##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocCheck.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BiocCheck_1.41.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.41.2'
* 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 4.87   3.75  125.38
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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
  'F:/biocbuild/bbs-3.20-bioc/meat/BiocCheck.Rcheck/00check.log'
for details.

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


* installing to library 'F:/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)

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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.

> BiocGenerics:::testPackage("BiocCheck") 
Loading required package: usethis
    * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
      removed
* 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.
* Checking License: for restrictive use...
    * 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 of less
      than 3 sentences. Provide a more detailed description of the
      package.
* 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...
    * 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.
* Checking that provided CITATION file is correctly formatted...
    * WARNING: Unable to read CITATION file with
      'utils::readCitationFile()'
    * 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...
No man pages found.
No vignettes 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...
* Checking for recommended biocViews...
No man pages found.
No vignettes 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...
    * WARNING: Use biocViews from one category only (one of Software,
      ExperimentData, AnnotationData, Workflow)
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide "BugReports" field(s) in DESCRIPTION
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide "URL" field(s) in DESCRIPTION
* Checking for recommended DESCRIPTION fields...
* 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.
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
    * ERROR: Dependencies in the DESCRIPTION file contain '=='
    * ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is
      deprecated and does not work on Windows.
    * ERROR: Vignette(s) found with duplicate chunk labels
    * 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: 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.
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqMJhiJ\file11786f453940\file11783cfb7b75/DESCRIPTION' ... OK

* preparing 'file11783cfb7b75':

* 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 'file11783cfb7b75/R'

* building 'file11783cfb7b75_0.0.1.tar.gz'



    * 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
      (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.
    * 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...
    * NOTE: License 'GPL-3.0' unknown; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.
* 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; refer to
      $R_HOME/share/licenses/license.db
      and https://choosealicense.com/appendix/ for more info.
* 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 4.4.0.
    * 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"



$`* 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] "F:\\biocbuild\\bbs-3.20-bioc\\tmpdir\\RtmpqMJhiJ/unitTestTempDir/inst/NEWS.Rd"
[2] "F:\\biocbuild\\bbs-3.20-bioc\\tmpdir\\RtmpqMJhiJ/unitTestTempDir/./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 4.4.0."


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



$`* 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...`
$`* Checking that provided CITATION file is correctly formatted...`$checkForCitationFile
$`* Checking that provided CITATION file is correctly formatted...`$checkForCitationFile[[1]]
[1] "* WARNING: Unable to read CITATION file with 'utils::readCitationFile()'"


$`* Checking that provided CITATION file is correctly formatted...`$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 biocViews validity...`
list()

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

$`* 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 '=='"


$`* Checking for pinned package versions in DESCRIPTION...`$checkDeprecatedPackages
$`* Checking for pinned package versions in DESCRIPTION...`$checkDeprecatedPackages[[1]]
[1] "* ERROR: Use 'BiocParallel' instead of 'multicore'. 'multicore' is deprecated and does not work on Windows."


$`* Checking for pinned package versions in DESCRIPTION...`$checkDupChunkLabels
$`* Checking for pinned package versions in DESCRIPTION...`$checkDupChunkLabels[[1]]
[1] "* ERROR:  Vignette(s) found with duplicate chunk labels"

$`* Checking for pinned package versions in DESCRIPTION...`$checkDupChunkLabels[[2]]
[1] "Found in files:"

$`* Checking for pinned package versions in DESCRIPTION...`$checkDupChunkLabels[[3]]
[1] "dupChunks.Rmd"


$`* Checking for pinned package versions in DESCRIPTION...`$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"


$`* Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess
$`* Checking for pinned package versions in DESCRIPTION...`$checkForDirectSlotAccess[[1]]
[1] "* NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes."


$`* Checking for pinned package versions in DESCRIPTION...`$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)"


$`* Checking for pinned package versions in DESCRIPTION...`$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] "a.Rd"      "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)"


$`* Checking for pinned package versions in DESCRIPTION...`$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 ..."


$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes
$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes[[1]]
[1] "* WARNING: Package files exceed the 5MB size limit."

$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes[[2]]
[1] "Files over the limit: "

$`* Checking for pinned package versions in DESCRIPTION...`$checkIndivFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"


$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes
$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[1]]
[1] "* WARNING: Data files exceed the 5MB size limit."

$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[2]]
[1] "Use 'ExperimentHub' or 'AnnotationHub' for the files: "

$`* Checking for pinned package versions in DESCRIPTION...`$checkDataFileSizes[[3]]
[1] "fileA.rda" "fileB.rds"


$`* Checking for pinned package versions in DESCRIPTION...`$checkInstDocFolder
$`* Checking for pinned package versions in DESCRIPTION...`$checkInstDocFolder[[1]]
[1] "* ERROR: Remove 'inst/doc' folder from the package source"



    * 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 odd in devel
    * WARNING: BiocInstaller code found in vignette(s)
    * ERROR: Installation calls found in vignette(s)
    * NOTE: 'sessionInfo' not found in vignette(s)
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpqMJhiJ\file11786b7b3240\file1178331377e6/DESCRIPTION' ... OK

* preparing 'file1178331377e6':

* 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 'file1178331377e6/R'

* building 'file1178331377e6_0.99.0.tar.gz'



    * 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette
      Title}'.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * 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/.
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * 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)
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
    * NOTE: 'sessionInfo' not found in vignette(s)
    * 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)
    * 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'
    * 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)
    * NOTE: Potential intermediate files found:


RUNIT TEST PROTOCOL -- Mon Jun 10 00:22:06 2024 
*********************************************** 
Number of test functions: 55 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocCheck RUnit Tests - 55 test functions, 0 errors, 0 failures
Number of test functions: 55 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  41.82   13.92  391.34