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Package 103/658HostnameOS / ArchBUILDCHECKBUILD BIN
cellHTS 1.29.0
Ligia Bras
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellHTS
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: cellHTS
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS_1.29.0.tar.gz
StartedAt: 2013-03-24 03:21:14 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 03:24:22 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 187.8 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cellHTS.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 'cellHTS/DESCRIPTION' ... OK
* this is package 'cellHTS' version '1.29.0'
* 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/20s] 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.

cellHTS.Rcheck/00install.out:

* 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)

cellHTS.Rcheck/cellHTS-Ex.timings:

nameusersystemelapsed
Bscore0.5320.0400.579
ROC0.0300.0090.040
annotate0.0120.0020.014
bdgpbiomart0.6740.0230.706
configure0.0060.0030.010
data-KcViab0.2440.0160.264
data-KcViabSmall0.0390.0100.049
getEnVisionRawData0.0720.0060.085
getLibraryPlate0.0590.0060.064
getMatrix0.0380.0050.043
imageScreen0.1200.0070.128
normalizeChannels0.0730.0030.076
normalizePlates0.0550.0050.061
oneRowPerId0.0290.0010.030
plotPlateLibrary1.2340.0421.300
plotSpatialEffects0.4880.0160.510
print.cellHTS0.0290.0080.037
readPlateData0.1980.0110.210
screenMatch0.6520.0290.686
summarizeChannels0.1070.0030.111
summarizeReplicates0.0910.0090.104
write.tabdel0.0570.0160.073
writeReport0.0320.0110.042
writeTab0.0360.0090.045