BioC 2.12: CHECK report for cellHTS on pelham

Package: cellHTS

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS_1.30.0.tar.gz

StartedAt: 2013-05-01 03:24:58 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:28:11 -0700 (Wed, 01 May 2013)

EllapsedTime: 193.7 seconds

RetCode: 0

Status: OK

CheckDir: cellHTS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellHTS.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cellHTS/DESCRIPTION' ... OK
* this is package 'cellHTS' version '1.30.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'cellHTS' can be installed ... [19s/21s] 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 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
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 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 ... [15s/15s] 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-2.12-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
** testing if installed package can be loaded
* DONE (cellHTS)

name	user	system	elapsed
Bscore	0.781	0.036	0.829
ROC	0.028	0.010	0.040
annotate	0.012	0.003	0.016
bdgpbiomart	0.655	0.020	0.677
configure	0.026	0.001	0.027
data-KcViab	0.606	0.019	0.638
data-KcViabSmall	0.043	0.011	0.054
getEnVisionRawData	0.087	0.005	0.094
getLibraryPlate	0.052	0.006	0.058
getMatrix	0.044	0.005	0.049
imageScreen	0.140	0.008	0.149
normalizeChannels	0.089	0.005	0.106
normalizePlates	0.050	0.005	0.055
oneRowPerId	0.038	0.003	0.042
plotPlateLibrary	1.380	0.032	1.433
plotSpatialEffects	0.511	0.030	0.542
print.cellHTS	0.026	0.011	0.038
readPlateData	0.200	0.013	0.217
screenMatch	0.672	0.027	0.707
summarizeChannels	0.084	0.005	0.089
summarizeReplicates	0.097	0.011	0.107
write.tabdel	0.102	0.008	0.110
writeReport	0.321	0.012	0.334
writeTab	0.033	0.009	0.041

Summary

Command output