK 
test_BiocCheck.R..............   43 tests OK     * WARNING: Data files exceed the 5MB size limit.

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..............   44 tests OK 
test_BiocCheck.R..............   44 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..............   44 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   45 tests OK 
test_BiocCheck.R..............   46 tests OK 
test_BiocCheck.R..............   46 tests OK     * WARNING: Description field in the DESCRIPTION file is too concise

test_BiocCheck.R..............   46 tests OK 
test_BiocCheck.R..............   47 tests OK 
test_BiocCheck.R..............   47 tests OK     * 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..............   47 tests OK 
test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   48 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 'file2e32852391d7a' must match Package:
      field (got 'Foo').

test_BiocCheck.R..............   48 tests OK 
test_BiocCheck.R..............   49 tests OK 
test_BiocCheck.R..............   50 tests OK 
test_BiocCheck.R..............   50 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..............   50 tests OK 
test_BiocCheck.R..............   51 tests OK 
test_BiocCheck.R..............   51 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..............   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 * 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..............   52 tests OK 
test_BiocCheck.R..............   53 tests OK 
test_BiocCheck.R..............   53 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...
    * 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..............   53 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   54 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.
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'

test_BiocCheck.R..............   54 tests OK 
test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   55 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.
    * NOTE: Invalid ORCID iD for Bioconductor Package Maintainer

test_BiocCheck.R..............   55 tests OK 
test_BiocCheck.R..............   56 tests OK 
test_BiocCheck.R..............   57 tests OK 
test_BiocCheck.R..............   57 tests OK 
test_BiocCheck.R..............   57 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..............   57 tests OK 
test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   58 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].
    * NOTE: Invalid ORCID iD for Bioconductor Package Maintainer

test_BiocCheck.R..............   58 tests OK 
test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   59 tests OK 
test_BiocCheck.R..............   59 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..............   59 tests OK 
test_BiocCheck.R..............   60 tests OK 
test_BiocCheck.R..............   60 tests OK 
test_BiocCheck.R..............   60 tests OK * Checking that provided CITATION file is correctly formatted...
    * WARNING: Unable to read CITATION file with
      'utils::readCitationFile()'

test_BiocCheck.R..............   60 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   61 tests OK     * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html

test_BiocCheck.R..............   61 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   62 tests OK 
test_BiocCheck.R..............   63 tests OK 
test_BiocCheck.R..............   63 tests OK     * NOTE: skip_on_bioc() found in testthat files: a_test.R

test_BiocCheck.R..............   63 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   64 tests OK 
test_BiocCheck.R..............   65 tests OK 
test_BiocCheck.R..............   65 tests OK 
test_BiocCheck.R..............   66 tests OK 
test_BiocCheck.R..............   66 tests OK 
test_BiocCheck.R..............   67 tests OK 
test_BiocCheck.R..............   67 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   68 tests OK 
test_BiocCheck.R..............   69 tests OK 
test_BiocCheck.R..............   69 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..............   71 tests OK 
test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   71 tests OK 
test_BiocCheck.R..............   72 tests OK 
test_BiocCheck.R..............   72 tests OK 
test_BiocCheck.R..............   72 tests OK 
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..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpyIpjgY\file2e32835126ecc\file2e328577aa8d/DESCRIPTION' ... OK

* preparing 'file2e328577aa8d':

* 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 'file2e328577aa8d/R'

* building 'file2e328577aa8d_0.99.0.tar.gz'




test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   75 tests OK 
test_BiocCheck.R..............   76 tests OK 
test_BiocCheck.R..............   76 tests OK 
test_BiocCheck.R..............   76 tests OK 
test_BiocCheck.R..............   76 tests OK     * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is
      deprecated and does not work on Windows.

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 
test_BiocCheck.R..............   77 tests OK 
test_BiocCheck.R..............   78 tests OK 
test_BiocCheck.R..............   78 tests OK 
test_BiocCheck.R..............   78 tests OK 
test_BiocCheck.R..............   79 tests OK 
test_BiocCheck.R..............   79 tests OK 
test_BiocCheck.R..............   79 tests OK 
test_BiocCheck.R..............   79 tests OK 
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..............   81 tests OK 
test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   81 tests OK 
test_BiocCheck.R..............   82 tests OK 
test_BiocCheck.R..............   82 tests OK 
test_BiocCheck.R..............   82 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 
test_BiocCheck.R..............   83 tests OK 
test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   84 tests OK     * ERROR: Installation calls found in vignette(s)

test_BiocCheck.R..............   84 tests OK 
test_BiocCheck.R..............   85 tests OK 
test_BiocCheck.R..............   86 tests OK 
test_BiocCheck.R..............   86 tests OK 
test_BiocCheck.R..............   86 tests OK     * ERROR: Vignette(s) found with duplicate chunk labels

test_BiocCheck.R..............   86 tests OK 
test_BiocCheck.R..............   87 tests OK 
test_BiocCheck.R..............   88 tests OK 
test_BiocCheck.R..............   88 tests OK     * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE

test_BiocCheck.R..............   88 tests OK 
test_BiocCheck.R..............   89 tests OK 
test_BiocCheck.R..............   89 tests OK 
test_BiocCheck.R..............   89 tests OK     * NOTE: 'sessionInfo' not found in vignette(s)

test_BiocCheck.R..............   89 tests OK 
test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   90 tests OK     Found install() in R/bad_coding.R (line 41, column 18)
    Found install() in vignettes/testpkg0.Rmd

test_BiocCheck.R..............   90 tests OK 
test_BiocCheck.R..............   91 tests OK 
test_BiocCheck.R..............   91 tests OK     * WARNING: BiocInstaller code found in vignette(s)

test_BiocCheck.R..............   91 tests OK 
test_BiocCheck.R..............   92 tests OK 
test_BiocCheck.R..............   92 tests OK 
test_BiocCheck.R..............   92 tests OK 
test_BiocCheck.R..............   92 tests OK 
test_BiocCheck.R..............   92 tests OK 
test_BiocCheck.R..............   93 tests OK 
test_BiocCheck.R..............   93 tests OK 
test_BiocCheck.R..............   93 tests OK * Checking for recommended DESCRIPTION fields...
    * NOTE: Provide "BugReports" field(s) in DESCRIPTION

test_BiocCheck.R..............   93 tests OK 
test_BiocCheck.R..............   94 tests OK 
test_BiocCheck.R..............   94 tests OK 
test_BiocCheck.R..............   94 tests OK * Checking for recommended DESCRIPTION fields...
    * NOTE: Provide "URL" field(s) in DESCRIPTION

test_BiocCheck.R..............   94 tests OK 
test_BiocCheck.R..............   95 tests OK 
test_BiocCheck.R..............   95 tests OK 
test_BiocCheck.R..............   95 tests OK * Checking for recommended DESCRIPTION fields...

test_BiocCheck.R..............   95 tests OK 
test_BiocCheck.R..............   96 tests OK 
test_BiocCheck.R..............   96 tests OK 
test_BiocCheck.R..............   96 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..............   96 tests OK 
test_BiocCheck.R..............   97 tests OK 
test_BiocCheck.R..............   97 tests OK 
test_BiocCheck.R..............   97 tests OK * Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (100%).

test_BiocCheck.R..............   97 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   98 tests OK * Checking for pinned package versions in DESCRIPTION...
    * ERROR: Dependencies in the DESCRIPTION file contain '=='

test_BiocCheck.R..............   98 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK 
test_BiocCheck.R..............   99 tests OK     * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION

test_BiocCheck.R..............   99 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..............  102 tests OK 
test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  102 tests OK     * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed

test_BiocCheck.R..............  102 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  103 tests OK 
test_BiocCheck.R..............  103 tests OK     * WARNING: Avoid the use of 'library' or 'require' in R code

test_BiocCheck.R..............  103 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..............  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..............  106 tests OK 
test_BiocCheck.R..............  106 tests OK     * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.

test_BiocCheck.R..............  106 tests OK 
test_BiocCheck.R..............  107 tests OK 
test_BiocCheck.R..............  108 tests OK 
test_BiocCheck.R..............  108 tests OK 
test_BiocCheck.R..............  108 tests OK 
test_BiocCheck.R..............  108 tests OK     * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.

test_BiocCheck.R..............  108 tests OK 
test_BiocCheck.R..............  109 tests OK 
test_BiocCheck.R..............  109 tests OK     * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 67% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.

test_BiocCheck.R..............  109 tests OK 
test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  110 tests OK     * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.

test_BiocCheck.R..............  110 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  111 tests OK     * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.

test_BiocCheck.R..............  111 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  112 tests OK     * NOTE: More than 1 NEWS file found. See ?news for recognition
      ordering.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.

test_BiocCheck.R..............  112 tests OK 
test_BiocCheck.R..............  113 tests OK 
test_BiocCheck.R..............  114 tests OK 
test_BiocCheck.R..............  114 tests OK 
test_BiocCheck.R..............  114 tests OK     * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 52 lines
      (9%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.

test_BiocCheck.R..............  114 tests OK 
test_BiocCheck.R..............  115 tests OK 
test_BiocCheck.R..............  115 tests OK 
test_BiocCheck.R..............  115 tests OK     * NOTE: Auto-generated '%% ~' comments found in Rd man pages.

test_BiocCheck.R..............  115 tests OK 
test_BiocCheck.R..............  116 tests OK 
test_BiocCheck.R..............  116 tests OK 
test_BiocCheck.R..............  116 tests OK 
test_BiocCheck.R..............  116 tests OK 
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..............  122 tests OK 
test_BiocCheck.R..............  122 tests OK     Maintainer is registered at support site.
    * ERROR: Unable to find your email in the Support Site: HTTP 404
      Not Found.
    Maintainer is registered at support site.
    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
    Package is in the Support Site Watched Tags.
    Package is in the Support Site Watched Tags.

test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK ── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'C:\Users\biocbuild\bbs-3.20-bioc\tmpdir\RtmpyIpjgY\file2e328217558e0\file2e328692f4cc0/DESCRIPTION' ... OK

* preparing 'file2e328692f4cc0':

* 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 'file2e328692f4cc0/R'

* building 'file2e328692f4cc0_0.0.1.tar.gz'




test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK 
test_BiocCheck.R..............  129 tests OK     * ERROR: Version number in tarball filename must match Version
      field in DESCRIPTION. (Tip: create tarball with R CMD build)

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..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK 
test_BiocCheck.R..............  130 tests OK     Found @ in ./FooBar
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.

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..............  132 tests OK 
test_BiocCheck.R..............  132 tests OK 
test_BiocCheck.R..............  132 tests OK     * NOTE: Update R version dependency from 1.0.0 to 4.4.0.

test_BiocCheck.R..............  132 tests OK 
test_BiocCheck.R..............  133 tests OK 
test_BiocCheck.R..............  133 tests OK 
test_BiocCheck.R..............  133 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..............  134 tests OK 
test_BiocCheck.R..............  135 tests OK 
test_BiocCheck.R..............  135 tests OK 
test_BiocCheck.R..............  135 tests OK 
test_BiocCheck.R..............  135 tests OK 
test_BiocCheck.R..............  136 tests OK 
test_BiocCheck.R..............  136 tests OK 
test_BiocCheck.R..............  136 tests OK 
test_BiocCheck.R..............  136 tests OK 
test_BiocCheck.R..............  136 tests OK 
test_BiocCheck.R..............  137 tests OK 
test_BiocCheck.R..............  138 tests OK 
test_BiocCheck.R..............  138 tests OK 
test_BiocCheck.R..............  138 tests OK 
test_BiocCheck.R..............  138 tests OK 
test_BiocCheck.R..............  139 tests OK 
test_BiocCheck.R..............  140 tests OK 
test_BiocCheck.R..............  141 tests OK 
test_BiocCheck.R..............  141 tests OK 
test_BiocCheck.R..............  141 tests OK 
test_BiocCheck.R..............  141 tests OK 
test_BiocCheck.R..............  142 tests OK 
test_BiocCheck.R..............  143 tests OK 
test_BiocCheck.R..............  143 tests OK 
test_BiocCheck.R..............  143 tests OK 
test_BiocCheck.R..............  143 tests OK 
test_BiocCheck.R..............  144 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..............  144 tests OK 
test_BiocCheck.R..............  145 tests OK     * ERROR: 'GenomicRanges' already exists in Bioconductor.

test_BiocCheck.R..............  145 tests OK 
test_BiocCheck.R..............  145 tests OK 
test_BiocCheck.R..............  146 tests OK     * ERROR: 'gwascatData' already exists in Bioconductor.

test_BiocCheck.R..............  146 tests OK 
test_BiocCheck.R..............  146 tests OK 
test_BiocCheck.R..............  147 tests OK     * ERROR: 'TENxBrainData' already exists in Bioconductor.

test_BiocCheck.R..............  147 tests OK 
test_BiocCheck.R..............  147 tests OK 
test_BiocCheck.R..............  148 tests OK     * ERROR: 'annotation' already exists in Bioconductor.

test_BiocCheck.R..............  148 tests OK 
test_BiocCheck.R..............  148 tests OK 
test_BiocCheck.R..............  149 tests OK 
test_BiocCheck.R..............  149 tests OK 
test_BiocCheck.R..............  150 tests OK 
test_BiocCheck.R..............  150 tests OK 
test_BiocCheck.R..............  151 tests OK 
test_BiocCheck.R..............  151 tests OK 
test_BiocCheck.R..............  152 tests OK 
test_BiocCheck.R..............  152 tests OK 
test_BiocCheck.R..............  153 tests OK 
test_BiocCheck.R..............  153 tests OK 
test_BiocCheck.R..............  154 tests OK 
test_BiocCheck.R..............  154 tests OK 
test_BiocCheck.R..............  155 tests OK 
test_BiocCheck.R..............  155 tests OK 
test_BiocCheck.R..............  156 tests OK 
test_BiocCheck.R..............  156 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  157 tests OK 
test_BiocCheck.R..............  158 tests OK 
test_BiocCheck.R..............  159 tests OK 
test_BiocCheck.R..............  159 tests OK 
test_BiocCheck.R..............  159 tests OK 
test_BiocCheck.R..............  159 tests OK $undefined
$undefined$checkVignetteDir
$undefined$checkVignetteDir[[1]]
[1] "* ERROR: No vignette sources in vignettes/ directory."


$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE:  '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]]
[1] "* WARNING: 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]]
[1] "* NOTE:  '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]]
[1] "* WARNING: Remove vignette sources from inst/doc; they belong in vignettes/."


$undefined$checkInstContents
$undefined$checkInstContents[[1]]
[1] "* WARNING: Remove vignette sources from inst/doc; they belong in vignettes/."


$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
[1] "* WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes."

$undefined$checkVigTypeRNW[[2]]
[1] "Rnw vignette(s) found:"

$undefined$checkVigTypeRNW[[3]]
[1] "testpkg0.Rnw"


$undefined$checkVigBuilder
$undefined$checkVigBuilder[[1]]
[1] "* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"

$undefined$checkVigBuilder[[2]]
[1] "knitr"


$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE:  '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]]
[1] "* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"

$undefined$checkVigBuilder[[2]]
[1] "knitr"


$undefined$checkVigTypeRNW
$undefined$checkVigTypeRNW[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE:  '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]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE:  '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]]
[1] "* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"

$undefined$checkVigBuilder[[2]]
[1] "knitr"


$undefined$checkVigMetadata
$undefined$checkVigMetadata[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* ERROR: No 'VignetteEngine' specified in vignette or DESCRIPTION. "

$undefined$checkVigEngine[[2]]
[1] "Add a 'VignetteEngine' to the following files or a default 'VignetteBuilder' in DESCRIPTION: "

$undefined$checkVigEngine[[3]]
[1] "dupChunks.Rmd"      "evalfalse.Rmd"      "testpkg0.Rmd"      
[4] "testpkg0_child.Rmd"


$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* ERROR:  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]]
[1] "* WARNING:  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]]
[1] "* ERROR: Installation calls found in vignette(s)"

$undefined$checkVigInstalls[[2]]
[1] "Found in files:"

$undefined$checkVigInstalls[[3]]
$undefined$checkVigInstalls[[3]]$`vignettes/testpkg0.Rmd`
[1] "vignettes/testpkg0.Rmd (code line 16, column 18)"
[2] "vignettes/testpkg0.Rmd (code line 24, column 20)"

$undefined$checkVigInstalls[[3]]$`vignettes/testpkg0.Rmd`
[1] "vignettes/testpkg0.Rmd (code line 18, column 1)"



$undefined$checkVigClassUsage
$undefined$checkVigClassUsage[[1]]
[1] "* WARNING:  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]]
[1] "* WARNING:  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]]
[1] "* NOTE:  '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]]
[1] "* WARNING:  Vignette set global option 'eval=FALSE'"

$undefined$checkVigEvalAllFalse[[2]]
[1] "Found in files:"

$undefined$checkVigEvalAllFalse[[3]]
[1] "/evalfalse.Rmd (line 10)"


$undefined$checkVigFiles
$undefined$checkVigFiles[[1]]
[1] "* NOTE: Potential intermediate files found:"

$undefined$checkVigFiles[[2]]
[1] "vignettes/testpkg0.html"


$undefined$checkVigBuilder
$undefined$checkVigBuilder[[1]]
[1] "* ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes:"

$undefined$checkVigBuilder[[2]]
[1] "FailBuilder"


$undefined$checkVigMetadata
$undefined$checkVigMetadata[[1]]
[1] "* WARNING: 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]]
[1] "* ERROR: 'VignetteEngine' specified but not in the DESCRIPTION."

$undefined$checkVigEngine[[2]]
[1] "Add 'VignetteEngine' to DESCRIPTION from the following:"

$undefined$checkVigEngine[[3]]
[1] "testpkg0.Rmd"


$undefined$checkVigSuggests
$undefined$checkVigSuggests[[1]]
[1] "* WARNING: 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]]
[1] "* WARNING: Evaluate more vignette chunks."


$undefined$checkTFSymbolUsage
$undefined$checkTFSymbolUsage[[1]]
[1] "* WARNING:  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 2, column 7)"


$undefined$checkVigSessionInfo
$undefined$checkVigSessionInfo[[1]]
[1] "* NOTE:  'sessionInfo' not found in vignette(s)"

$undefined$checkVigSessionInfo[[2]]
[1] "Missing from file(s):"

$undefined$checkVigSessionInfo[[3]]
  vignettes/testpkg0.Rmd 
"vignettes/testpkg0.Rmd" 


$undefined$checkVigFiles
$undefined$checkVigFiles[[1]]
[1] "* NOTE: Potential intermediate files found:"

$undefined$checkVigFiles[[2]]
[1] "vignettes/testpkg0.html"


$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
[1] "* ERROR: Invalid package Version, see https://contributions.bioconductor.org/versionnum.html"


$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
[1] "* ERROR: Invalid package Version, see https://contributions.bioconductor.org/versionnum.html"


$undefined$checkVersionNumber
$undefined$checkVersionNumber[[1]]
[1] "* WARNING: y of x.y.z version should be odd in devel"


$undefined$checkNewPackageVersionNumber
$undefined$checkNewPackageVersionNumber[[1]]
[1] "* WARNING: 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]]
[1] "* ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3"


$undefined$checkBiocCheckOutputFolder
$undefined$checkBiocCheckOutputFolder[[1]]
[1] "* ERROR: Remove 'file2e328416879b9.BiocCheck' from the package directory"


$undefined$checkInstDocFolder
$undefined$checkInstDocFolder[[1]]
[1] "* ERROR: 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]]
[1] "* WARNING: 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]]
[1] "* ERROR: 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]]
[1] "* WARNING: 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]]
[1] "* WARNING: 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]]
[1] "* ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both."


$`* Checking for valid maintainer...`$checkBBScompatibility
$`* Checking for valid maintainer...`$checkBBScompatibility[[1]]
[1] "* ERROR: Designate only one maintainer with Authors@R [cre]."


$`* Checking for valid maintainer...`$checkBBScompatibility
$`* Checking for valid maintainer...`$checkBBScompatibility[[1]]
[1] "* NOTE: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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]]
[1] "* ERROR: 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]]
[1] "* ERROR: 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]]
$`* Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[3]]$`vignettes/testpkg0.Rmd`
[1] "vignettes/testpkg0.Rmd (code line 16, column 18)"
[2] "vignettes/testpkg0.Rmd (code line 24, column 20)"

$`* Checking that provided CITATION file is correctly formatted...`$checkVigInstalls[[3]]$`vignettes/testpkg0.Rmd`
[1] "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]]
[1] "* ERROR:  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]]
[1] "* WARNING:  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]]
[1] "* NOTE:  '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]]
[1] "* WARNING:  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]]
[1] "* ERROR: Dependencies in the DESCRIPTION file contain '=='"


$`* Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage
$`* Checking for pinned package versions in DESCRIPTION...`$checkRemotesUsage[[1]]
[1] "* ERROR: 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]]
[1] "* NOTE: '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]]
[1] "* WARNING:  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]]
[1] "* NOTE: 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.14 
"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]]
[1] "* ERROR: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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]]
[1] "* WARNING: 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]]
[1] "* NOTE: 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] "C:\\Users\\biocbuild\\bbs-3.20-bioc\\tmpdir\\RtmpyIpjgY/unitTestTempDir/inst/NEWS.Rd"
[2] "C:\\Users\\biocbuild\\bbs-3.20-bioc\\tmpdir\\RtmpyIpjgY/unitTestTempDir/./NEWS.md"   


$`* Checking for pinned package versions in DESCRIPTION...`$`3`
$`* Checking for pinned package versions in DESCRIPTION...`$`3`[[1]]
[1] "* WARNING: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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#L82    ..."                                      
 [2] "R/bad_coding.R#L83    ..."                                      
 [3] "R/bad_coding.R#L84    ..."                                      
 [4] "R/bad_coding.R#L85    ..."                                      
 [5] "R/bad_coding.R#L86    ..."                                      
 [6] "R/bad_coding.R#L87    ..."                                      
 [7] "R/bad_coding.R#L88    ..."                                      
 [8] "R/bad_coding.R#L89    ..."                                      
 [9] "R/bad_coding.R#L90    ..."                                      
[10] "R/bad_coding.R#L91    ..."                                      
[11] "R/bad_coding.R#L92    ..."                                      
[12] "R/bad_coding.R#L93    ..."                                      
[13] "R/bad_coding.R#L94    ..."                                      
[14] "R/bad_coding.R#L95    ..."                                      
[15] "R/bad_coding.R#L96    ..."                                      
[16] "R/bad_coding.R#L97    ..."                                      
[17] "R/bad_coding.R#L98    ..."                                      
[18] "R/bad_coding.R#L99    ..."                                      
[19] "R/bad_coding.R#L100    ..."                                     
[20] "R/bad_coding.R#L101    ..."                                     
[21] "R/bad_coding.R#L102    ..."                                     
[22] "R/bad_coding.R#L103    ..."                                     
[23] "R/bad_coding.R#L104    ..."                                     
[24] "R/bad_coding.R#L105    ..."                                     
[25] "R/bad_coding.R#L106    ..."                                     
[26] "R/bad_coding.R#L107    ..."                                     
[27] "R/bad_coding.R#L108    ..."                                     
[28] "R/bad_coding.R#L109    ..."                                     
[29] "R/bad_coding.R#L110    ..."                                     
[30] "R/bad_coding.R#L111    ..."                                     
[31] "R/bad_coding.R#L112    ..."                                     
[32] "R/bad_coding.R#L113    ..."                                     
[33] "R/bad_coding.R#L114    ..."                                     
[34] "R/bad_coding.R#L115    ..."                                     
[35] "R/bad_coding.R#L116    ..."                                     
[36] "R/bad_coding.R#L117    ..."                                     
[37] "R/bad_coding.R#L118    ..."                                     
[38] "R/bad_coding.R#L119    ..."                                     
[39] "R/bad_coding.R#L120    ..."                                     
[40] "R/bad_coding.R#L121    ..."                                     
[41] "R/bad_coding.R#L122    ..."                                     
[42] "R/bad_coding.R#L123    ..."                                     
[43] "R/bad_coding.R#L124    ..."                                     
[44] "R/bad_coding.R#L125    ..."                                     
[45] "R/bad_coding.R#L126    ..."                                     
[46] "R/bad_coding.R#L127    ..."                                     
[47] "R/bad_coding.R#L128    ..."                                     
[48] "R/bad_coding.R#L129    ..."                                     
[49] "R/bad_coding.R#L130    ..."                                     
[50] "R/bad_coding.R#L131    ..."                                     
[51] "R/bad_coding.R#L132   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]]
[1] "* NOTE: 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]]
[1] "* ERROR: 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]]
[1] "* ERROR: 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]]
[1] "* ERROR: 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]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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]]
[1] "* WARNING: 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]]
[1] "* ERROR: 'GenomicRanges' already exists in Bioconductor."


$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
[1] "* ERROR: 'gwascatData' already exists in Bioconductor."


$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
[1] "* ERROR: 'TENxBrainData' already exists in Bioconductor."


$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse
$`* Checking for pinned package versions in DESCRIPTION...`$checkIsPackageNameAlreadyInUse[[1]]
[1] "* ERROR: 'annotation' already exists in Bioconductor."


$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont
$`* Checking for pinned package versions in DESCRIPTION...`$checkUsageOfDont[[1]]
[1] "* NOTE: 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]]
[1] "* NOTE: 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..............  159 tests OK 
test_BiocCheck.R..............  160 tests OK 
test_BiocCheck.R..............  161 tests OK 
test_BiocCheck.R..............  161 tests OK 
test_BiocCheck.R..............  161 tests OK 
test_BiocCheck.R..............  161 tests OK 
test_BiocCheck.R..............  161 tests OK 
test_BiocCheck.R..............  162 tests OK 
test_BiocCheck.R..............  162 tests OK 
test_BiocCheck.R..............  162 tests OK 
test_BiocCheck.R..............  162 tests OK 
test_BiocCheck.R..............  163 tests OK 
test_BiocCheck.R..............  163 tests OK 
test_BiocCheck.R..............  164 tests OK 
test_BiocCheck.R..............  165 tests OK 
test_BiocCheck.R..............  165 tests OK 
test_BiocCheck.R..............  165 tests OK 
test_BiocCheck.R..............  166 tests OK 
test_BiocCheck.R..............  167 tests OK 2.7s
All ok, 167 results (2m 42.3s)
Warning message:
In file.remove(newname) :
  cannot remove file 'C:/Users/biocbuild/bbs-3.20-bioc/tmpdir/RtmpyIpjgY/file2e328217558e0/file2e328692f4cc0_9.9.9.tar.gz', reason 'No such file or directory'
> 
> proc.time()
   user  system elapsed 
  59.50    6.70  164.29 

Example timings

BiocCheck.Rcheck/BiocCheck-Ex.timings

nameusersystemelapsed
BiocCheck-class000
BiocCheck 4.13 1.4725.79
BiocCheckGitClone0.340.030.38
BiocPackage-class000