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BioC 3.2: CHECK report for cellHTS on moscato1

This page was generated on 2015-08-20 13:18:20 -0700 (Thu, 20 Aug 2015).

Package 145/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS 1.39.1
Andrzej Oles
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellHTS
Last Changed Rev: 104630 / Revision: 107602
Last Changed Date: 2015-06-06 03:55:08 -0700 (Sat, 06 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cellHTS
Version: 1.39.1
Command: rm -rf cellHTS.buildbin-libdir cellHTS.Rcheck && mkdir cellHTS.buildbin-libdir cellHTS.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS.buildbin-libdir cellHTS_1.39.1.tar.gz >cellHTS.Rcheck\00install.out 2>&1 && cp cellHTS.Rcheck\00install.out cellHTS-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cellHTS.buildbin-libdir --install="check:cellHTS-install.out" --force-multiarch --no-vignettes --timings cellHTS_1.39.1.tar.gz
StartedAt: 2015-08-20 02:19:03 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 02:22:46 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 223.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: cellHTS.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cellHTS.buildbin-libdir cellHTS.Rcheck && mkdir cellHTS.buildbin-libdir cellHTS.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS.buildbin-libdir cellHTS_1.39.1.tar.gz >cellHTS.Rcheck\00install.out 2>&1 && cp cellHTS.Rcheck\00install.out cellHTS-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=cellHTS.buildbin-libdir --install="check:cellHTS-install.out" --force-multiarch --no-vignettes --timings cellHTS_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/cellHTS.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellHTS/DESCRIPTION' ... OK
* this is package 'cellHTS' version '1.39.1'
* 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 whether package 'cellHTS' can be installed ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See 'D:/biocbld/bbs-3.2-bioc/meat/cellHTS.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  '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 ... WARNING
  Error in if (dep$op != ">=") next : argument is of length zero
  Calls: <Anonymous>
  Execution halted
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [10s] 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: 2 WARNINGs, 4 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/cellHTS.Rcheck/00check.log'
for details.


cellHTS.Rcheck/00install.out:


install for i386

WARNING: omitting pointless dependence on 'R' without a version requirement
* 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

install for x64

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'cellHTS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS' as cellHTS_1.39.1.zip
* DONE (cellHTS)

cellHTS.Rcheck/examples_i386/cellHTS-Ex.timings:

nameusersystemelapsed
Bscore0.510.000.51
ROC0.030.000.04
annotate000
bdgpbiomart0.300.020.31
configure000
data-KcViab0.250.000.25
data-KcViabSmall0.020.000.02
getEnVisionRawData0.030.000.03
getLibraryPlate0.030.000.03
getMatrix0.010.000.02
imageScreen0.260.000.27
normalizeChannels000
normalizePlates0.020.020.03
oneRowPerId000
plotPlateLibrary0.680.000.69
plotSpatialEffects0.450.000.45
print.cellHTS0.020.000.01
readPlateData0.180.000.19
screenMatch0.270.000.27
summarizeChannels000
summarizeReplicates0.050.000.05
write.tabdel0.050.000.05
writeReport0.030.000.03
writeTab0.260.000.84

cellHTS.Rcheck/examples_x64/cellHTS-Ex.timings:

nameusersystemelapsed
Bscore0.670.020.69
ROC0.020.000.05
annotate000
bdgpbiomart0.360.000.36
configure000
data-KcViab0.190.000.19
data-KcViabSmall000
getEnVisionRawData0.050.000.05
getLibraryPlate0.020.000.01
getMatrix0.010.000.01
imageScreen0.10.00.1
normalizeChannels000
normalizePlates0.010.020.03
oneRowPerId000
plotPlateLibrary1.030.001.03
plotSpatialEffects0.460.010.49
print.cellHTS0.020.000.01
readPlateData0.160.021.06
screenMatch0.250.000.25
summarizeChannels0.010.000.02
summarizeReplicates0.060.000.06
write.tabdel0.030.000.03
writeReport0.020.000.02
writeTab0.030.000.22