BioC 3.2: CHECK report for MSGFplus on moscato1

Package: MSGFplus

Version: 1.4.0

Command: rm -rf MSGFplus.buildbin-libdir MSGFplus.Rcheck && mkdir MSGFplus.buildbin-libdir MSGFplus.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.4.0.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.4.0.tar.gz

StartedAt: 2016-04-23 05:05:06 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:07:09 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 123.2 seconds

RetCode: 0

Status:  OK

CheckDir: MSGFplus.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MSGFplus.buildbin-libdir MSGFplus.Rcheck && mkdir MSGFplus.buildbin-libdir MSGFplus.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.4.0.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.4.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MSGFplus.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MSGFplus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSGFplus' version '1.4.0'
* 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 whether package 'MSGFplus' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [3s]
 [3s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [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

Status: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/MSGFplus.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MSGFplus' ...
** 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.
* MD5 sums
packaged installation of 'MSGFplus' as MSGFplus_1.4.0.zip
* DONE (MSGFplus)

name	user	system	elapsed
chargeRange	0	0	0
db	0	0	0
enzyme	0.02	0.00	0.02
fragmentation	0	0	0
getMSGFpar	0.02	0.00	0.01
instrument	0	0	0
isotopeError	0.00	0.01	0.02
lengthRange	0	0	0
matches	0	0	0
mods	0.01	0.00	0.01
msgfAsync-class	0	0	0
msgfPar-class	0	0	0
msgfPar	0.03	0.00	0.03
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0.02	0.00	0.02
msgfParFragmentation-class	0	0	0
msgfParFromID	0	0	0
msgfParGUI	0	0	0
msgfParInstrument-class	0	0	0
msgfParIsotopeError-class	0	0	0
msgfParLengthRange-class	0	0	0
msgfParMatches-class	0	0	0
msgfParModification-class	0	0	0
msgfParModificationList-class	0.02	0.00	0.02
msgfParNtt-class	0	0	0
msgfParProtocol-class	0	0	0
msgfParTda-class	0	0	0
msgfParTolerance-class	0	0	0
ntt	0.01	0.00	0.02
protocol	0	0	0
runMSGF	0	0	0
tda	0.02	0.00	0.01
tolerance	0	0	0

name	user	system	elapsed
chargeRange	0	0	0
db	0.01	0.00	0.02
enzyme	0.02	0.00	0.01
fragmentation	0	0	0
getMSGFpar	0	0	0
instrument	0	0	0
isotopeError	0.02	0.00	0.01
lengthRange	0	0	0
matches	0	0	0
mods	0.00	0.02	0.03
msgfAsync-class	0	0	0
msgfPar-class	0.01	0.00	0.01
msgfPar	0.03	0.00	0.03
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0.02	0.00	0.02
msgfParFragmentation-class	0	0	0
msgfParFromID	0	0	0
msgfParGUI	0	0	0
msgfParInstrument-class	0.01	0.00	0.01
msgfParIsotopeError-class	0	0	0
msgfParLengthRange-class	0	0	0
msgfParMatches-class	0	0	0
msgfParModification-class	0.02	0.00	0.02
msgfParModificationList-class	0	0	0
msgfParNtt-class	0	0	0
msgfParProtocol-class	0	0	0
msgfParTda-class	0	0	0
msgfParTolerance-class	0	0	0
ntt	0.01	0.00	0.02
protocol	0	0	0
runMSGF	0.02	0.00	0.01
tda	0	0	0
tolerance	0	0	0