Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P [Q] R  S  T  U  V  W  X  Y  Z 

BioC 3.2: CHECK report for QUALIFIER on perceval

This page was generated on 2015-10-27 17:34:57 -0400 (Tue, 27 Oct 2015).

Package 824/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QUALIFIER 1.14.0
Mike Jiang
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/QUALIFIER
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QUALIFIER
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QUALIFIER_1.14.0.tar.gz
StartedAt: 2015-10-27 11:18:33 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:20:35 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 121.4 seconds
RetCode: 0
Status:  OK 
CheckDir: QUALIFIER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QUALIFIER_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QUALIFIER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QUALIFIER’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘flowCore’ ‘flowViz’ ‘ncdfFlow’ ‘flowWorkspace’ ‘data.table’
  ‘reshape’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘QUALIFIER’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘flowViz’ ‘flowWorkspace’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘flowViz’ ‘grDevices’ ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘data.table’ ‘flowCore’ ‘flowViz’ ‘ncdfFlow’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘flowWorkspace:::mkformula’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
  ‘flowWorkspace:::.formulaParser’ ‘flowWorkspace:::.getNodeInd’
  ‘flowWorkspace:::.getPopStat’ ‘lattice:::calculateGridLayout’
  ‘lattice:::checkArgsAndCall’ ‘lattice:::chooseFace’
  ‘lattice:::compute.layout’ ‘lattice:::drawInViewport’
  ‘lattice:::evaluate.legend’ ‘lattice:::getFunctionOrName’
  ‘lattice:::getLabelList’ ‘lattice:::grobFromLabelList’
  ‘lattice:::lattice.getStatus’ ‘lattice:::lattice.setStatus’
  ‘lattice:::layoutNCol’ ‘lattice:::layoutNRow’
  ‘lattice:::paste.and.draw’ ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getName’ ‘height’ ‘width’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addStats: no visible global function definition for ‘getData’
.addStats: no visible binding for global variable ‘value’
.addStats: no visible global function definition for ‘:=’
.addStats: no visible binding for global variable ‘stats’
.addStats: no visible binding for global variable ‘sid’
.addStats: no visible binding for global variable ‘channel’
.addStats: no visible binding for global variable ‘stain’
.addStats: no visible binding for global variable ‘population’
.addStats: no visible binding for global variable ‘node’
.addStats: no visible global function definition for ‘setcolorder’
.addStats: no visible global function definition for ‘rbindlist’
.getQAStats.env: no visible global function definition for ‘:=’
.getQAStats.env: no visible global function definition for ‘rbindlist’
.getQAStats.env: no visible binding for global variable ‘sid’
.getQAStats.gh: no visible global function definition for ‘getSample’
.getQAStats.gh: no visible global function definition for ‘getNodes’
.getQAStats.gh: no visible global function definition for ‘getData’
.getQAStats.gh: no visible global function definition for ‘pData’
.getQAStats.gh: no visible global function definition for ‘parameters’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘getGate’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘parameters’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘data.table’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘exprs’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘rbindlist’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘getData’
.getQAStats.gh : <anonymous>: no visible global function definition for
  ‘:=’
.getQAStats.gh : <anonymous>: no visible binding for global variable
  ‘node’
.getQAStats.gh : <anonymous>: no visible binding for global variable
  ‘population’
.getQAStats.gh: no visible global function definition for ‘rbindlist’
.parseTubeID: no visible global function definition for ‘pData’
.parseTubeID: no visible global function definition for ‘pData<-’
.qaCheck: no visible global function definition for ‘getData’
.qaCheck: no visible global function definition for ‘rename’
.qaCheck : .funcOutlierGrp: no visible binding for global variable
  ‘.SD’
.qaCheck : .funcOutlierGrp: no visible binding for global variable ‘V1’
.qaCheck : .funcOutlierGrp: no visible binding for global variable
  ‘sid’
.qaCheck: no visible binding for global variable ‘.SD’
.qaCheck: no visible binding for global variable ‘V1’
.qaCheck : .funcOutlier: no visible binding for global variable ‘sid’
.queryStats : <anonymous>: no visible global function definition for
  ‘pData’
.queryStats: no visible global function definition for ‘pData’
.queryStats: no visible binding for global variable ‘stats’
.read.qaTask : <anonymous>: no visible binding for global variable
  ‘aoutlierFunc_args’
.setupPlotTheme: no visible global function definition for
  ‘standard.theme’
.timelineplot: no visible global function definition for ‘exprs’
.TubeNameMapping: no visible global function definition for ‘pData’
clearCheck: no visible global function definition for ‘getData’
createDbSchema: no visible global function definition for ‘rename’
load_db: no visible global function definition for ‘l_ply’
load_db : <anonymous>: no visible global function definition for
  ‘load_gs’
panel.bwplotEx: no visible global function definition for
  ‘trellis.par.get’
panel.bwplotEx: no visible global function definition for
  ‘current.panel.limits’
panel.bwplotEx: no visible global function definition for ‘:=’
panel.bwplotEx: no visible binding for global variable ‘.BY’
panel.bwplotEx: no visible binding for global variable ‘.SD’
panel.bwplotEx: no visible global function definition for
  ‘panel.polygon’
panel.bwplotEx: no visible global function definition for
  ‘panel.segments’
panel.bwplotEx: no visible global function definition for
  ‘panel.points’
panel.bwplotEx: no visible binding for global variable ‘outlier’
panel.bwplotEx: no visible binding for global variable ‘gOutlier’
panel.xyplot.flowsetEx: no visible global function definition for
  ‘panel.xyplot.flowset’
panel.xyplot.qa: no visible global function definition for ‘panel.text’
panel.xyplot.qa: no visible global function definition for
  ‘panel.abline’
panel.xyplotEx: no visible global function definition for
  ‘trellis.par.get’
panel.xyplotEx: no visible binding for global variable ‘panel.grid’
panel.xyplotEx: no visible binding for global variable ‘panel.abline’
panel.xyplotEx: no visible global function definition for
  ‘panel.superpose’
panel.xyplotEx: no visible global function definition for
  ‘panel.points’
panel.xyplotEx: no visible global function definition for ‘panel.lines’
panel.xyplotEx: no visible global function definition for
  ‘panel.lmline’
panel.xyplotEx: no visible global function definition for ‘panel.loess’
panel.xyplotEx: no visible global function definition for
  ‘panel.linejoin’
plot.qaTask: no visible global function definition for ‘description’
plot.qaTask: no visible global function definition for
  ‘lattice.options’
plot.qaTask: no visible global function definition for ‘getData’
plot.qaTask: no visible global function definition for ‘:=’
plot.qaTask: no visible binding for global variable ‘outlier’
plot.qaTask: no visible binding for global variable ‘gOutlier’
plot.qaTask: no visible global function definition for ‘rename’
plot.trellisEx: no visible binding for global variable
  ‘packet.panel.default’
plot.trellisEx: no visible global function definition for
  ‘lattice.getOption’
plot.trellisEx: no visible global function definition for
  ‘trellis.device’
plot.trellisEx: no visible global function definition for
  ‘trellis.par.get’
plot.trellisEx: no visible global function definition for
  ‘trellis.par.set’
plot.trellisEx: no visible global function definition for
  ‘lattice.options’
plot.trellisEx: no visible global function definition for
  ‘trellis.grobname’
plot.trellisEx: no visible global function definition for
  ‘trellis.vpname’
plot.trellisEx: no visible global function definition for ‘panel.fill’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getGate’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getProp’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘pData’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘parameters’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getData’
qa.GroupPlot : <anonymous>: no visible binding for global variable
  ‘channel’
qa.GroupPlot : <anonymous>: no visible global function definition for
  ‘getParent’
qa.GroupPlot: no visible global function definition for ‘flowSet’
qa.GroupPlot: no visible binding for global variable ‘name’
qaWrite.list: no visible global function definition for ‘getData’
qaWrite.summary: no visible global function definition for ‘getData’
qaWrite.summary: no visible global function definition for ‘pData’
qaWrite.summary: no visible global function definition for ‘cast’
qaWrite.task: no visible global function definition for ‘getData’
qaWrite.task: no visible global function definition for ‘pData’
qaWrite.task: no visible global function definition for ‘rename’
qaWrite.task: no visible global function definition for ‘description’
qaWrite.task: no visible global function definition for ‘melt’
qaWrite.task: no visible global function definition for ‘cast’
qaWrite.task : <anonymous>: no visible global function definition for
  ‘getData’
read.qaTask: no visible global function definition for ‘fread’
save_db: no visible global function definition for ‘l_ply’
save_db : <anonymous>: no visible global function definition for
  ‘save_gs’
saveToDB: no visible global function definition for ‘pData’
saveToDB: no visible global function definition for ‘fread’
saveToDB: no visible binding for global variable ‘name’
saveToDB: no visible global function definition for ‘sampleNames’
saveToDB: no visible global function definition for ‘pData<-’
saveToDB: no visible global function definition for ‘getData’
stripEx: no visible global function definition for ‘trellis.par.get’
stripEx: no visible global function definition for ‘trellis.grobname’
getQAStats,GatingSet: no visible global function definition for ‘pData’
getQAStats,GatingSet: no visible global function definition for
  ‘sampleNames’
queryStats,qaTask : .local: no visible global function definition for
  ‘getData’
show,qaTask: no visible global function definition for ‘description’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/5s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/QUALIFIER.Rcheck/00check.log’
for details.

QUALIFIER.Rcheck/00install.out:

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

QUALIFIER.Rcheck/QUALIFIER-Ex.timings:

nameusersystemelapsed
getQAStats0.0010.0000.001
initDB0.0040.0000.005
plot-methods0.0010.0000.001
qaCheck-methods0.0010.0000.002
qaPreprocess0.0000.0000.001
qaReport0.0010.0000.001
read.qaTask0.0010.0010.000
saveToDB0.0010.0000.001
save_db0.0000.0000.001