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BioC 3.2: CHECK report for MSGFplus on zin1

This page was generated on 2015-08-24 10:50:11 -0700 (Mon, 24 Aug 2015).

Package 654/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.3.0
Thomas Lin Pedersen
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSGFplus
Last Changed Rev: 104958 / Revision: 107696
Last Changed Date: 2015-06-15 05:08:15 -0700 (Mon, 15 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSGFplus
Version: 1.3.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSGFplus_1.3.0.tar.gz
StartedAt: 2015-08-24 01:58:42 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:59:19 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 36.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MSGFplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSGFplus_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MSGFplus.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.0’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [2s/2s]
 [2s/2s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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
* DONE (MSGFplus)

MSGFplus.Rcheck/MSGFplus-Ex.timings:

nameusersystemelapsed
chargeRange0.0030.0000.004
db0.0020.0000.002
enzyme0.0100.0000.009
fragmentation0.0060.0000.007
getMSGFpar0.0080.0000.008
instrument0.0060.0000.006
isotopeError0.0030.0000.002
lengthRange0.0020.0000.003
matches0.0020.0040.002
mods0.0040.0000.007
msgfAsync-class0.0010.0000.000
msgfPar-class0.0070.0000.007
msgfPar0.0200.0000.021
msgfParChargeRange-class0.0010.0000.001
msgfParEnzyme-class0.0030.0000.003
msgfParFragmentation-class0.0030.0000.003
msgfParFromID0.0010.0000.000
msgfParGUI0.0000.0000.001
msgfParInstrument-class0.0030.0000.004
msgfParIsotopeError-class0.0010.0000.000
msgfParLengthRange-class0.0000.0000.001
msgfParMatches-class0.0010.0000.000
msgfParModification-class0.0020.0000.003
msgfParModificationList-class0.0040.0000.004
msgfParNtt-class0.0010.0000.000
msgfParProtocol-class0.0040.0000.004
msgfParTda-class0.0000.0000.001
msgfParTolerance-class0.0020.0000.001
ntt0.0020.0000.002
protocol0.0060.0000.005
runMSGF0.0000.0000.001
tda0.0020.0000.002
tolerance0.0040.0000.003