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BioC 3.5: CHECK report for prada on veracruz2

This page was generated on 2017-08-16 13:27:16 -0400 (Wed, 16 Aug 2017).

Package 1003/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
prada 1.52.0
Florian Hahne
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/prada
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: prada
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prada_1.52.0.tar.gz
StartedAt: 2017-08-16 06:38:56 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:39:46 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 50.0 seconds
RetCode: 0
Status:  OK 
CheckDir: prada.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings prada_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/prada.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.52.0’
* 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 ‘prada’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘grid’ ‘methods’ ‘RColorBrewer’ ‘rrcov’
A package should be listed in only one of these fields.
* 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 ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
analysePlate: no visible binding for global variable ‘dat’
gatePoints: no visible binding for global variable ‘prev’
killProgress: no visible binding for global variable
  ‘.tkprogress.canceled’
killProgress: no visible global function definition for ‘tkdestroy’
killProgress: no visible binding for global variable
  ‘.tkprogress.window’
progress: no visible global function definition for ‘tktoplevel’
progress: no visible global function definition for ‘tclVar’
progress: no visible global function definition for ‘tkwm.geometry’
progress: no visible binding for global variable ‘.tkprogress.window’
progress: no visible global function definition for ‘tkwm.title’
progress: no visible global function definition for ‘tkconfigure’
progress: no visible global function definition for ‘tkframe’
progress: no visible global function definition for ‘tkfont.create’
progress: no visible binding for '<<-' assignment to
  ‘.tkprogress.labelText’
progress: no visible binding for global variable
  ‘.tkprogress.labelText’
progress: no visible global function definition for ‘tclvalue<-’
progress: no visible global function definition for ‘tklabel’
progress: no visible global function definition for ‘tclvalue’
progress: no visible global function definition for ‘tkgrid’
progress: no visible global function definition for ‘tclRequire’
progress: no visible global function definition for ‘tkwidget’
progress: no visible binding for global variable ‘.tkprogress.iterator’
progress: no visible binding for global variable
  ‘.tkprogress.fallbackIterator’
progress: no visible global function definition for ‘tkbind’
progress : <anonymous>: no visible binding for '<<-' assignment to
  ‘.tkprogress.canceled’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.iterator’
updateProgress: no visible binding for global variable
  ‘.tkprogress.iterator’
updateProgress: no visible global function definition for ‘tclvalue<-’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for global variable
  ‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.labelText’
updateProgress: no visible binding for global variable
  ‘.tkprogress.labelText’
updateProgress: no visible global function definition for ‘tcl’
Undefined global functions or variables:
  .tkprogress.canceled .tkprogress.fallbackIterator
  .tkprogress.iterator .tkprogress.labelText .tkprogress.window dat
  prev tcl tclRequire tclVar tclvalue tclvalue<- tkbind tkconfigure
  tkdestroy tkfont.create tkframe tkgrid tklabel tktoplevel tkwidget
  tkwm.geometry tkwm.title
* checking Rd files ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/prada.Rcheck/00check.log’
for details.


prada.Rcheck/00install.out:

* installing *source* package ‘prada’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inPolygon.c -o inPolygon.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o prada.so inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/prada.Rcheck/prada/libs
** 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 (prada)

prada.Rcheck/prada-Ex.timings:

nameusersystemelapsed
analysePlate0.0000.0000.001
as.all0.0010.0010.000
barploterrbar0.010.000.01
combineFrames0.2330.0090.250
csApply0.0620.0030.069
cytoFrame-class0.1110.0030.114
cytoSet-class0.0480.0010.055
data-cytoFrame0.0160.0030.019
data-cytoSet0.0030.0020.004
devDims0.0000.0000.001
devRes0.0030.0000.003
fitNorm20.0910.0030.095
gate-class0.1620.0020.171
gateSet-class0.0140.0010.015
getAlphaNumeric0.0170.0020.020
getPradaPar0.0010.0010.002
plotNorm20.2310.0060.243
plotPlate1.2710.0151.329
readCytoSet000
readFCS0.0380.0020.040
removeCensored0.0040.0010.004
tcltkProgress0.0010.0000.001
threePanelPlot0.1850.0070.204
thresholds0.0020.0000.001
vpLocation0.0030.0000.003