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BioC 3.0: CHECK report for MSGFplus on perceval

This page was generated on 2015-04-10 10:00:26 -0700 (Fri, 10 Apr 2015).

Package 580/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.0.5
Thomas Lin Pedersen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MSGFplus
Last Changed Rev: 98993 / Revision: 102249
Last Changed Date: 2015-02-03 00:52:21 -0800 (Tue, 03 Feb 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

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

Command output

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


* 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.

MSGFplus.Rcheck/00install.out:

* 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)

MSGFplus.Rcheck/MSGFplus-Ex.timings:

nameusersystemelapsed
chargeRange0.0060.0010.007
db0.0040.0010.005
enzyme0.0140.0020.016
fragmentation0.0090.0020.012
getMSGFpar0.0140.0010.016
instrument0.0090.0010.011
isotopeError0.0050.0020.006
lengthRange0.0060.0010.008
matches0.0050.0000.006
mods0.0080.0010.009
msgfAsync-class0.0010.0000.001
msgfPar-class0.1200.0020.122
msgfPar0.0320.0020.035
msgfParChargeRange-class0.0010.0000.001
msgfParEnzyme-class0.0050.0010.007
msgfParFragmentation-class0.0050.0010.007
msgfParFromID0.0010.0000.001
msgfParGUI0.0000.0010.001
msgfParInstrument-class0.0060.0020.007
msgfParIsotopeError-class0.0010.0000.001
msgfParLengthRange-class0.0010.0000.001
msgfParMatches-class0.0010.0000.001
msgfParModification-class0.0040.0010.008
msgfParModificationList-class0.0070.0000.007
msgfParNtt-class0.0010.0000.002
msgfParProtocol-class0.0050.0000.005
msgfParTda-class0.0020.0000.001
msgfParTolerance-class0.0020.0010.002
ntt0.0040.0010.006
protocol0.0090.0020.010
runMSGF0.0010.0000.001
tda0.0050.0010.007
tolerance0.0060.0010.007