Multiple platform build/check report for BioC 3.8 - CHECK report for BiocCheck on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocCheck_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BiocCheck.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.18.0’
* 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:::RdTags’
  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 or elapsed time > 5s
           user system elapsed
BiocCheck 5.369  0.553    6.72
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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") 
    * ERROR: System Files found that should not be git tracked:
        something.Rproj
* Checking for blank lines in DESCRIPTION...
* 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.
* Checking for blank lines in DESCRIPTION...
* 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 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 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 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 for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: No Maintainer or Authors@R field in DESCRIPTION file.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Maintainer field in DESCRIPTION file is malformed.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking for blank lines in DESCRIPTION...
* 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 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 'parallel' 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
* 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 3 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_fun (update.packages)
      has_devel (R)
      iambad (colone)
    Found browser() in R/morecode.R (line 1, column 12)
    Found @ in
    * NOTE: Use accessors; don't access S4 class slots via '@' in
      examples/vignettes.
    * NOTE: Remove generated comments from man pages a.Rd, baddep.Rd

    * 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/
    * 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.
    * ERROR: New package version starting with 0.99.* (e.g., 0.99.0,
      0.99.1, ...); got '1.2.3'.
    * WARNING: Update R version dependency from 1.0.0 to 3.5.
    * WARNING: Register native routines; see
      http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
    * 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
    * NOTE: install, biocLite, install.packages, or update.packages
      found in R files
    bad_coding.R: 3
    * 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

    * ERROR: No 'vignettes' directory.
    * ERROR: No vignette sources in vignettes/ directory.
    # of chunks: 0, # of eval=FALSE: 0 (0%)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    * 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
    # of chunks: 0, # of eval=FALSE: 0 (0%)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    # of chunks: 0, # of eval=FALSE: 0 (0%)
    * WARNING: Remove vignette sources from inst/doc; they belong in
      vignettes/.
    # of chunks: 0, # of eval=FALSE: 0 (0%)
    * ERROR: VignetteBuilder listed in DESCRIPTION but not found as
      VignetteEngine in any vignettes:
      knitr
    * WARNING: Vignette[s] still using 'VignetteIndexEntry{Vignette
      Title}' Update the following files from using template values:
      testpkg0.Rmd
    # of chunks: 2, # of eval=FALSE: 1 (50%)
    * WARNING: Evaluate more vignette chunks.
    * NOTE: Potential intermediate files found:
        vignettes/testpkg0.html
    * ERROR: VignetteBuilder listed in DESCRIPTION but not found as
      VignetteEngine in any vignettes:
      FailBuilder
    * ERROR: VignetteEngine specified but not in DESCRIPTION. Add the
      VignetteEngine from the following files to DESCRIPTION:
      testpkg0.Rmd
    # of chunks: 2, # of eval=FALSE: 1 (50%)
    * WARNING: Evaluate more vignette chunks.
    * NOTE: Potential intermediate files found:
        vignettes/testpkg0.html


RUNIT TEST PROTOCOL -- Mon Apr 15 22:35:56 2019 
*********************************************** 
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocCheck RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29 
Number of errors: 0 
Number of failures: 0 
There were 25 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 17.140   2.106  19.897

CHECK report for BiocCheck on merida1

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
BiocCheck	5.369	0.553	6.720
BiocCheckGitClone	0.055	0.003	0.057