flowQ 1.31.0
Mike Jiang
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowQ_1.31.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowQ.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.31.0’
* 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 ... [9s/9s] 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
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’
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
‘simpleKey’
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.DensityPlot: no visible global function definition for
‘brewer.pal’
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
‘calout.detect’
qaProcess.ECDFPlot: no visible global function definition for
‘brewer.pal’
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
‘calout.detect’
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
‘calout.detect’
qaProcess.marginevents: no visible global function definition for
‘levelplot’
qaProcess.timeflow: no visible global function definition for
‘timeLinePlot’
qaProcess.timeline: no visible global function definition for
‘timeLinePlot’
outliers,flowSet: no visible binding for global variable ‘variance’
Undefined global functions or variables:
Aliquot KLdist.matrix barchart brewer.pal calout.detect
chisq.out.test densityplot dixon.test ecdfplot grubbs.test levelplot
listLen panel.xyplot pcout simpleKey timeLinePlot trellis.panelArgs
variance warpSet xyplot
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
qaProcess.2DStatsPlot 11.143 0.600 8.784
qaProcess.ECDFPlot 6.340 0.366 6.586
qaProcess.DensityPlot 5.413 0.344 5.626
qaProcess.KLDistPlot 5.295 0.326 5.489
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/flowQ.Rcheck/00check.log’
for details.