BioC 2.14: CHECK report for mzID on petty

Package: mzID

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mzID_1.2.1.tar.gz

StartedAt: 2014-10-07 23:10:34 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:12:08 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 93.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: mzID.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mzID_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/mzID.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzID’ version ‘1.2.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘mzID’ can be installed ... [6s/6s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mzID: no visible binding for global variable ‘i’
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'length,mzID-method':
  ‘length-mzID-method.Rd’ ‘length.Rd’
Rd files with duplicated alias 'length,mzIDdatabase-method':
  ‘length-mzIDdatabase-method.Rd’ ‘length.Rd’
Rd files with duplicated alias 'length,mzIDevidence-method':
  ‘length-mzIDevidence-method.Rd’ ‘length.Rd’
Rd files with duplicated alias 'length,mzIDparameters-method':
  ‘length-mzIDparameters-method.Rd’ ‘length.Rd’
Rd files with duplicated alias 'length,mzIDpeptides-method':
  ‘length-mzIDpeptides-method.Rd’ ‘length.Rd’
Rd files with duplicated alias 'length,mzIDpsm-method':
  ‘length-mzIDpsm-method.Rd’ ‘length.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'names' and siglist 'mzIDCollection'
  generic 'names<-' and siglist 'mzIDCollection,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'Utilities':
  ‘\S4method{names}{mzIDCollection}’

Bad \usage lines found in documentation object 'Utilities':
  <unescaped bksl>S4method{names<-}{mzIDCollection}(x, value)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/19s] OK
Examples with CPU or elapsed time > 5s
      user system elapsed
mzID 6.013  0.087  12.282
* 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

WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/mzID.Rcheck/00check.log’
for details.

* installing *source* package ‘mzID’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzID)

name	user	system	elapsed
flatten-methods	1.127	0.030	2.633
mzID	6.013	0.087	12.282