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Package 210/609HostnameOS / ArchBUILDCHECKBUILD BIN
flowStats 1.16.0
Greg Finak and Mike Jiang
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/flowStats
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: flowStats
Version: 1.16.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings flowStats_1.16.0.tar.gz
StartedAt: 2013-03-25 01:04:47 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:11:12 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 384.9 seconds
RetCode: 0
Status:  OK 
CheckDir: flowStats.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/flowStats.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.16.0’
* 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 whether package ‘flowStats’ can be installed ... OK
* checking installed package size ... OK
* 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 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 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
%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’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
* checking Rd files ... NOTE
prepare_Rd: normalizeGatingSet.Rd:53-55: Dropping empty section \note
prepare_Rd: normalizeGatingSet.Rd:47-49: Dropping empty section \references
prepare_Rd: normalizeGatingSet.Rd:62-63: 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
warpSet      48.372  0.152  49.946
gaussNorm    14.853  0.112  15.539
lymphGate    14.837  0.056  15.028
gpaSet        9.973  0.032  10.144
quadrantGate  9.609  0.224  10.639
density1d     9.364  0.084   9.583
rangeGate     8.488  0.072   8.738
autoGate      7.469  0.136   7.778
* 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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-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: replacing previous import ‘plot’ when loading ‘graphics’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GettingStartedWithFlowStats.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘plot’ when loading ‘graphics’

* DONE (flowStats)

flowStats.Rcheck/flowStats-Ex.timings:

nameusersystemelapsed
autoGate7.4690.1367.778
binByRef1.1600.0361.200
calcPBChiSquare1.1840.0241.225
calcPearsonChi1.2480.0321.282
curvPeaks1.1040.0201.142
density1d9.3640.0849.583
gaussNorm14.853 0.11215.539
gpaSet 9.973 0.03210.144
iProcrustes0.3360.0080.343
idFeaturesByBackgating2.3720.0042.772
landmarkMatrix1.5120.0201.549
lymphGate14.837 0.05615.028
plotBins1.5160.0201.543
proBin0.6080.0280.646
quadrantGate 9.609 0.22410.639
rangeGate8.4880.0728.738
warpSet48.372 0.15249.946