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BioC 3.5: CHECK report for MSGFplus on tokay2

This page was generated on 2017-08-16 13:23:46 -0400 (Wed, 16 Aug 2017).

Package 858/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.10.1
Thomas Lin Pedersen
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MSGFplus
Last Changed Rev: 130536 / Revision: 131943
Last Changed Date: 2017-06-19 17:34:07 -0400 (Mon, 19 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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.


MSGFplus.Rcheck/00install.out:


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)

MSGFplus.Rcheck/examples_i386/MSGFplus-Ex.timings:

nameusersystemelapsed
chargeRange0.010.000.02
db0.070.000.06
enzyme0.020.000.01
fragmentation0.010.000.02
getMSGFpar000
instrument000
isotopeError000
lengthRange000
matches000
mods0.000.010.01
msgfAsync-class000
msgfPar-class0.030.000.03
msgfPar0.050.000.05
msgfParChargeRange-class0.010.000.02
msgfParEnzyme-class000
msgfParFragmentation-class000
msgfParFromID000
msgfParGUI000
msgfParInstrument-class000
msgfParIsotopeError-class000
msgfParLengthRange-class000
msgfParMatches-class000
msgfParModification-class000
msgfParModificationList-class000
msgfParNtt-class000
msgfParProtocol-class000
msgfParTda-class000
msgfParTolerance-class0.020.000.01
ntt000
protocol000
runMSGF0.020.000.02
tda000
tolerance000

MSGFplus.Rcheck/examples_x64/MSGFplus-Ex.timings:

nameusersystemelapsed
chargeRange000
db0.080.000.08
enzyme0.010.000.01
fragmentation0.020.000.02
getMSGFpar000
instrument000
isotopeError000
lengthRange000
matches000
mods0.000.020.01
msgfAsync-class000
msgfPar-class0.030.000.03
msgfPar0.060.000.07
msgfParChargeRange-class000
msgfParEnzyme-class000
msgfParFragmentation-class0.020.000.01
msgfParFromID000
msgfParGUI000
msgfParInstrument-class000
msgfParIsotopeError-class000
msgfParLengthRange-class000
msgfParMatches-class000
msgfParModification-class000
msgfParModificationList-class000
msgfParNtt-class0.020.000.01
msgfParProtocol-class000
msgfParTda-class000
msgfParTolerance-class000
ntt000
protocol0.020.000.02
runMSGF000
tda000
tolerance0.010.000.02