##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocCheck_1.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocCheck.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.36.1’
* 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 R 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:::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 5.483  0.773  15.929
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BiocCheck.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocCheck
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘BiocCheck’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocCheck)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> BiocGenerics:::testPackage("BiocCheck") 
Loading required package: usethis
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
    * ERROR: System files found that should not be Git tracked.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
    * ERROR: Remove whitespace from DESCRIPTION field names.
* Checking for blank lines in DESCRIPTION...
    * ERROR: Remove blank lines from DESCRIPTION.
    * WARNING: Description field in the DESCRIPTION file is too concise
    * NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got 'Foo').
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
    * ERROR: No 'Version:' field in DESCRIPTION.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* 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 must evaluate to 'person' object.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* 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 in DESCRIPTION file is malformed.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* 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] field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got '%s unitTestTempDir').
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
    * ERROR: Use Authors@R field not Author/Maintainer fields. Do not
      use both.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * NOTE: Invalid ORCID iD for Bioconductor Package Maintainer
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* 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.
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Designated only one maintainer with Authors@R [cre].
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* 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="...")'
* Checking that provided CITATION file is correctly formatted...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted
    * ERROR: Remove 'testpkg.BiocCheck' from the package directory
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
* 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...
* 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...
* 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)
    * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is
      deprecated and does not work on Windows.
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
    * 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{}.
    Found @ in ./FooBar
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    Found install() in R/bad_coding.R (line 41, column 18)
    Found install() in vignettes/testpkg0.Rmd
    * WARNING: Avoid the use of 'library' or 'require' in R code
    * NOTE: Auto-generated '%% ~' comments found in Rd man pages.
    Maintainer is registered at support site.
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/
    Maintainer is registered at support site.
    Package name is in support site watched tags.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.
    Package name is in support site watched tags.
    Package name is in support site watched tags.

    * ERROR: Version number in tarball filename must match Version
      field in DESCRIPTION. (Tip: create tarball with R CMD build)
    * 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
      (11%) 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.
    * WARNING: Package files exceed the 5MB size limit.
    * WARNING: Data files exceed the 5MB size limit.
    * ERROR: Remove 'inst/doc' folder from the package source
* Checking License: for restrictive use...
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0' restricts use
* Checking License: for restrictive use...
    * ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts use
* Checking License: for restrictive use...
    * NOTE: License 'UNKNOWN' unknown; licenses cannot restrict use
* Checking License: for restrictive use...
    * NOTE: malformed 'License:' field 'NA'
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
    * WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will
      not be included in Bioconductor release announcements.
    * 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.
    * WARNING: New package x version starting with non-zero value
      (e.g., 1.y.z, 2.y.z); got '1.99.3'.
    * ERROR: New package 'y' version not 99 (i.e., x.99.z); Package
      version: 0.2.3
    * NOTE: Update R version dependency from 1.0.0 to 4.3.0.
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      https://contributions.bioconductor.org/tests.html
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
$undefined
$undefined$checkLazyDataUsage
$undefined$checkLazyDataUsage[[1]]
[1] "* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed"


$undefined$checkBadFiles
$undefined$checkBadFiles[[1]]
[1] "* ERROR: System files found that should not be Git tracked."

$undefined$checkBadFiles[[2]]
[1] "something.Rproj"



$`* Checking for blank lines in DESCRIPTION...`
list()

$`* Checking if DESCRIPTION is well formatted...`
list()

$`* Checking for proper Description: field...`
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...`
$`* Checking for valid maintainer...`$checkBBScompatibility
$`* Checking for valid maintainer...`$checkBBScompatibility[[1]]
[1] "* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID=\"...\")'"



$`* Checking that provided CITATION file is correctly formatted...`
$`* Checking that provided CITATION file is correctly formatted...`$`3`
$`* Checking that provided CITATION file is correctly formatted...`$`3`[[1]]
[1] "* NOTE: CITATION file might be not correctly formatted"


$`* Checking that provided CITATION file is correctly formatted...`$checkBiocCheckOutputFolder
$`* Checking that provided CITATION file is correctly formatted...`$checkBiocCheckOutputFolder[[1]]
[1] "* ERROR: Remove 'testpkg.BiocCheck' from the package directory"



$`* 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)"


$`* Checking that biocViews come from the same category...`$checkDeprecatedPackages
$`* Checking that biocViews come from the same category...`$checkDeprecatedPackages[[1]]
[1] "* ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows."


$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import devtools in NAMESPACE as well as DESCRIPTION."


$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import BiocCheck in NAMESPACE as well as DESCRIPTION."


$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency
$`* Checking that biocViews come from the same category...`$checkDescriptionNamespaceConsistency[[1]]
[1] "* WARNING: Import devtools in DESCRIPTION as well as NAMESPACE."


$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented
$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[1]]
[1] "* ERROR: At least 80% of man pages documenting exported objects must have runnable examples."

$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[2]]
[1] "The following pages do not:"

$`* Checking that biocViews come from the same category...`$checkExportsAreDocumented[[3]]
[1] "baddep.Rd"


$`* Checking that biocViews come from the same category...`$checkUsageOfDont
$`* Checking that biocViews come from the same category...`$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."

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"


$`* Checking that biocViews come from the same category...`$checkUsageOfDont
$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"


$`* Checking that biocViews come from the same category...`$checkForDirectSlotAccess
$`* Checking that biocViews come from the same category...`$checkForDirectSlotAccess[[1]]
[1] "* NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes."


$`* Checking that biocViews come from the same category...`$checkForLibraryRequire
$`* Checking that biocViews come from the same category...`$checkForLibraryRequire[[1]]
[1] "* WARNING:  Avoid the use of 'library' or 'require' in R code"

$`* Checking that biocViews come from the same category...`$checkForLibraryRequire[[2]]
[1] "Found in files:"

$`* Checking that biocViews come from the same category...`$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)"


$`* Checking that biocViews come from the same category...`$checkForPromptComments
$`* Checking that biocViews come from the same category...`$checkForPromptComments[[1]]
[1] "* NOTE: Auto-generated '%% ~' comments found in Rd man pages."

$`* Checking that biocViews come from the same category...`$checkForPromptComments[[2]]
[1] "a.Rd"      "baddep.Rd"


$`* Checking that biocViews come from the same category...`$checkSupportReg
$`* Checking that biocViews come from the same category...`$checkSupportReg[[1]]
[1] "* ERROR: Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/"


$`* Checking that biocViews come from the same category...`$checkWatchedTag
$`* Checking that biocViews come from the same category...`$checkWatchedTag[[1]]
[1] "* ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."


$`* Checking that biocViews come from the same category...`$checkForVersionNumberMismatch
$`* Checking that biocViews come from the same category...`$checkForVersionNumberMismatch[[1]]
[1] "* ERROR: Version number in tarball filename must match Version field in DESCRIPTION. (Tip: create tarball with R CMD build)"


$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$checkFormatting[[3]]
[1] "R/morebadcode.R#L2 # this is a really long line with many c..."


$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$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..."


$`* Checking that biocViews come from the same category...`$checkFormatting
$`* Checking that biocViews come from the same category...`$checkFormatting[[1]]
[1] "* NOTE: Consider multiples of 4 spaces for line indents; 52 lines (11%) are not."

$`* Checking that biocViews come from the same category...`$checkFormatting[[2]]
[1] "First few lines:"

$`* Checking that biocViews come from the same category...`$checkFormatting[[3]]
 [1] "R/bad_coding.R#L 77   ..."                                       
 [2] "R/bad_coding.R#L 78   ..."                                       
 [3] "R/bad_coding.R#L 79   ..."                                       
 [4] "R/bad_coding.R#L 80   ..."                                       
 [5] "R/bad_coding.R#L 81   ..."                                       
 [6] "R/bad_coding.R#L 82   ..."                                       
 [7] "R/bad_coding.R#L 83   ..."                                       
 [8] "R/bad_coding.R#L 84   ..."                                       
 [9] "R/bad_coding.R#L 85   ..."                                       
[10] "R/bad_coding.R#L 86   ..."                                       
[11] "R/bad_coding.R#L 87   ..."                                       
[12] "R/bad_coding.R#L 88   ..."                                       
[13] "R/bad_coding.R#L 89   ..."                                       
[14] "R/bad_coding.R#L 90   ..."                                       
[15] "R/bad_coding.R#L 91   ..."                                       
[16] "R/bad_coding.R#L 92   ..."                                       
[17] "R/bad_coding.R#L 93   ..."                                       
[18] "R/bad_coding.R#L 94   ..."                                       
[19] "R/bad_coding.R#L 95   ..."                                       
[20] "R/bad_coding.R#L 96   ..."                                       
[21] "R/bad_coding.R#L 97   ..."                                       
[22] "R/bad_coding.R#L 98   ..."                                       
[23] "R/bad_coding.R#L 99   ..."                                       
[24] "R/bad_coding.R#L100   ..."                                       
[25] "R/bad_coding.R#L101   ..."                                       
[26] "R/bad_coding.R#L102   ..."                                       
[27] "R/bad_coding.R#L103   ..."                                       
[28] "R/bad_coding.R#L104   ..."                                       
[29] "R/bad_coding.R#L105   ..."                                       
[30] "R/bad_coding.R#L106   ..."                                       
[31] "R/bad_coding.R#L107   ..."                                       
[32] "R/bad_coding.R#L108   ..."                                       
[33] "R/bad_coding.R#L109   ..."                                       
[34] "R/bad_coding.R#L110   ..."                                       
[35] "R/bad_coding.R#L111   ..."                                       
[36] "R/bad_coding.R#L112   ..."                                       
[37] "R/bad_coding.R#L113   ..."                                       
[38] "R/bad_coding.R#L114   ..."                                       
[39] "R/bad_coding.R#L115   ..."                                       
[40] "R/bad_coding.R#L116   ..."                                       
[41] "R/bad_coding.R#L117   ..."                                       
[42] "R/bad_coding.R#L118   ..."                                       
[43] "R/bad_coding.R#L119   ..."                                       
[44] "R/bad_coding.R#L120   ..."                                       
[45] "R/bad_coding.R#L121   ..."                                       
[46] "R/bad_coding.R#L122   ..."                                       
[47] "R/bad_coding.R#L123   ..."                                       
[48] "R/bad_coding.R#L124   ..."                                       
[49] "R/bad_coding.R#L125   ..."                                       
[50] "R/bad_coding.R#L126   ..."                                       
[51] "R/bad_coding.R#L127   return(TRUE)..."                           
[52] "R/morebadcode.R#L  6      # something other than a multiple o..."


$`* Checking that biocViews come from the same category...`$checkIndivFileSizes
$`* Checking that biocViews come from the same category...`$checkIndivFileSizes[[1]]
[1] "* WARNING: Package files exceed the 5MB size limit."

$`* Checking that biocViews come from the same category...`$checkIndivFileSizes[[2]]
[1] "Files over the limit: "

$`* Checking that biocViews come from the same category...`$checkIndivFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"


$`* Checking that biocViews come from the same category...`$checkDataFileSizes
$`* Checking that biocViews come from the same category...`$checkDataFileSizes[[1]]
[1] "* WARNING: Data files exceed the 5MB size limit."

$`* Checking that biocViews come from the same category...`$checkDataFileSizes[[2]]
[1] "Use 'ExperimentHub' or 'AnnotationHub' for the files: "

$`* Checking that biocViews come from the same category...`$checkDataFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"


$`* Checking that biocViews come from the same category...`$checkInstDocFolder
$`* Checking that biocViews come from the same category...`$checkInstDocFolder[[1]]
[1] "* ERROR: Remove 'inst/doc' folder from the package source"



$`* Checking biocViews validity...`
list()

$`* Checking for recommended biocViews...`
list()

$`* Checking License: for restrictive use...`
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse
$`* Checking License: for restrictive use...`$.checkLicenseForRestrictiveUse[[1]]
[1] "* NOTE: malformed 'License:' field 'NA'"


$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."


$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."


$`* Checking License: for restrictive use...`$checkNEWS
$`* Checking License: for restrictive use...`$checkNEWS[[1]]
[1] "* NOTE: More than 1  NEWS file found. See ?news for recognition ordering."

$`* Checking License: for restrictive use...`$checkNEWS[[2]]
[1] "Please remove one of the following: "

$`* Checking License: for restrictive use...`$checkNEWS[[3]]
[1] "/inst/NEWS.Rd" "/./NEWS.md"   


$`* Checking License: for restrictive use...`$`3`
$`* Checking License: for restrictive use...`$`3`[[1]]
[1] "* WARNING: Fix formatting of NEWS.Rd. Malformed package NEWS will not be included in Bioconductor release announcements."


$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$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'."


$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber
$`* Checking License: for restrictive use...`$checkNewPackageVersionNumber[[1]]
[1] "* ERROR: New package 'y' version not 99 (i.e., x.99.z); Package version: 0.2.3"


$`* Checking License: for restrictive use...`$checkRVersionDependency
$`* Checking License: for restrictive use...`$checkRVersionDependency[[1]]
[1] "* NOTE: Update R version dependency from 1.0.0 to 4.3.0."


$`* Checking License: for restrictive use...`$checkTFSymbolUsage
$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[1]]
[1] "* WARNING:  Avoid T/F variables; If logical, use TRUE/FALSE"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkTFSymbolUsage[[3]]
[1] "vignettes/testpkg0.Rmd (code line 47, column 5)"


$`* Checking License: for restrictive use...`$checkUnitTests
$`* Checking License: for restrictive use...`$checkUnitTests[[1]]
[1] "* NOTE: Consider adding unit tests. We strongly encourage them. See\n  https://contributions.bioconductor.org/tests.html"


$`* Checking License: for restrictive use...`$checkSkipOnBioc
$`* Checking License: for restrictive use...`$checkSkipOnBioc[[1]]
[1] "* NOTE: skip_on_bioc() found in testthat files: a_test.R"


$`* Checking License: for restrictive use...`$checkUsageOfDont
$`* Checking License: for restrictive use...`$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."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "a.Rd"      "baddep.Rd"


$`* Checking License: for restrictive use...`$checkUsageOfDont
$`* Checking License: for restrictive use...`$checkUsageOfDont[[1]]
[1] "* NOTE: Use donttest{} instead of dontrun{}."

$`* Checking License: for restrictive use...`$checkUsageOfDont[[2]]
[1] "Found in files:"

$`* Checking License: for restrictive use...`$checkUsageOfDont[[3]]
[1] "baddep.Rd"



    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * ERROR: Invalid package Version, see
      https://contributions.bioconductor.org/versionnum.html
    * WARNING: y of x.y.z version should be even in release
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)

    * NOTE: The recommended function length is 50 lines or less. There
      are 25 functions greater than 50 lines.
    * NOTE: The recommended function length is 50 lines or less. There
      is 1 function greater than 50 lines.
    * WARNING: The package already exists on CRAN. Packages submitted
      to Bioconductor must be removed from CRAN before the next
      Bioconductor release.
    * ERROR: 'GenomicRanges' already exists in Bioconductor.
    * ERROR: 'gwascatData' already exists in Bioconductor.
    * ERROR: 'TENxBrainData' already exists in Bioconductor.
    * ERROR: 'annotation' already exists in Bioconductor.
    * ERROR: Package dependencies must be on CRAN or Bioconductor.
      Remove 'Remotes:' from DESCRIPTION
    * ERROR: No vignette sources in vignettes/ directory.
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
      'VignetteEngine' in any vignettes:
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * 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: 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}'.
    * WARNING: Evaluate more vignette chunks.
        7 code chunks / 14 total = 50% percent unevaluated
        0 non-exec code chunks (e.g., '``` r')
    * 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'
    * 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 code chunks / 2 total = 50% percent unevaluated
        1 non-exec code chunks (e.g., '``` r')
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
    * NOTE: 'sessionInfo' not found in vignette(s)
    * NOTE: Potential intermediate files found:


RUNIT TEST PROTOCOL -- Tue Oct 17 05:24:11 2023 
*********************************************** 
Number of test functions: 53 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocCheck RUnit Tests - 53 test functions, 0 errors, 0 failures
Number of test functions: 53 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 53.804   5.372 113.142