Multiple platform build/check report for BioC 3.7 - CHECK report for BiocCheck on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiocCheck.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiocCheck_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BiocCheck.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.16.0’
* 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:
  ‘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
* 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-3.7-bioc/meat/BiocCheck.Rcheck/00check.log’
for details.


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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") 
* 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)
    * 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 (function)
        RJSONIO::isValidJSON (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().
    object (function)
      update.packages (bad_fun)
      R (has_devel)
      colone (iambad)
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.
    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
    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/.
    * NOTE: skip_on_bioc() found in testthat files: a_test.R
    * NOTE: biocLite, install.packages, or update.packages found in R
      files
    bad_coding.R: 3
    * NOTE: Avoid sapply(); use vapply() found in files:
    bad_coding.R (line 9, column 5)
    * NOTE: Avoid 1:...; use seq_len() or seq_along() found in files:
    bad_coding.R (line 5, column 15)
    * 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.
    * 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.


RUNIT TEST PROTOCOL -- Mon Oct 15 22:46:51 2018 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
 11.220   0.796  18.135

CHECK report for BiocCheck on malbec2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
BiocCheck	1.812	0.120	2.744