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BioC 3.1: CHECK report for cellHTS on zin2

This page was generated on 2015-10-09 09:23:06 -0700 (Fri, 09 Oct 2015).

Package 140/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS 1.38.0
Ligia Bras
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cellHTS
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellHTS
Version: 1.38.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS_1.38.0.tar.gz
StartedAt: 2015-10-08 23:09:15 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:10:47 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 92.2 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/cellHTS.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS/DESCRIPTION’ ... OK
* this is package ‘cellHTS’ version ‘1.38.0’
* 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 ... [8s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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’ ‘RColorBrewer’ ‘genefilter’ ‘prada’
  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’
* 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'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
QMbyPlate: no visible global function definition for ‘brewer.pal’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘plotPlate’
envisionPlateReader: no visible global function definition for
  ‘listLen’
imageScreen: no visible global function definition for ‘brewer.pal’
makePlot: no visible global function definition for ‘devDims’
plotPlateLibrary: no visible global function definition for
  ‘brewer.pal’
plotPlateLibrary: no visible global function definition for
  ‘pushViewport’
plotPlateLibrary: no visible global function definition for ‘viewport’
plotPlateLibrary: no visible global function definition for
  ‘grid.layout’
plotPlateLibrary: no visible global function definition for ‘plotPlate’
plotPlateLibrary: no visible global function definition for
  ‘popViewport’
plotSpatialEffects: no visible global function definition for
  ‘pushViewport’
plotSpatialEffects: no visible global function definition for
  ‘viewport’
plotSpatialEffects: no visible global function definition for
  ‘grid.layout’
plotSpatialEffects: no visible global function definition for
  ‘plotPlate’
plotSpatialEffects: no visible global function definition for
  ‘brewer.pal’
plotSpatialEffects: no visible global function definition for
  ‘popViewport’
scaleByPlateShorth: no visible global function definition for ‘shorth’
writeReport: no visible global function definition for ‘progress’
writeReport: no visible global function definition for ‘killProgress’
writeReport: no visible global function definition for ‘updateProgress’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/7s] 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
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/cellHTS.Rcheck/00check.log’
for details.


cellHTS.Rcheck/00install.out:

* installing *source* package ‘cellHTS’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cellHTS)

cellHTS.Rcheck/cellHTS-Ex.timings:

nameusersystemelapsed
Bscore0.2200.0160.236
ROC0.0090.0000.009
annotate000
bdgpbiomart0.1880.0040.196
configure0.0010.0000.000
data-KcViab0.3260.0000.473
data-KcViabSmall0.010.000.01
getEnVisionRawData0.0380.0000.037
getLibraryPlate0.0140.0000.015
getMatrix0.010.000.01
imageScreen0.0320.0040.039
normalizeChannels0.0010.0000.001
normalizePlates0.0130.0000.012
oneRowPerId0.0040.0000.004
plotPlateLibrary0.4760.0230.564
plotSpatialEffects0.2430.0000.310
print.cellHTS0.010.000.01
readPlateData0.1290.0040.277
screenMatch0.1490.0000.218
summarizeChannels0.0020.0000.001
summarizeReplicates0.0390.0000.038
write.tabdel0.0210.0000.021
writeReport0.0110.0000.010
writeTab0.0170.0000.018