Package: cellHTS2

Version: 2.23.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.23.2.tar.gz

StartedAt: 2013-03-25 01:36:31 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:43:12 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 400.6 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellHTS2.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.23.2'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'cellHTS2' can be installed ... [30s/31s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.7Mb
* checking package directory ... 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
annotate,cellHTS: warning in read.table(file.path(path, file), sep =
  "\t", header = TRUE, stringsAsFactors = FALSE, na.string = "", quote
  = "", fill = FALSE): partial argument match of 'na.string' to
  'na.strings'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [63s/63s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
Bscore 6.903  0.076   6.982
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [63s/64s]
 [63s/64s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'GO.db' 'KEGG.db'
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.

* installing *source* package 'cellHTS2' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'lines' from package 'graphics' in package 'cellHTS2'
** help
*** installing help indices
** building package indices
** installing vignettes
   'cellhts2.Rnw' 
   'cellhts2Complete.Rnw' 
   'twoChannels.Rnw' 
   'twoWay.Rnw' 
** testing if installed package can be loaded
* DONE (cellHTS2)

name	user	system	elapsed
Bscore	6.903	0.076	6.982
ROC-class	0.604	0.025	0.629
ROC	2.037	0.024	2.062
annotate	2.130	0.026	2.158
bdgpbiomart	0.486	0.017	0.505
buildCellHTS2	0.531	0.014	0.545
cellHTS-class	4.190	0.093	4.285
configurationAsScreenPlot	4.372	0.072	4.447
configure	1.309	0.014	1.324
convertOldCellHTS	1.943	0.016	1.960
convertWellCoordinates	0.010	0.009	0.018
data-KcViab	0.248	0.014	0.263
data-KcViabSmall	0.040	0.007	0.047
data-dualCh	0.038	0.007	0.046
data-oldKcViabSmall	0.035	0.007	0.042
getAlphaNumeric	0.012	0.007	0.020
getDynamicRange	0.881	0.019	0.902
getEnVisionRawData	0.044	0.011	0.057
getMeasureRepAgreement	0.836	0.013	0.851
getTopTable	1.644	0.018	1.663
getZfactor	0.627	0.017	0.644
imageScreen	1.380	0.023	1.405
normalizePlates	1.822	0.024	1.849
oneRowPerId	0.019	0.006	0.025
plotSpatialEffects	3.255	0.014	3.271
readHTAnalystData	1.290	0.013	1.303
readPlateList	1.369	0.022	1.393
rsa	1.003	0.015	1.019
scoreReplicates	1.453	0.013	1.466
scores2calls	1.544	0.022	1.568
setSettings	0.018	0.013	0.030
spatialNormalization	1.805	0.029	1.835
summarizeChannels	2.551	0.043	2.595
summarizeReplicates	1.573	0.015	1.587
templateDescriptionFile	0.016	0.008	0.024
updateCellHTS	0.200	0.008	0.208
write.tabdel	0.120	0.016	0.137
writeReport	0.032	0.013	0.045
writeTab	0.034	0.008	0.113