Package: prada

Version: 1.60.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:prada.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings prada_1.60.0.tar.gz

StartedAt: 2019-10-16 04:02:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:03:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 53.3 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:prada.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings prada_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/prada.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.60.0’
* 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 : : 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 ... NOTE
Note: information on .o files is not available
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/prada.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL prada
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘prada’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c inPolygon.c -o inPolygon.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o prada.so inPolygon.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-prada/00new/prada/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (prada)

name	user	system	elapsed
analysePlate	0	0	0
as.all	0	0	0
barploterrbar	0.006	0.000	0.006
combineFrames	0.092	0.000	0.110
csApply	0.022	0.000	0.023
cytoFrame-class	0.055	0.000	0.055
cytoSet-class	0.038	0.000	0.038
data-cytoFrame	0.022	0.000	0.040
data-cytoSet	0.003	0.000	0.003
devDims	0	0	0
devRes	0.002	0.000	0.002
fitNorm2	0.147	0.000	0.147
gate-class	0.02	0.00	0.02
gateSet-class	0.015	0.000	0.015
getAlphaNumeric	0	0	0
getPradaPar	0.002	0.000	0.002
plotNorm2	0.134	0.000	0.134
plotPlate	1.343	0.000	1.343
readCytoSet	0	0	0
readFCS	0.027	0.000	0.027
removeCensored	0.003	0.000	0.003
tcltkProgress	0	0	0
threePanelPlot	0.302	0.000	0.302
thresholds	0.001	0.000	0.001
vpLocation	0.002	0.000	0.003