BioC 3.5: CHECK report for MSGFplus on tokay2

Package: MSGFplus

Version: 1.10.1

Command: rm -rf MSGFplus.buildbin-libdir MSGFplus.Rcheck && mkdir MSGFplus.buildbin-libdir MSGFplus.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.10.1.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.10.1.tar.gz

StartedAt: 2017-08-16 01:26:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:27:36 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 81.7 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MSGFplus.buildbin-libdir MSGFplus_1.10.1.tar.gz >MSGFplus.Rcheck\00install.out 2>&1 && cp MSGFplus.Rcheck\00install.out MSGFplus-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MSGFplus.buildbin-libdir --install="check:MSGFplus-install.out" --force-multiarch --no-vignettes --timings MSGFplus_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MSGFplus.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.1'
* 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 ... 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
* 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
Namespace in Imports field not imported from: 'ProtGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-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
* MD5 sums
packaged installation of 'MSGFplus' as MSGFplus_1.10.1.zip
* DONE (MSGFplus)

name	user	system	elapsed
chargeRange	0.01	0.00	0.02
db	0.07	0.00	0.06
enzyme	0.02	0.00	0.01
fragmentation	0.01	0.00	0.02
getMSGFpar	0	0	0
instrument	0	0	0
isotopeError	0	0	0
lengthRange	0	0	0
matches	0	0	0
mods	0.00	0.01	0.01
msgfAsync-class	0	0	0
msgfPar-class	0.03	0.00	0.03
msgfPar	0.05	0.00	0.05
msgfParChargeRange-class	0.01	0.00	0.02
msgfParEnzyme-class	0	0	0
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	0	0
msgfParNtt-class	0	0	0
msgfParProtocol-class	0	0	0
msgfParTda-class	0	0	0
msgfParTolerance-class	0.02	0.00	0.01
ntt	0	0	0
protocol	0	0	0
runMSGF	0.02	0.00	0.02
tda	0	0	0
tolerance	0	0	0

name	user	system	elapsed
chargeRange	0	0	0
db	0.08	0.00	0.08
enzyme	0.01	0.00	0.01
fragmentation	0.02	0.00	0.02
getMSGFpar	0	0	0
instrument	0	0	0
isotopeError	0	0	0
lengthRange	0	0	0
matches	0	0	0
mods	0.00	0.02	0.01
msgfAsync-class	0	0	0
msgfPar-class	0.03	0.00	0.03
msgfPar	0.06	0.00	0.07
msgfParChargeRange-class	0	0	0
msgfParEnzyme-class	0	0	0
msgfParFragmentation-class	0.02	0.00	0.01
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	0	0
msgfParNtt-class	0.02	0.00	0.01
msgfParProtocol-class	0	0	0
msgfParTda-class	0	0	0
msgfParTolerance-class	0	0	0
ntt	0	0	0
protocol	0.02	0.00	0.02
runMSGF	0	0	0
tda	0	0	0
tolerance	0.01	0.00	0.02