QUALIFIER 1.12.1
Mike Jiang
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/QUALIFIER | | Last Changed Rev: 106586 / Revision: 109384 | | Last Changed Date: 2015-07-20 12:03:07 -0700 (Mon, 20 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && mkdir QUALIFIER.buildbin-libdir QUALIFIER.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QUALIFIER.buildbin-libdir QUALIFIER_1.12.1.tar.gz >QUALIFIER.Rcheck\00install.out 2>&1 && cp QUALIFIER.Rcheck\00install.out QUALIFIER-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=QUALIFIER.buildbin-libdir --install="check:QUALIFIER-install.out" --force-multiarch --no-vignettes --timings QUALIFIER_1.12.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/QUALIFIER.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QUALIFIER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QUALIFIER' version '1.12.1'
* 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 whether package 'QUALIFIER' can be installed ... 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
* 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
** checking loading without being on the library search path ... 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 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
.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 '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'
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 ...
** running examples for arch 'i386' ... [3s] OK
** running examples for arch 'x64' ... [4s] OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/QUALIFIER.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'QUALIFIER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QUALIFIER' as QUALIFIER_1.12.1.zip
* DONE (QUALIFIER)