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: 2011-07-07 02:05:52 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:12:46 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 413.9 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) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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  6.3Mb
  sub-directories of 1Mb or more:
    data     1.2Mb
    doc      1.5Mb
    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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                     old_size new_size compress
  KcViab.rda            636Kb    331Kb       xz
  KcViabSmall.rda        41Kb     22Kb       xz
  bdgpbiomart.rda       462Kb    269Kb       xz
  dualCh.rda             43Kb     23Kb       xz
  oldKcViabSmall.rda     39Kb     22Kb       xz
* 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 1.3-01)
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 1.3-01)

* DONE (cellHTS2)

name	user	system	elapsed
Bscore	2.942	0.030	3.029
ROC-class	0.482	0.010	0.512
ROC	1.849	0.016	1.897
annotate	1.367	0.014	1.468
bdgpbiomart	0.306	0.007	0.339
buildCellHTS2	0.524	0.002	0.532
cellHTS-class	1.328	0.027	1.379
configurationAsScreenPlot	0.790	0.033	0.837
configure	1.186	0.012	1.219
convertOldCellHTS	1.610	0.008	1.648
convertWellCoordinates	0.001	0.000	0.001
data-KcViab	0.202	0.009	0.226
data-KcViabSmall	0.015	0.001	0.018
data-dualCh	0.016	0.003	0.032
data-oldKcViabSmall	0.014	0.002	0.020
getDynamicRange	0.911	0.011	0.944
getEnVisionRawData	0.034	0.003	0.038
getMeasureRepAgreement	0.927	0.009	0.953
getTopTable	1.913	0.015	1.960
getZfactor	0.621	0.007	0.664
imageScreen	1.630	0.011	1.686
normalizePlates	2.465	0.016	2.532
oneRowPerId	0.005	0.000	0.005
plotSpatialEffects	1.977	0.012	2.037
readHTAnalystData	1.809	0.013	1.864
readPlateList	1.193	0.012	1.228
rsa	1.411	0.009	1.439
scoreReplicates	1.821	0.018	1.927
scores2calls	1.601	0.012	1.626
setSettings	0.007	0.005	0.012
spatialNormalization	2.171	0.041	2.419
summarizeChannels	2.648	0.024	2.724
summarizeReplicates	1.554	0.013	1.626
templateDescriptionFile	0.001	0.002	0.003
updateCellHTS	0.030	0.002	0.031
write.tabdel	0.031	0.003	0.034
writeReport	0.014	0.001	0.015
writeTab	0.026	0.003	0.028