Package: cellHTS2

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.21.0.tar.gz

StartedAt: 2012-06-20 22:35:42 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:42:54 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 432.5 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/cellHTS2.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '2.21.0'
* 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 'cellHTS2' can be installed ... 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 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 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 ... 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 installed files from '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 ... 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 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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	6.824	0.057	7.081
ROC-class	0.529	0.014	0.561
ROC	1.715	0.013	1.739
annotate	2.129	0.016	2.256
bdgpbiomart	0.397	0.012	0.414
buildCellHTS2	0.460	0.002	0.466
cellHTS-class	4.023	0.053	4.162
configurationAsScreenPlot	4.149	0.055	4.284
configure	1.460	0.011	1.481
convertOldCellHTS	1.804	0.008	1.858
convertWellCoordinates	0.001	0.000	0.001
data-KcViab	0.288	0.011	0.303
data-KcViabSmall	0.021	0.001	0.023
data-dualCh	0.022	0.001	0.024
data-oldKcViabSmall	0.020	0.002	0.022
getAlphaNumeric	0.001	0.000	0.000
getDynamicRange	1.082	0.010	1.113
getEnVisionRawData	0.060	0.004	0.068
getMeasureRepAgreement	1.111	0.010	1.131
getTopTable	2.387	0.014	2.426
getZfactor	0.728	0.007	0.746
imageScreen	1.860	0.024	1.988
normalizePlates	2.680	0.015	2.742
oneRowPerId	0.004	0.001	0.005
plotSpatialEffects	4.365	0.034	4.465
readHTAnalystData	1.746	0.009	1.918
readPlateList	1.327	0.013	1.353
rsa	1.356	0.009	1.399
scoreReplicates	1.389	0.010	1.434
scores2calls	1.428	0.013	1.575
setSettings	0.006	0.005	0.011
spatialNormalization	2.383	0.027	2.556
summarizeChannels	2.401	0.020	2.444
summarizeReplicates	1.384	0.009	1.406
templateDescriptionFile	0.001	0.001	0.002
updateCellHTS	0.288	0.003	0.298
write.tabdel	0.128	0.004	0.133
writeReport	0.020	0.002	0.021
writeTab	0.031	0.003	0.034