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Package 157/462HostnameOS / ArchBUILDCHECKBUILD BIN
flowStats 1.11.0
Florian Hahne and Chao-Jen Wong
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats
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: flowStats
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowStats_1.11.0.tar.gz
StartedAt: 2011-05-09 14:30:53 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:39:05 -0700 (Mon, 09 May 2011)
EllapsedTime: 492.6 seconds
RetCode: 0
Status:  OK 
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/flowStats.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.11.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘flowStats’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.7Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
    doc   15.3Mb
* 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
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
.usingSVD: no visible global function definition for ‘s.nan’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
warpSet: no visible binding for global variable ‘wfuns’
* 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘GettingStartedWithFlowStats.pdf’ from 15.3Mb to 2.7Mb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

flowStats.Rcheck/00install.out:

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
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

Loading required package: splines
Loading required package: zoo
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:fda’:

    melanoma

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

    salinity

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

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

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GettingStartedWithFlowStats.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')    
--------


* DONE (flowStats)

flowStats.Rcheck/flowStats-Ex.timings:

nameusersystemelapsed
autoGate6.1190.4196.607
binByRef2.0460.1452.256
calcPBChiSquare1.8750.1262.070
calcPearsonChi1.9770.1272.142
curvPeaks2.7570.1973.143
density1d35.799 2.54940.433
gaussNorm34.446 4.34539.294
gpaSet13.314 2.06015.982
iProcrustes0.5690.0630.635
idFeaturesByBackgating3.6820.0313.872
landmarkMatrix3.1130.4403.628
lymphGate36.647 3.70341.247
plotBins2.2740.1602.448
proBin1.8520.1041.969
quadrantGate39.161 3.47243.509
rangeGate31.139 3.05634.922
warpSet67.75324.42795.863