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BioC 3.5: CHECK report for MSGFplus on malbec2

This page was generated on 2017-10-18 14:16:13 -0400 (Wed, 18 Oct 2017).

Package 858/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSGFplus 1.10.1
Thomas Lin Pedersen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MSGFplus
Branch: RELEASE_3_5
Last Commit: 51b755d
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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MSGFplus_1.10.1.tar.gz
StartedAt: 2017-10-18 01:00:48 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:01:25 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 37.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MSGFplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MSGFplus_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MSGFplus.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.10.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.5-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
chargeRange0.0000.0000.003
db0.0480.0000.049
enzyme0.0120.0000.010
fragmentation0.0080.0000.006
getMSGFpar0.0040.0000.006
instrument0.0040.0000.005
isotopeError0.0040.0000.002
lengthRange0.0000.0000.002
matches0.0000.0000.002
mods0.0040.0000.004
msgfAsync-class000
msgfPar-class0.0240.0000.027
msgfPar0.1000.0000.101
msgfParChargeRange-class0.0000.0000.001
msgfParEnzyme-class0.0040.0000.002
msgfParFragmentation-class0.0040.0000.002
msgfParFromID000
msgfParGUI000
msgfParInstrument-class0.0040.0000.003
msgfParIsotopeError-class000
msgfParLengthRange-class0.0000.0000.001
msgfParMatches-class000
msgfParModification-class0.0040.0000.002
msgfParModificationList-class0.0040.0000.003
msgfParNtt-class000
msgfParProtocol-class0.0040.0000.002
msgfParTda-class000
msgfParTolerance-class0.0040.0000.001
ntt0.0000.0000.002
protocol0.0040.0000.004
runMSGF0.0000.0000.001
tda0.0000.0000.002
tolerance0.0000.0000.003