Package: cellHTS2

Version: 2.20.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS2_2.20.0.tar.gz

StartedAt: 2012-04-01 00:07:06 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:11:15 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 248.9 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/cellHTS2.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.20.0'
* 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  5.8Mb
  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 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
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.

* installing *source* package 'cellHTS2' ...
** R
** data
** inst
** preparing package for lazy loading
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
** installing vignettes
   'cellhts2.Rnw' 
   'cellhts2Complete.Rnw' 
   'twoChannels.Rnw' 
   'twoWay.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (cellHTS2)

name	user	system	elapsed
Bscore	3.856	0.016	3.890
ROC-class	0.280	0.004	0.286
ROC	0.920	0.000	0.933
annotate	1.088	0.004	1.094
bdgpbiomart	0.172	0.000	0.180
buildCellHTS2	0.248	0.004	0.252
cellHTS-class	2.124	0.000	2.144
configurationAsScreenPlot	2.309	0.008	2.328
configure	0.740	0.004	0.748
convertOldCellHTS	0.944	0.000	0.960
convertWellCoordinates	0	0	0
data-KcViab	0.128	0.000	0.136
data-KcViabSmall	0.008	0.004	0.019
data-dualCh	0.012	0.000	0.023
data-oldKcViabSmall	0.012	0.000	0.021
getAlphaNumeric	0.000	0.000	0.001
getDynamicRange	0.580	0.000	0.592
getEnVisionRawData	0.028	0.004	0.035
getMeasureRepAgreement	0.572	0.000	0.582
getTopTable	1.336	0.000	1.350
getZfactor	0.360	0.000	0.374
imageScreen	0.992	0.000	1.002
normalizePlates	1.588	0.000	1.606
oneRowPerId	0.004	0.000	0.003
plotSpatialEffects	2.412	0.004	2.428
readHTAnalystData	1.020	0.000	1.026
readPlateList	0.772	0.004	0.784
rsa	0.824	0.004	0.845
scoreReplicates	0.828	0.004	0.841
scores2calls	0.864	0.004	0.879
setSettings	0.000	0.004	0.005
spatialNormalization	1.301	0.004	1.314
summarizeChannels	1.432	0.000	1.443
summarizeReplicates	0.804	0.004	0.816
templateDescriptionFile	0.000	0.000	0.001
updateCellHTS	0.164	0.000	0.174
write.tabdel	0.072	0.004	0.087
writeReport	0.008	0.004	0.023
writeTab	0.032	0.000	0.040