Package: prada

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch prada_1.30.0.tar.gz

StartedAt: 2012-03-24 03:21:08 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:22:52 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 103.7 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/prada.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'prada/DESCRIPTION' ... OK
* this is package 'prada' version '1.30.0'
* 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 whether package 'prada' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* 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 binding for global variable
  '.tkprogress.window'
progress: no visible binding for global variable '.tkprogress.window'
progress: no visible binding for '<<-' assignment to
  '.tkprogress.labelText'
progress: no visible binding for global variable
  '.tkprogress.labelText'
progress: no visible binding for global variable '.tkprogress.iterator'
progress: no visible binding for global variable
  '.tkprogress.fallbackIterator'
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 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'
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'prada' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c inPolygon.c -o inPolygon.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.9-bioc/meat/prada.Rcheck/prada/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Creating a generic function for 'split' from package 'base' in package 'prada'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'norm2.Rnw' 
   'prada2cellHTS.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (prada)

name	user	system	elapsed
analysePlate	0	0	0
as.all	0	0	0
barploterrbar	0.009	0.001	0.011
combineFrames	0.187	0.054	0.345
csApply	0.132	0.024	0.164
cytoFrame-class	0.133	0.019	0.242
cytoSet-class	0.073	0.012	0.116
data-cytoFrame	0.038	0.010	0.649
data-cytoSet	0.004	0.002	0.009
devDims	0.001	0.000	0.001
devRes	0.006	0.001	0.008
fitNorm2	0.318	0.030	0.786
gate-class	0.025	0.005	0.635
gateSet-class	0.031	0.006	0.270
getPradaPar	0.002	0.000	0.002
plotNorm2	0.295	0.024	1.358
plotPlate	1.802	0.045	4.364
readCytoSet	0	0	0
readFCS	0.059	0.013	0.073
removeCensored	0.009	0.003	0.012
tcltkProgress	0.001	0.000	0.000
threePanelPlot	0.633	0.063	0.723
thresholds	0.000	0.000	0.001
vpLocation	0.004	0.001	0.004