BioC 3.4: CHECK report for BiocCheck on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocCheck_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BiocCheck.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocCheck/DESCRIPTION’ ... OK
* this is package ‘BiocCheck’ version ‘1.10.1’
* 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:
  ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
BiocCheck 2.97  0.166   8.044
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
   
  1 Test Suite : 
  BiocCheck RUnit Tests - 29 test functions, 0 errors, 1 failure
  FAILURE in test_checkForBiocDevelSubscription: Error in checkTrue(stillZero()) : Test not TRUE
  
  
  Test files with failing tests
  
     test_BiocCheck.R 
       test_checkForBiocDevelSubscription 
  
  
  Error in BiocGenerics:::testPackage("BiocCheck") : 
    unit tests failed for package BiocCheck
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.


R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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") 
* 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 dir/tarball name...
    * ERROR: Package dir 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 dir/tarball name...
    * ERROR: Package dir unitTestTempDir must match Package: field (
      got )!
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches dir/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 dir/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: One author with maintainer (cre) role.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches dir/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: 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 dir/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
    * ERROR: Email address in Maintainer field.
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches dir/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 dir/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking that biocViews are present...
    * ERROR: Add some biocViews!
* Checking that biocViews are present...
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
    * WARNING: Use valid biocViews. Invalid ones: foo, Cancer, bar, baz
* Checking for recommended biocViews...
* Checking that biocViews are present...
* 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 for non-trivial biocViews...
* Checking that biocViews come from the same category...
    * WARNING: Use biocViews from one category only (one of Software,
      ExperimentData, AnnotationData)
    * 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 (RJSONIO) which provide isValidJSON (used in
      baddep) should be imported in the NAMESPACE file, otherwise
      packages that import testpkg0 could fail.
* Checking to see if we understand object initialization....
    * NOTE: Consider clarifying how objects 'R, colone' (used in
      has_devel, iambad) were initialized. Maybe they are part of a
      data set loaded with data(), or perhaps part of an object
      referenced in with() or within().
    * ERROR: Maintainer should subscribe to the bioc-devel mailing
      list. Subscribe here:
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
    * ERROR: Maintainer should subscribe to the bioc-devel mailing
      list. Subscribe here:
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
Timing stopped at: 0.046 0.003 3.517 
Error in checkTrue(stillZero()) : Test not TRUE

Loading required namespace: knitr
      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.
    * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain
      tabs.
    * NOTE: Consider indenting lines with a multiple of 4 spaces; 1
      lines (0%) are not.
  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 3.3.
    * WARNING: Register native routines! see
      http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines
      Found T in R/morecode.R (line 10, column 8)
      Found F in R/morecode.R (line 7, column 5)
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
    * ERROR: Valid package Version, see
      http://www.bioconductor.org/developers/how-to/version-numbering/
    * ERROR: Valid 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: 'vignettes' directory!
    * ERROR: vignette sources in vignettes/ directory.
      # 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%)
      # of chunks: 0, # of eval=FALSE: 0 (0%)
      # of chunks: 2, # of eval=FALSE: 1 (50%)
    * WARNING: Evaluate more vignette chunks.


RUNIT TEST PROTOCOL -- Fri Apr 14 23:11:49 2017 
*********************************************** 
Number of test functions: 29 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
BiocCheck RUnit Tests - 29 test functions, 0 errors, 1 failure
FAILURE in test_checkForBiocDevelSubscription: Error in checkTrue(stillZero()) : Test not TRUE


Test files with failing tests

   test_BiocCheck.R 
     test_checkForBiocDevelSubscription 


Error in BiocGenerics:::testPackage("BiocCheck") : 
  unit tests failed for package BiocCheck
Execution halted

BioC 3.4: CHECK report for BiocCheck on morelia

Summary

Command output