BioC 2.12: CHECK report for cellHTS2 on petty

Package: cellHTS2

Version: 2.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS2_2.24.1.tar.gz

StartedAt: 2013-10-08 21:51:06 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:59:30 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 503.8 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 3.0.1 (2013-05-16)
* 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 '2.24.1'
* 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 ... [33s/34s] 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 ... [76s/77s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
Bscore                    7.770  0.088   7.896
configurationAsScreenPlot 5.036  0.060   5.232
plotSpatialEffects        5.021  0.044   5.104
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [86s/90s]
 [87s/91s] 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
** testing if installed package can be loaded
* DONE (cellHTS2)

name	user	system	elapsed
Bscore	7.770	0.088	7.896
ROC-class	0.654	0.022	0.679
ROC	2.380	0.022	2.406
annotate	2.375	0.024	2.456
bdgpbiomart	0.433	0.015	0.450
buildCellHTS2	0.560	0.015	0.577
cellHTS-class	4.131	0.071	4.232
configurationAsScreenPlot	5.036	0.060	5.232
configure	1.663	0.015	1.712
convertOldCellHTS	2.038	0.017	2.088
convertWellCoordinates	0.038	0.002	0.041
data-KcViab	0.293	0.023	0.317
data-KcViabSmall	0.052	0.009	0.061
data-dualCh	0.039	0.008	0.047
data-oldKcViabSmall	0.035	0.008	0.044
getAlphaNumeric	0.018	0.001	0.023
getDynamicRange	1.589	0.019	1.632
getEnVisionRawData	0.063	0.007	0.072
getMeasureRepAgreement	1.111	0.011	1.142
getTopTable	2.559	0.022	2.591
getZfactor	0.690	0.018	0.708
imageScreen	1.955	0.025	1.999
normalizePlates	2.811	0.023	2.853
oneRowPerId	0.016	0.003	0.019
plotSpatialEffects	5.021	0.044	5.104
readHTAnalystData	2.093	0.008	2.122
readPlateList	1.722	0.015	1.743
rsa	1.657	0.017	1.681
scoreReplicates	1.669	0.011	1.685
scores2calls	1.720	0.016	1.752
setSettings	0.044	0.010	0.055
spatialNormalization	2.640	0.026	2.686
summarizeChannels	2.915	0.025	2.950
summarizeReplicates	1.694	0.012	1.720
templateDescriptionFile	0.012	0.005	0.016
updateCellHTS	0.299	0.017	0.318
write.tabdel	0.161	0.017	0.179
writeReport	0.040	0.012	0.051
writeTab	0.044	0.008	0.052