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BioC 2.14: CHECK report for flowStats on moscato2

This page was generated on 2014-10-08 08:52:53 -0700 (Wed, 08 Oct 2014).

Package 293/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowStats 3.22.6
Greg Finak and Mike Jiang
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowStats
Last Changed Rev: 91304 / Revision: 95116
Last Changed Date: 2014-06-11 15:59:43 -0700 (Wed, 11 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: flowStats
Version: 3.22.6
Command: rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowStats.buildbin-libdir flowStats_3.22.6.tar.gz >flowStats-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=flowStats.buildbin-libdir --install="check:flowStats-install.out" --force-multiarch --no-vignettes --timings flowStats_3.22.6.tar.gz
StartedAt: 2014-10-08 01:07:47 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:14:41 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 413.1 seconds
RetCode: 0
Status:  OK  
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowStats.buildbin-libdir flowStats_3.22.6.tar.gz >flowStats-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=flowStats.buildbin-libdir --install="check:flowStats-install.out" --force-multiarch --no-vignettes --timings flowStats_3.22.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/flowStats.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '3.22.6'
* 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 whether package 'flowStats' 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:
  '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
* 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
* 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 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'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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'
.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'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
glpolygon,curv1Filter-ANY: no visible global function definition for
  'evalError'
glpolygon,curv2Filter-ANY: no visible global function definition for
  'evalError'
* 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' ... [96s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
warpSet   33.06   0.29   33.35
gaussNorm 11.39   0.09   11.53
lymphGate  9.70   0.06    9.76
rangeGate  5.99   0.16    6.15
density1d  5.76   0.18    6.55
** running examples for arch 'x64' ... [102s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
warpSet   34.33   0.39   34.86
lymphGate 10.81   0.08   10.88
gaussNorm 10.49   0.22   10.72
density1d  6.81   0.14    6.96
rangeGate  5.62   0.07    5.70
gpaSet     5.41   0.05    5.46
* 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

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/flowStats.Rcheck/00check.log'
for details.

flowStats.Rcheck/00install.out:


install for i386

* installing *source* package 'flowStats' ...
** 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 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_3.22.6.zip
* DONE (flowStats)

flowStats.Rcheck/examples_i386/flowStats-Ex.timings:

nameusersystemelapsed
autoGate3.700.033.73
binByRef1.090.031.12
calcPBChiSquare1.140.021.16
calcPearsonChi1.190.061.25
curv1Filter-class0.420.000.45
curv2Filter-class2.220.022.24
curvPeaks1.010.041.06
density1d5.760.186.55
gaussNorm11.39 0.0911.53
gpaSet4.820.034.85
iProcrustes0.240.000.24
idFeaturesByBackgating1.960.001.96
landmarkMatrix1.220.021.24
lymphGate9.700.069.76
normalize000
plotBins1.590.011.61
proBin0.830.020.84
quadrantGate000
rangeGate5.990.166.15
singletGate000
warpSet33.06 0.2933.35

flowStats.Rcheck/examples_x64/flowStats-Ex.timings:

nameusersystemelapsed
autoGate4.240.034.27
binByRef1.580.051.62
calcPBChiSquare1.120.051.17
calcPearsonChi1.220.001.22
curv1Filter-class0.640.000.64
curv2Filter-class2.620.012.64
curvPeaks1.000.000.99
density1d6.810.146.96
gaussNorm10.49 0.2210.72
gpaSet5.410.055.46
iProcrustes0.30.00.3
idFeaturesByBackgating2.040.002.04
landmarkMatrix1.310.001.31
lymphGate10.81 0.0810.88
normalize000
plotBins1.600.061.69
proBin0.730.020.75
quadrantGate000
rangeGate5.620.075.70
singletGate000
warpSet34.33 0.3934.86