QUALIFIER 1.14.1
Mike Jiang
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/QUALIFIER | | Last Changed Rev: 110425 / Revision: 116712 | | Last Changed Date: 2015-11-06 14:54:45 -0800 (Fri, 06 Nov 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings QUALIFIER_1.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/QUALIFIER.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.14.1’
* 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 ... [9s/11s] 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:::.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
.TubeNameMapping: no visible global function definition for ‘pData’
.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 ‘sampleNames’
.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’
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’
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’
save_db: no visible global function definition for ‘l_ply’
save_db : <anonymous>: no visible global function definition for
‘save_gs’
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 ... [4s/4s] 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.