flowQ 1.35.1
Mike Jiang
| Snapshot Date: 2017-04-11 17:17:07 -0400 (Tue, 11 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ | | Last Changed Rev: 127583 / Revision: 128559 | | Last Changed Date: 2017-03-21 13:32:42 -0400 (Tue, 21 Mar 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | 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 flowQ_1.35.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowQ.Rcheck’
* using R version 3.4.0 beta (2017-04-08 r72499)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQ’ version ‘1.35.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘outliers’ ‘lattice’ ‘flowViz’ ‘mvoutlier’ ‘bioDist’
‘parody’ ‘RColorBrewer’ ‘latticeExtra’
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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowQ’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘flowViz’
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
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
All declared Imports should be used.
Packages in Depends field not imported from:
‘RColorBrewer’ ‘bioDist’ ‘flowViz’ ‘lattice’ ‘latticeExtra’
‘mvoutlier’ ‘outliers’ ‘parody’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mySd: no visible binding for global variable ‘sd’
.mySd: no visible global function definition for ‘sd’
.mybw.nrd0: no visible global function definition for ‘IQR’
evaluateProcess: multiple local function definitions for ‘efun’ with
different formal arguments
failedProcesses: no visible global function definition for ‘listLen’
normalizeSets : <anonymous>: no visible global function definition for
‘warpSet’
outlierD : <anonymous>: no visible global function definition for
‘dixon.test’
outlierG : <anonymous>: no visible global function definition for
‘grubbs.test’
outlierX2 : <anonymous>: no visible global function definition for
‘chisq.out.test’
outlierX2 : <anonymous>: no visible global function definition for
‘var’
qaProcess.2DStatsPlot: no visible global function definition for
‘colorRampPalette’
qaProcess.2DStatsPlot: no visible global function definition for
‘brewer.pal’
qaProcess.2DStatsPlot: no visible global function definition for
‘pcout’
qaProcess.2DStatsPlot: no visible global function definition for
‘xyplot’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.2DStatsPlot: no visible global function definition for
‘extendrange’
qaProcess.2DStatsPlot: no visible global function definition for
‘simpleKey’
qaProcess.2DStatsPlot: no visible global function definition for
‘dev.off’
qaProcess.BoundaryPlot: no visible global function definition for
‘colorRampPalette’
qaProcess.BoundaryPlot: no visible global function definition for
‘brewer.pal’
qaProcess.BoundaryPlot: no visible global function definition for
‘barchart’
qaProcess.BoundaryPlot: no visible global function definition for
‘simpleKey’
qaProcess.BoundaryPlot: no visible global function definition for
‘dev.off’
qaProcess.DensityPlot: no visible global function definition for
‘colorRampPalette’
qaProcess.DensityPlot: no visible global function definition for
‘brewer.pal’
qaProcess.DensityPlot: no visible global function definition for
‘density’
qaProcess.DensityPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.DensityPlot: no visible global function definition for
‘xyplot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible global function definition for
‘simpleKey’
qaProcess.DensityPlot: no visible global function definition for
‘densityplot’
qaProcess.DensityPlot : <anonymous>: no visible binding for global
variable ‘panel.xyplot’
qaProcess.DensityPlot : <anonymous>: no visible global function
definition for ‘trellis.panelArgs’
qaProcess.DensityPlot: no visible global function definition for
‘dev.off’
qaProcess.DensityPlot: no visible global function definition for
‘calout.detect’
qaProcess.ECDFPlot: no visible global function definition for
‘colorRampPalette’
qaProcess.ECDFPlot: no visible global function definition for
‘brewer.pal’
qaProcess.ECDFPlot: no visible global function definition for ‘ppoints’
qaProcess.ECDFPlot: no visible global function definition for
‘quantile’
qaProcess.ECDFPlot: no visible global function definition for ‘xyplot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible global function definition for
‘simpleKey’
qaProcess.ECDFPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.ECDFPlot: no visible global function definition for
‘ecdfplot’
qaProcess.ECDFPlot: no visible global function definition for
‘densityplot’
qaProcess.ECDFPlot : <anonymous>: no visible binding for global
variable ‘panel.xyplot’
qaProcess.ECDFPlot : <anonymous>: no visible global function definition
for ‘trellis.panelArgs’
qaProcess.ECDFPlot: no visible global function definition for ‘dev.off’
qaProcess.ECDFPlot: no visible global function definition for
‘calout.detect’
qaProcess.KLDistPlot: no visible global function definition for
‘colorRampPalette’
qaProcess.KLDistPlot: no visible global function definition for
‘brewer.pal’
qaProcess.KLDistPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.KLDistPlot: no visible global function definition for
‘levelplot’
qaProcess.KLDistPlot: no visible global function definition for
‘dev.off’
qaProcess.KLDistPlot: no visible global function definition for
‘calout.detect’
qaProcess.cellnumber: no visible global function definition for ‘par’
qaProcess.cellnumber: no visible global function definition for
‘barplot’
qaProcess.cellnumber: no visible global function definition for
‘abline’
qaProcess.cellnumber: no visible global function definition for ‘text’
qaProcess.cellnumber: no visible global function definition for
‘dev.off’
qaProcess.marginevents: no visible global function definition for
‘colorRampPalette’
qaProcess.marginevents: no visible global function definition for
‘levelplot’
qaProcess.marginevents: no visible global function definition for
‘dev.off’
qaProcess.marginevents: no visible global function definition for ‘par’
qaProcess.marginevents: no visible global function definition for
‘density’
qaProcess.marginevents: no visible global function definition for
‘extendrange’
qaProcess.marginevents: no visible global function definition for
‘polygon’
qaProcess.marginevents: no visible global function definition for
‘text’
qaProcess.timeflow: no visible global function definition for ‘median’
qaProcess.timeflow: no visible global function definition for
‘timeLinePlot’
qaProcess.timeflow: no visible global function definition for ‘text’
qaProcess.timeflow: no visible global function definition for ‘dev.off’
qaProcess.timeline: no visible global function definition for ‘median’
qaProcess.timeline: no visible global function definition for
‘timeLinePlot’
qaProcess.timeline: no visible global function definition for ‘text’
qaProcess.timeline: no visible global function definition for ‘dev.off’
writeQATextReport: no visible global function definition for
‘write.table’
outliers,flowSet: no visible binding for global variable ‘variance’
Undefined global functions or variables:
Aliquot IQR KLdist.matrix abline barchart barplot brewer.pal
calout.detect chisq.out.test colorRampPalette density densityplot
dev.off dixon.test ecdfplot extendrange grubbs.test levelplot listLen
median panel.xyplot par pcout polygon ppoints quantile sd simpleKey
text timeLinePlot trellis.panelArgs var variance warpSet write.table
xyplot
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "extendrange")
importFrom("graphics", "abline", "barplot", "par", "polygon", "text")
importFrom("stats", "IQR", "density", "median", "ppoints", "quantile",
"sd", "var")
importFrom("utils", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'qaProcess.timeflow.Rd':
‘[flowViz:timeLinePlot-methods]{timeLinePlot}’
Missing link or links in documentation object 'qaProcess.timeline.Rd':
‘[flowViz:timeLinePlot-methods]{timeLinePlot}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qaProcess.2DStatsPlot 10.742 0.895 11.974
qaProcess.DensityPlot 9.111 0.544 9.886
qaProcess.KLDistPlot 8.802 0.541 9.545
qaProcess.ECDFPlot 8.641 0.515 9.376
qaProcess.BoundaryPlot 7.428 0.524 8.192
* 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 WARNING, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/flowQ.Rcheck/00check.log’
for details.