##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocCheck.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings BiocCheck_1.31.36.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/BiocCheck.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocCheck/DESCRIPTION' ... OK
* this is package 'BiocCheck' version '1.31.36'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'codetoolsBioC'
* 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 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:
  'BiocManager:::.version_bioc' '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.
* 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 5.78   0.38   15.54
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/BiocCheck.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BiocCheck
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BiocCheck' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocCheck'
    finding HTML links ... done
    BiocCheck                               html  
    BiocCheckGitClone                       html  
    Context                                 html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MsBackendMassbank' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'RCy3' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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:something.Rproj
        something.Rproj
* 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...
    * ERROR: Package directory 'unitTestTempDir' must match Package:
      field (got '').
* 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 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].
* 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...
* Checking that provided CITATION file is correctly formatted...
* Checking that provided CITATION file is correctly formatted...
    * NOTE: CITATION file might be not correctly formatted
* 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: 'foo' is an invalid BiocViews term.
    * WARNING: 'Cancer' is an invalid BiocViews term.
    * WARNING: 'bar' is an invalid BiocViews term. Did you mean: 'ag'
    * WARNING: 'baz' is an invalid BiocViews term. Did you mean: 'ag'
* 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. The following pages do not:
      baddep.Rd
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      67% of man pages use one of these cases.
      Found in the following files:
        a.Rd
        baddep.Rd
    * NOTE: Use donttest{} instead of dontrun{}.
      Found in the following files:
        baddep.Rd
* Checking if other packages can import this one...
    * ERROR: Packages providing 1 object(s) used in this package should
      be imported in the NAMESPACE file, otherwise packages importing
      this package may fail.
    
      package::object in function()
        RJSONIO::isValidJSON in baddep()
      
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 6 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
    function (object)
      bad_cat (setMethod)
      bad_dl (download.file)
      bad_fun (update.packages)
      has_devel (R)
      iambad (colone)
      invalid_ref (BiocCheck)
    Found @ in ./FooBar
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    Found install() in R/bad_coding.R (line 31, column 18)
    Found install() in vignettes/testpkg0.Rmd
    * WARNING: Avoid the use of 'library' or 'require' in R code
      Found in files:
        library() in R/requireme.R (line 3, column 5)
        library() in R/requireme.R (line 5, column 5)
        library() in R/requireme.R (line 7, column 5)
        library() in R/requireme.R (line 8, column 5)
        library() in R/requireme.R (line 13, column 5)
        require() in R/requireme.R (line 4, column 5)
        require() in R/requireme.R (line 6, column 5)
        require() in R/requireme.R (line 9, column 5)
        require() in R/requireme.R (line 10, column 5)
        require() in R/requireme.R (line 11, column 5)
        require() in R/requireme.R (line 12, column 5)
        require() in R/requireme.R (line 14, column 5)
        require() in R/requireme.R (line 17, column 5)
        require() in R/requireme.R (line 18, column 5)
    * NOTE: Remove generated comments from man pages a.Rd, baddep.Rd
    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.
    First 1 lines:
      R/morebadcode.R:2 # this is a really long line with many characters in ...
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
      tabs.
    First 2 lines:
      man/a.Rd:48 ##--	or do  help(data=index)  for the standard data sets.
      man/baddep.Rd:41 ##--	or do  help(data=index)  for the standard data sets.
    * NOTE: Consider multiples of 4 spaces for line indents, 1
      lines(0%) are not.
    First 1 lines:
      R/morebadcode.R:6      # something other than a multiple of 5 spaces!
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* 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. Please remove one of the following:
        D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEbjynK/unitTestTempDir/inst/NEWS.Rd
        D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpEbjynK/unitTestTempDir/./NEWS.md
    * 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 (e.g., x.99.z, x.99.z, ...);
      got '0.2.3'.
    * NOTE: Update R version dependency from 1.0.0 to 4.2.0.
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
    * ERROR: Invalid package Version, see
      http://www.bioconductor.org/developers/how-to/version-numbering/
    * ERROR: Invalid package Version, see
      http://www.bioconductor.org/developers/how-to/version-numbering/
    * WARNING: y of x.y.z version should be odd in devel
    * NOTE: Update R version dependency from 4.0 to 4.1.0.
    * WARNING: BiocInstaller code found in vignette(s)
      Found in file(s):
        testpkg0.Rmd (line 21)
    * ERROR: Installation calls found in vignette(s)
      Found in file(s):
        vignettes/testpkg0.Rmd (code line 12, column 18)
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/testpkg0_child.Rmd

    * NOTE: Recommended function length <= 50 lines.
      There are 25 functions > 50 lines.
      The longest 5 functions are:
        _anonymous_.326() (R/DataFrame-class.R, line 326): 147 lines
        _anonymous_.392() (R/RangedData-class.R, line 392): 113 lines
        .CompressedIRangesList.coverage() (R/coverage-methods.R, line
      101): 92 lines
        normalizeSingleBracketSubscript() (R/subsetting-utils.R, line
      8): 92 lines
        _anonymous_.343() (R/Rle-class.R, line 343): 91 lines
    * ERROR: Package must be removed from CRAN.
    * ERROR: 'GenomicRanges' already exists in Bioconductor.
    * ERROR: 'GO.db' 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}'. Update the following files:
        test.Rnw
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/test.Rnw
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/test.Rnw
    * 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:
        knitr
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested. Add the following to Suggests in
      DESCRIPTION:
        knitr
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/test.Rnw
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/test.Rnw
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested. Add the following to Suggests in
      DESCRIPTION:
        Sweave
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/test.Rnw
    * ERROR: VignetteBuilder listed in DESCRIPTION but not found as
      VignetteEngine in any vignettes:
        knitr
    * WARNING: Vignette[s] missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html ; Update the following
      files:
        testpkg0.Rmd
        testpkg0_child.Rmd
    * ERROR: No VignetteEngine specified in vignette or DESCRIPTION.
      Add VignetteEngine to the following files or add a default
      VignetteBuilder in DESCRIPTION:
        testpkg0.Rmd
        testpkg0_child.Rmd
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested. Add the following to Suggests in
      DESCRIPTION:
        knitr
    * WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette
      Title}' Update the following files from using template values:
        testpkg0.Rmd
    * WARNING: Vignette[s] missing '\%VignetteIndexEntry{Vignette
      Title}'. Update the following files:
        testpkg0_child.Rmd
    * WARNING: Evaluate more vignette chunks.
        # of code chunks: 9
        # of eval=FALSE: 5
        # of nonexecutable code chunks by syntax: 0
        # total unevaluated 5 (55%)
    * WARNING: BiocInstaller code found in vignette(s)
      Found in file(s):
        testpkg0.Rmd (line 21)
    * ERROR: Installation calls found in vignette(s)
      Found in file(s):
        vignettes/testpkg0.Rmd (code line 12, column 18)
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
      Found in file(s):
        testpkg0.Rmd (code line 36, column 10)
        testpkg0_child.Rmd (code line 3, column 10)
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/testpkg0_child.Rmd
    * NOTE: Potential intermediate files found:
        vignettes/testpkg0.html
    * ERROR: VignetteBuilder listed in DESCRIPTION but not found as
      VignetteEngine in any vignettes:
        FailBuilder
    * WARNING: Vignette[s] missing Vignette metadata. See
      http://r-pkgs.had.co.nz/vignettes.html ; Update the following
      files:
        testpkg0.Rmd
    * ERROR: VignetteEngine specified but not in DESCRIPTION. Add the
      VignetteEngine from the following files to DESCRIPTION:
        testpkg0.Rmd
    * WARNING: Package listed as VignetteEngine or VignetteBuilder but
      not currently Suggested. Add the following to Suggests in
      DESCRIPTION:
        ThisWillFail
        FailBuilder
    * WARNING: Evaluate more vignette chunks.
        # of code chunks: 2
        # of eval=FALSE: 0
        # of nonexecutable code chunks by syntax: 1
        # total unevaluated 1 (50%)
    * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
      Found in file(s):
        vignettes/testpkg0.Rmd (code line 2, column 7)
    * NOTE: 'sessionInfo' not found in vignette(s)
      Missing from file(s):
        vignettes/testpkg0.Rmd
    * NOTE: Potential intermediate files found:
        vignettes/testpkg0.html


RUNIT TEST PROTOCOL -- Thu Mar 17 18:34:03 2022 
*********************************************** 
Number of test functions: 46 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocCheck RUnit Tests - 46 test functions, 0 errors, 0 failures
Number of test functions: 46 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In sprintf("Package: ", UNIT_TEST_PKG) :
  one argument not used by format 'Package: '
2: In sprintf("Depends: multicore", UNIT_TEST_PKG) :
  one argument not used by format 'Depends: multicore'
> 
> proc.time()
   user  system elapsed 
  35.31    1.31   71.40