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BioC 3.2: CHECK report for flowQ on oaxaca

This page was generated on 2015-08-24 10:55:33 -0700 (Mon, 24 Aug 2015).

Package 355/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowQ 1.29.0
Mike Jiang
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flowQ
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.29.0.tar.gz
StartedAt: 2015-08-23 23:54:28 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 23:57:51 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 203.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowQ.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowQ.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.29.0’
* 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 ... [13s/14s] 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 : .local: no visible binding for global variable
  ‘variance’
* 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 ... [59s/61s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
qaProcess.2DStatsPlot  12.172  0.673  13.867
qaProcess.DensityPlot   9.791  0.390  10.926
qaProcess.ECDFPlot      9.395  0.369   9.933
qaProcess.KLDistPlot    9.380  0.368   9.934
qaProcess.BoundaryPlot  6.330  0.338   6.721
* 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-3.2-bioc/meat/flowQ.Rcheck/00check.log’
for details.


flowQ.Rcheck/00install.out:

* installing *source* package ‘flowQ’ ...
** 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 (flowQ)

flowQ.Rcheck/flowQ-Ex.timings:

nameusersystemelapsed
aggregatorList-class0.0020.0000.003
binaryAggregator-class0.0010.0010.001
discreteAggregator-class0.0010.0000.001
evaluateProcess000
factorAggregator-class0.0010.0010.001
flowQ-package0.0010.0000.000
numericAggregator-class0.0020.0000.002
outlier-class0.0010.0000.001
outlierResult-class0.0010.0000.000
qaAggregator-class0.0010.0000.001
qaGraph-class0.0010.0000.001
qaGraphList-class0.0020.0010.001
qaProcess-class0.0020.0000.002
qaProcess.2DStatsPlot12.172 0.67313.867
qaProcess.BoundaryPlot6.3300.3386.721
qaProcess.DensityPlot 9.791 0.39010.926
qaProcess.ECDFPlot9.3950.3699.933
qaProcess.KLDistPlot9.3800.3689.934
qaProcess.cellnumber0.0010.0000.001
qaProcess.marginevents0.0010.0000.001
qaProcess.timeflow0.0000.0000.001
qaProcess.timeline0.0000.0000.001
qaProcessFrame-class0.0010.0010.002
qaReport0.0000.0000.001
rangeAggregator-class0.0010.0000.001
stringAggregator-class0.0010.0010.001
txtFormatQAObject3.1200.4143.628
writeQAReport0.0010.0010.001
writeQATextReport0.0010.0000.001