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Package 156/462HostnameOS / ArchBUILDCHECKBUILD BIN
flowQ 1.13.0
F. Hahne
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: flowQ
Version: 1.13.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings flowQ_1.13.0.tar.gz
StartedAt: 2011-05-09 12:24:08 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:27:13 -0700 (Mon, 09 May 2011)
EllapsedTime: 185.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowQ.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/flowQ.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-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 ‘1.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowQ’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    9.8Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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
normalizeSets : <anonymous>: no visible global function definition for
  ‘warpSet’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘flowStats’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

flowQ.Rcheck/00install.out:

* installing *source* package ‘flowQ’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: flowCore
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

Attaching package: ‘flowCore’

The following object(s) are masked from ‘package:stats’:

    alias, filter

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: compositions
Loading required package: rgl
Loading required package: tensorA

Attaching package: ‘tensorA’

The following object(s) are masked from ‘package:base’:

    norm

Loading required package: energy
Loading required package: boot

Attaching package: ‘boot’

The following object(s) are masked from ‘package:robustbase’:

    salinity

The following object(s) are masked from ‘package:lattice’:

    melanoma

Loading required package: MASS
Welcome to compositions, a package for compositional data analysis.

Get help with "? compositions"
Version info: to ensure compatibility with R > 2.7.0.
 ".inv" in function names has globaly been replaced by "Inv"
 similarly ".row" and ".col" respectively by "Row" and "Col".

WARNING
Please, take into account that this piece of software does complex   
geometric operations in high-dimensional spaces, possibly using      
different incompatible geometries. In particular, be advised that    
arithmetic operations (+ and *) might have non-conventional meanings.
Double-check that you are doing reasonable things. The mere fact that
the package computes something does not imply that this is reasonable

Attaching package: ‘compositions’

The following object(s) are masked from ‘package:flowCore’:

    normalize

The following object(s) are masked from ‘package:stats’:

    cor, cov, dist, var

The following object(s) are masked from ‘package:base’:

    %*%, scale, scale.default

Loading required package: robCompositions
Loading required package: car
Loading required package: nnet
Loading required package: survival
Loading required package: splines

Attaching package: ‘survival’

The following object(s) are masked from ‘package:boot’:

    aml

The following object(s) are masked from ‘package:robustbase’:

    heart


Attaching package: ‘car’

The following object(s) are masked from ‘package:boot’:

    logit


--------

for references have a look at
citation('robCompositions')    
--------


Attaching package: ‘robCompositions’

The following object(s) are masked from ‘package:compositions’:

    alr, clr, ilr

Loading required package: KernSmooth
Loading required package: tools

Attaching package: ‘latticeExtra’

The following object(s) are masked from ‘package:flowViz’:

    ecdfplot

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘DataQualityAssessment.Rnw’ 
   ‘Extending-flowQ.Rnw’ 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Welcome to compositions, a package for compositional data analysis.

Get help with "? compositions"
Version info: to ensure compatibility with R > 2.7.0.
 ".inv" in function names has globaly been replaced by "Inv"
 similarly ".row" and ".col" respectively by "Row" and "Col".

WARNING
Please, take into account that this piece of software does complex   
geometric operations in high-dimensional spaces, possibly using      
different incompatible geometries. In particular, be advised that    
arithmetic operations (+ and *) might have non-conventional meanings.
Double-check that you are doing reasonable things. The mere fact that
the package computes something does not imply that this is reasonable

--------

for references have a look at
citation('robCompositions')    
--------

Using ImageMagic library at /usr/lib64/ImageMagick-6.6.5
(version 6.6.5)

* DONE (flowQ)

flowQ.Rcheck/flowQ-Ex.timings:

nameusersystemelapsed
aggregatorList-class0.0080.0000.009
binaryAggregator-class0.0000.0000.001
discreteAggregator-class000
evaluateProcess0.0000.0000.001
factorAggregator-class000
flowQ-package0.0000.0000.001
numericAggregator-class000
outlier-class0.0000.0000.001
outlierResult-class000
qaAggregator-class0.0000.0000.001
qaGraph-class000
qaGraphList-class0.0040.0000.001
qaProcess-class0.0000.0000.001
qaProcess.2DStatsPlot13.316 1.24813.538
qaProcess.BoundaryPlot5.8770.7846.248
qaProcess.DensityPlot10.888 0.77611.235
qaProcess.ECDFPlot11.069 0.75211.407
qaProcess.KLDistPlot9.1490.8289.852
qaProcess.cellnumber000
qaProcess.marginevents0.0000.0000.001
qaProcess.timeflow000
qaProcess.timeline000
qaProcessFrame-class0.0000.0000.001
qaReport0.0040.0000.000
rangeAggregator-class000
stringAggregator-class0.0040.0000.000
txtFormatQAObject4.3200.8284.690
writeQAReport000
writeQATextReport0.0000.0000.001