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BioC 3.2: CHECK report for flowStats on perceval

This page was generated on 2015-08-24 10:51:50 -0700 (Mon, 24 Aug 2015).

Package 359/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 3.27.0
Greg Finak and Mike Jiang
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats
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  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowStats
Version: 3.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowStats_3.27.0.tar.gz
StartedAt: 2015-08-24 00:44:54 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 00:49:45 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 290.7 seconds
RetCode: 0
Status:  OK 
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowStats_3.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowStats.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.27.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘flowStats’ can be installed ... [17s/17s] 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:
  ‘flowCore’ ‘fda’
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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘flowWorkspace::getDimensions’
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
  ‘flowCore:::findTimeChannel’ ‘flowCore:::inpolygon’
  ‘flowViz:::plotType’ ‘flowWorkspace:::.isBoolGate’
  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:
  ‘backGating’ ‘curvPeaks’ ‘getPeakRegions’ ‘idFeaturesByBackgating’
  ‘landmarkMatrixWithoutFilterResult’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
  parameters(table), preselection = pre, scale = table@scale, bwFac =
  table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
  partial argument match of 'eval' to 'evaluate'
.normalizeGatingSet: no visible global function definition for
  ‘getNodes’
.normalizeGatingSet: no visible global function definition for ‘clone’
.normalizeGatingSet: no visible global function definition for
  ‘getGate’
.normalizeGatingSet: no visible global function definition for
  ‘getParent’
.normalizeGatingSet: no visible global function definition for
  ‘flowData<-’
.normalizeGatingSet: no visible global function definition for
  ‘flowData’
.normalizeGatingSet: no visible global function definition for
  ‘recompute’
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
density1d_simple: no visible binding for global variable ‘y’
fdPar: no visible global function definition for ‘fd’
fdPar: no visible global function definition for ‘vec2Lfd’
fdPar: no visible global function definition for ‘norder.bspline’
fdPar: no visible global function definition for ‘int2Lfd’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
singletGate: no visible global function definition for ‘polygonGate’
warpSetNCDF: no visible global function definition for
  ‘clone.ncdfFlowSet’
addName,curv1Filter-character : .local: no visible global function
  definition for ‘identifier’
addName,curv1Filter-character : .local: no visible global function
  definition for ‘checkParameterMatch’
addName,curv1Filter-character : .local: no visible global function
  definition for ‘addName’
addName,curv1Filter-logical : .local: no visible global function
  definition for ‘addName’
addName,curv2Filter-character : .local: no visible global function
  definition for ‘identifier’
addName,curv2Filter-character : .local: no visible global function
  definition for ‘checkParameterMatch’
addName,curv2Filter-character : .local: no visible global function
  definition for ‘addName’
addName,curv2Filter-character : .local: no visible global function
  definition for ‘polygonGate’
addName,curv2Filter-logical : .local: no visible global function
  definition for ‘addName’
densityplot,view-missing : .local: no visible global function
  definition for ‘Data’
glines,curv1Filter-ANY : .local: no visible global function definition
  for ‘evalError’
glines,curv1Filter-flowFrame : .local: no visible global function
  definition for ‘glines’
glines,curv1Filter-missing : .local: no visible global function
  definition for ‘evalError’
glines,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
glines,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘brewer.pal’
glines,curv1Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘glines’
glines,curv2Filter-ANY : .local: no visible global function definition
  for ‘evalError’
glines,curv2Filter-flowFrame : .local: no visible global function
  definition for ‘glines’
glines,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
glines,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘brewer.pal’
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘glines’
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘polygonGate’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘flowViz.par.get’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘multFiltPoints’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘addName’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘flowViz.par.get’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘multFiltPoints’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘addName’
glpolygon,curv1Filter-ANY: no visible global function definition for
  ‘evalError’
glpolygon,curv1Filter-flowFrame : .local: no visible global function
  definition for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
glpolygon,curv2Filter-ANY: no visible global function definition for
  ‘evalError’
glpolygon,curv2Filter-flowFrame : .local: no visible global function
  definition for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘polygonGate’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘checkParameterMatch’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘identifier’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for ‘brewer.pal’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘checkParameterMatch’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘identifier’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for ‘brewer.pal’
gpolygon,curv1Filter-ANY : .local: no visible global function
  definition for ‘evalError’
gpolygon,curv1Filter-flowFrame : .local: no visible global function
  definition for ‘gpolygon’
gpolygon,curv1Filter-missing : .local: no visible global function
  definition for ‘evalError’
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for ‘brewer.pal’
gpolygon,curv1Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘gpolygon’
gpolygon,curv2Filter-ANY : .local: no visible global function
  definition for ‘evalError’
gpolygon,curv2Filter-flowFrame : .local: no visible global function
  definition for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘identifier’
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for ‘brewer.pal’
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for ‘polygonGate’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [110s/111s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   34.961  9.548  44.585
gaussNorm 10.126  0.842  11.131
lymphGate  9.774  0.784  10.672
density1d  5.917  0.754   6.694
rangeGate  5.643  0.818   6.484
gpaSet     4.904  0.197   5.303
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowStats.Rcheck/00check.log’
for details.

flowStats.Rcheck/00install.out:

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (flowStats)

flowStats.Rcheck/flowStats-Ex.timings:

nameusersystemelapsed
autoGate3.7010.1473.849
binByRef1.1550.1431.298
calcPBChiSquare1.2040.1161.328
calcPearsonChi1.2950.1371.438
curv1Filter-class0.3630.0410.407
curv2Filter-class2.3120.1542.469
curvPeaks0.7060.1230.830
density1d5.9170.7546.694
gaussNorm10.126 0.84211.131
gpaSet4.9040.1975.303
iProcrustes0.2660.0240.292
idFeaturesByBackgating1.7360.0571.808
landmarkMatrix1.5990.2091.827
lymphGate 9.774 0.78410.672
normalize0.0010.0000.002
plotBins1.5470.1731.800
proBin0.7190.1400.866
quadrantGate0.0010.0000.001
rangeGate5.6430.8186.484
singletGate0.0010.0000.001
warpSet34.961 9.54844.585