Package: cellHTS2

Version: 2.17.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.17.2.tar.gz

StartedAt: 2011-06-22 01:53:29 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 02:00:15 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 406.4 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/cellHTS2.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.17.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘cellHTS2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data     1.2Mb
    doc      1.3Mb
    KcViab   2.0Mb
* 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 ... OK
* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’
 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

* installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading

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: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Creating a generic function for "lines" from package "graphics" in package “cellHTS2”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘cellhts2.Rnw’ 
   ‘cellhts2Complete.Rnw’ 
   ‘twoChannels.Rnw’ 
   ‘twoWay.Rnw’ 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (cellHTS2)

name	user	system	elapsed
Bscore	2.876	0.024	3.604
ROC-class	0.454	0.010	0.469
ROC	1.734	0.016	2.015
annotate	1.290	0.010	1.439
bdgpbiomart	0.264	0.005	0.347
buildCellHTS2	0.426	0.002	0.514
cellHTS-class	1.365	0.022	1.766
configurationAsScreenPlot	0.904	0.020	1.161
configure	0.990	0.021	1.050
convertOldCellHTS	1.605	0.006	1.889
convertWellCoordinates	0.001	0.000	0.001
data-KcViab	0.186	0.004	0.190
data-KcViabSmall	0.015	0.001	0.015
data-dualCh	0.016	0.001	0.017
data-oldKcViabSmall	0.015	0.001	0.015
getDynamicRange	0.891	0.008	1.116
getEnVisionRawData	0.094	0.003	0.118
getMeasureRepAgreement	0.917	0.006	1.263
getTopTable	1.871	0.014	2.912
getZfactor	0.613	0.005	0.810
imageScreen	1.543	0.009	2.206
normalizePlates	2.392	0.013	2.960
oneRowPerId	0.005	0.000	0.005
plotSpatialEffects	1.789	0.010	2.022
readHTAnalystData	1.669	0.009	2.674
readPlateList	1.236	0.011	1.498
rsa	1.295	0.011	1.374
scoreReplicates	1.485	0.011	1.505
scores2calls	1.535	0.010	1.577
setSettings	0.013	0.005	0.023
spatialNormalization	2.098	0.033	2.306
summarizeChannels	2.556	0.019	2.908
summarizeReplicates	1.633	0.009	1.714
templateDescriptionFile	0.004	0.001	0.004
updateCellHTS	0.030	0.001	0.055
write.tabdel	0.033	0.002	0.156
writeReport	0.014	0.002	0.023
writeTab	0.030	0.002	0.033