BioC 3.0: CHECK report for MSGFplus on oaxaca

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 01:37:46 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:38:52 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 65.7 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-darwin13.4.0 (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 ... [4s/5s] 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/2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [2s/3s]
 [3s/3s] 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	0.007	0.001	0.008
db	0.005	0.001	0.006
enzyme	0.015	0.002	0.020
fragmentation	0.010	0.001	0.011
getMSGFpar	0.014	0.001	0.019
instrument	0.010	0.001	0.020
isotopeError	0.005	0.001	0.009
lengthRange	0.005	0.001	0.006
matches	0.005	0.001	0.022
mods	0.007	0.001	0.012
msgfAsync-class	0.001	0.001	0.001
msgfPar-class	0.012	0.001	0.027
msgfPar	0.085	0.001	0.115
msgfParChargeRange-class	0.001	0.000	0.001
msgfParEnzyme-class	0.005	0.000	0.004
msgfParFragmentation-class	0.005	0.000	0.006
msgfParFromID	0.001	0.000	0.000
msgfParGUI	0.000	0.000	0.001
msgfParInstrument-class	0.005	0.000	0.013
msgfParIsotopeError-class	0.001	0.000	0.001
msgfParLengthRange-class	0.001	0.000	0.003
msgfParMatches-class	0.001	0.000	0.001
msgfParModification-class	0.004	0.001	0.004
msgfParModificationList-class	0.007	0.001	0.008
msgfParNtt-class	0.001	0.001	0.001
msgfParProtocol-class	0.005	0.001	0.005
msgfParTda-class	0.001	0.000	0.001
msgfParTolerance-class	0.002	0.000	0.002
ntt	0.006	0.000	0.009
protocol	0.009	0.000	0.016
runMSGF	0.001	0.000	0.001
tda	0.005	0.001	0.009
tolerance	0.006	0.001	0.007