BioC 3.0: CHECK report for MSGFplus on perceval

Package: MSGFplus

Version: 1.0.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSGFplus_1.0.5.tar.gz

StartedAt: 2015-04-10 04:08:59 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:10:18 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 79.0 seconds

RetCode: 0

Status:  OK

CheckDir: MSGFplus.Rcheck

Warnings: 0

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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 MSGFplus_1.0.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MSGFplus.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSGFplus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSGFplus’ version ‘1.0.5’
* 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 ‘MSGFplus’ can be installed ... [6s/9s] 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
'library' or 'require' call to ‘gWidgets’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
msgfParGUI: no visible global function definition for ‘gwindow’
msgfParGUI: no visible global function definition for ‘glayout’
msgfParGUI: no visible global function definition for ‘gfilebrowse’
msgfParGUI: no visible global function definition for ‘ggroup’
msgfParGUI: no visible global function definition for ‘gedit’
msgfParGUI: no visible global function definition for ‘size’
msgfParGUI: no visible global function definition for ‘size<-’
msgfParGUI: no visible global function definition for ‘gcombobox’
msgfParGUI: no visible global function definition for ‘gspinbutton’
msgfParGUI: no visible global function definition for ‘svalue<-’
msgfParGUI: no visible global function definition for ‘glabel’
msgfParGUI: no visible global function definition for ‘gcheckbox’
msgfParGUI: no visible global function definition for ‘gbutton’
msgfParGUI: no visible global function definition for ‘addSpace’
msgfParGUI: no visible global function definition for ‘gtable’
msgfParGUI: no visible global function definition for ‘addSpring’
msgfParGUI: no visible global function definition for
  ‘addHandlerClicked’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘gbasicdialog’
msgfParGUI : <anonymous> : <anonymous>: no visible binding for global
  variable ‘svalue’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘glayout’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘gedit’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘gcombobox’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘visible’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘svalue’
msgfParGUI : <anonymous>: no visible global function definition for
  ‘dispose’
msgfParGUI: no visible global function definition for
  ‘addHandlerUnrealize’
msgfParGUI: no visible global function definition for ‘visible<-’
* 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 ... [2s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [3s/3s]
 [3s/4s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MSGFplus.Rcheck/00check.log’
for details.

* installing *source* package ‘MSGFplus’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  Java need to be at least version 1.7 for MS-GF+ to work. Please upgrade.
* DONE (MSGFplus)

name	user	system	elapsed
chargeRange	0.006	0.001	0.007
db	0.004	0.001	0.005
enzyme	0.014	0.002	0.016
fragmentation	0.009	0.002	0.012
getMSGFpar	0.014	0.001	0.016
instrument	0.009	0.001	0.011
isotopeError	0.005	0.002	0.006
lengthRange	0.006	0.001	0.008
matches	0.005	0.000	0.006
mods	0.008	0.001	0.009
msgfAsync-class	0.001	0.000	0.001
msgfPar-class	0.120	0.002	0.122
msgfPar	0.032	0.002	0.035
msgfParChargeRange-class	0.001	0.000	0.001
msgfParEnzyme-class	0.005	0.001	0.007
msgfParFragmentation-class	0.005	0.001	0.007
msgfParFromID	0.001	0.000	0.001
msgfParGUI	0.000	0.001	0.001
msgfParInstrument-class	0.006	0.002	0.007
msgfParIsotopeError-class	0.001	0.000	0.001
msgfParLengthRange-class	0.001	0.000	0.001
msgfParMatches-class	0.001	0.000	0.001
msgfParModification-class	0.004	0.001	0.008
msgfParModificationList-class	0.007	0.000	0.007
msgfParNtt-class	0.001	0.000	0.002
msgfParProtocol-class	0.005	0.000	0.005
msgfParTda-class	0.002	0.000	0.001
msgfParTolerance-class	0.002	0.001	0.002
ntt	0.004	0.001	0.006
protocol	0.009	0.002	0.010
runMSGF	0.001	0.000	0.001
tda	0.005	0.001	0.007
tolerance	0.006	0.001	0.007