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BioC 3.0: CHECK report for msQC on perceval

This page was generated on 2014-07-31 10:58:09 -0700 (Thu, 31 Jul 2014).

Package 536/858HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msQC 0.99.7
Bo Wen
Snapshot Date: 2014-07-30 16:20:07 -0700 (Wed, 30 Jul 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msQC
Last Changed Rev: 90682 / Revision: 93061
Last Changed Date: 2014-05-23 13:38:17 -0700 (Fri, 23 May 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.2) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: msQC
Version: 0.99.7
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch msQC_0.99.7.tar.gz
StartedAt: 2014-07-31 02:13:45 -0700 (Thu, 31 Jul 2014)
EndedAt: 2014-07-31 02:14:57 -0700 (Thu, 31 Jul 2014)
EllapsedTime: 72.1 seconds
RetCode: 0
Status:  OK 
CheckDir: msQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch msQC_0.99.7.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/msQC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msQC’ version ‘0.99.7’
* 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 ‘msQC’ can be installed ... [5s/6s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addSummaryChart: no visible binding for global variable ‘peplength’
addSummaryChart: no visible binding for global variable ‘..count..’
addSummaryChart: no visible binding for global variable ‘delta’
msQC.barplot: no visible binding for global variable ‘x’
msQC.barplot: no visible binding for global variable ‘y’
msQC.barplot: no visible binding for global variable ‘label’
plotMS1Error: no visible binding for '<<-' assignment to ‘curenv’
plotMS1Error: no visible binding for global variable ‘bioRep’
plotMS1Error: no visible binding for global variable ‘techRep’
plotMS1Error: no visible binding for global variable ‘fraction’
plotMS1Error: no visible binding for global variable ‘peptide_summary’
plotMS1Error: no visible binding for global variable ‘curenv’
plotMS1Error : <anonymous>: no visible binding for global variable
  ‘curenv’
plotMS2Error: no visible binding for global variable ‘bioRep’
plotMS2Error: no visible binding for global variable ‘techRep’
plotMS2Error: no visible binding for global variable ‘fraction’
plotMS2Error: no visible binding for global variable ‘peptide_summary’
plotSampleIDResultErrorBar: no visible binding for global variable
  ‘fraction’
plotSampleIDResultErrorBar: no visible binding for global variable
  ‘val’
plotSampleIDResultErrorBar: no visible binding for global variable ‘se’
qcHist: no visible binding for global variable ‘error’
qcHist: no visible binding for global variable ‘techRep’
qcHist: no visible binding for global variable ‘bioRep’
qcHist: no visible global function definition for ‘labs’
qcHist2: no visible binding for global variable ‘error’
qcHist2: no visible binding for global variable ‘fractile’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [3s/4s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/msQC.Rcheck/00check.log’
for details.

msQC.Rcheck/00install.out:

* installing *source* package ‘msQC’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (msQC)

msQC.Rcheck/msQC-Ex.timings:

nameusersystemelapsed
loadmsQCres0.0880.1180.329
msQCpipe0.0020.0000.002
print.msQCres0.0930.0920.356
reportHTML0.0870.0930.283
showEnzyme0.0120.0020.015
showMods0.0060.0010.008