Multiple platform build/check report for BioC 3.14 - CHECK results for BiocCheck on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BiocCheck_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BiocCheck.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.30.0’
* 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 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:
  ‘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 6.683  0.416  11.567
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
* 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 5 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_dl (download.file)
      bad_fun (update.packages)
      has_devel (R)
      iambad (colone)
      invalid_ref (BiocCheck)
    Found @ in
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    Found install() in R/bad_coding.R (line 45, column 18)
    Found install() in vignettes/testpkg0.Rmd
    * 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:
        /inst/NEWS.Rd
        /./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 4.1.0.
    * 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 even in release
    * 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

    * 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 'vignettes' directory.
    * 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 -- Tue Apr 12 06:33:52 2022 
*********************************************** 
Number of test functions: 44 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocCheck RUnit Tests - 44 test functions, 0 errors, 0 failures
Number of test functions: 44 
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 
 23.363   2.402  34.096

CHECK results for BiocCheck on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
BiocCheck	6.683	0.416	11.567
BiocCheckGitClone	0.007	0.000	0.006