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BioC 2.13: CHECK report for cellHTS on perceval

This page was generated on 2014-04-05 09:51:50 -0700 (Sat, 05 Apr 2014).

Package 115/750HostnameOS / ArchBUILDCHECKBUILD BIN
cellHTS 1.32.0
Ligia Bras
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/cellHTS
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: cellHTS
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cellHTS_1.32.0.tar.gz
StartedAt: 2014-04-05 00:03:56 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:06:58 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 181.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/cellHTS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS/DESCRIPTION’ ... OK
* this is package ‘cellHTS’ version ‘1.32.0’
* 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 ... [18s/18s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc      2.1Mb
    KcViab   2.0Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘prada’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘genefilter’ ‘prada’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘scaleByPlateMedian’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘cellhts.Rnw’, ‘twoChannels.Rnw’, ‘twoWay.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [14s/14s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (cellHTS)

cellHTS.Rcheck/cellHTS-Ex.timings:

nameusersystemelapsed
Bscore0.6800.0310.711
ROC0.0250.0060.031
annotate0.0070.0010.009
bdgpbiomart0.6100.0200.631
configure0.0060.0030.010
data-KcViab0.1810.0170.199
data-KcViabSmall0.0520.0090.061
getEnVisionRawData0.1180.0070.125
getLibraryPlate0.0430.0100.053
getMatrix0.0350.0070.042
imageScreen0.0910.0050.096
normalizeChannels0.0480.0050.053
normalizePlates0.0370.0090.046
oneRowPerId0.0250.0020.027
plotPlateLibrary0.8300.0330.869
plotSpatialEffects0.4670.0120.483
print.cellHTS0.0360.0050.041
readPlateData0.6740.0130.697
screenMatch0.6880.0330.724
summarizeChannels0.1000.0020.102
summarizeReplicates0.0880.0050.094
write.tabdel0.0870.0050.093
writeReport0.0230.0110.034
writeTab0.0250.0090.035