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: 2013-03-24 03:20:38 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:27:50 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 432.6 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellHTS2.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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 ... [29s/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 installed files from 'inst/doc' ... OK
* checking examples ... [64s/65s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
Bscore 6.094  0.076   6.735
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [72s/75s]
 [72s/75s] 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	6.094	0.076	6.735
ROC-class	0.512	0.018	0.531
ROC	1.669	0.015	1.697
annotate	2.094	0.018	2.129
bdgpbiomart	0.293	0.022	0.349
buildCellHTS2	0.490	0.012	0.570
cellHTS-class	3.946	0.084	4.090
configurationAsScreenPlot	4.383	0.078	4.513
configure	1.350	0.023	1.409
convertOldCellHTS	1.603	0.012	1.634
convertWellCoordinates	0.037	0.002	0.041
data-KcViab	0.245	0.017	0.264
data-KcViabSmall	0.034	0.011	0.048
data-dualCh	0.025	0.009	0.034
data-oldKcViabSmall	0.023	0.010	0.033
getAlphaNumeric	0.010	0.005	0.015
getDynamicRange	0.928	0.019	0.949
getEnVisionRawData	0.060	0.008	0.070
getMeasureRepAgreement	0.875	0.011	0.890
getTopTable	2.034	0.019	2.111
getZfactor	0.557	0.017	0.575
imageScreen	1.485	0.022	1.512
normalizePlates	2.149	0.030	2.189
oneRowPerId	0.018	0.005	0.024
plotSpatialEffects	4.072	0.032	4.125
readHTAnalystData	1.670	0.012	1.716
readPlateList	1.344	0.014	1.366
rsa	1.295	0.026	1.331
scoreReplicates	1.317	0.013	1.331
scores2calls	1.359	0.014	1.378
setSettings	0.030	0.013	0.043
spatialNormalization	2.211	0.023	2.247
summarizeChannels	2.359	0.026	2.397
summarizeReplicates	1.299	0.010	1.312
templateDescriptionFile	0.013	0.006	0.018
updateCellHTS	0.267	0.016	0.286
write.tabdel	0.150	0.014	0.165
writeReport	0.049	0.010	0.060
writeTab	0.050	0.009	0.059