Package: cellHTS

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS_1.26.0.tar.gz

StartedAt: 2012-09-23 23:36:50 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:39:37 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 166.9 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/cellHTS.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cellHTS/DESCRIPTION' ... OK
* this is package 'cellHTS' version '1.26.0'
* 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 'cellHTS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      2.1Mb
* 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 ... NOTE
File 'cellHTS/R/zzz.R':
  .onAttach calls:
    message(paste("\n-------------------------------------------------------------------",     "\nA note from the 'cellHTS' package:", "\nThe package 'cellHTS2' offers better functionality for working with",     "\nmultiple screens and with multi-channel screens. Please consider",     "\nusing 'cellHTS2' for new projects. However, 'cellHTS' will be",     "\nsupported for a while to help with your existing projects.",     "\n-------------------------------------------------------------------\n\n",     sep = ""))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in ?.onAttach.

annotate.cellHTS: warning in read.table(file.path(path, file), sep =
  "\t", header = TRUE, as.is = TRUE, na.string = "", quote = "", fill =
  TRUE): partial argument match of 'na.string' to 'na.strings'
configure.cellHTS: warning in read.table(file.path(ppath, confFile),
  sep = "\t", header = TRUE, as.is = TRUE, na.string = "", fill =
  TRUE): partial argument match of 'na.string' to 'na.strings'
configure.cellHTS: warning in read.table(file.path(ppath, logFile), sep
  = "\t", header = TRUE, as.is = TRUE, na.string = "", fill = TRUE):
  partial argument match of 'na.string' to 'na.strings'
tableOutput: warning in read.table(fn, sep = "\t", header = header,
  na.string = "", as.is = TRUE): partial argument match of 'na.string'
  to 'na.strings'
* checking Rd files ... NOTE
prepare_Rd: oneRowPerId.Rd:19: Dropping empty section \details
* 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' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* 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 4 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/cellHTS.Rcheck/00check.log'
for details.

* installing *source* package 'cellHTS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cellhts.Rnw' 
   'twoChannels.Rnw' 
   'twoWay.Rnw' 
** testing if installed package can be loaded

* DONE (cellHTS)

name	user	system	elapsed
Bscore	0.850	0.020	0.869
ROC	0.018	0.001	0.020
annotate	0	0	0
bdgpbiomart	0.465	0.019	0.484
configure	0	0	0
data-KcViab	0.370	0.015	0.384
data-KcViabSmall	0.023	0.002	0.024
getEnVisionRawData	0.069	0.006	0.075
getLibraryPlate	0.033	0.002	0.035
getMatrix	0.022	0.002	0.024
imageScreen	0.318	0.005	0.324
normalizeChannels	0.000	0.000	0.001
normalizePlates	0.028	0.003	0.031
oneRowPerId	0.008	0.000	0.009
plotPlateLibrary	1.296	0.011	1.308
plotSpatialEffects	0.549	0.003	0.552
print.cellHTS	0.018	0.001	0.020
readPlateData	0.139	0.011	0.151
screenMatch	0.451	0.012	0.467
summarizeChannels	0.001	0.000	0.001
summarizeReplicates	0.081	0.003	0.084
write.tabdel	0.044	0.003	0.047
writeReport	0.023	0.001	0.025
writeTab	0.043	0.003	0.046