Package: prada

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch prada_1.36.0.tar.gz

StartedAt: 2013-05-01 09:29:14 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:30:51 -0700 (Wed, 01 May 2013)

EllapsedTime: 97.3 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/prada.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'prada/DESCRIPTION' ... OK
* this is package 'prada' version '1.36.0'
* 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 ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 installed files from 'inst/doc' ... OK
* checking examples ... [8s/9s] OK
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/prada.Rcheck/00check.log'
for details.

* installing *source* package 'prada' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inPolygon.c -o inPolygon.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-2.12-bioc/meat/prada.Rcheck/prada/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'split' from package 'base' in package 'prada'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (prada)

name	user	system	elapsed
analysePlate	0.121	0.002	0.123
as.all	0.011	0.001	0.012
barploterrbar	0.015	0.002	0.017
combineFrames	0.182	0.018	0.200
csApply	0.180	0.008	0.189
cytoFrame-class	0.198	0.012	0.210
cytoSet-class	0.121	0.011	0.134
data-cytoFrame	0.042	0.007	0.067
data-cytoSet	0.023	0.002	0.025
devDims	0.113	0.002	0.118
devRes	0.008	0.000	0.009
fitNorm2	0.244	0.016	0.308
gate-class	0.078	0.010	0.095
gateSet-class	0.058	0.007	0.078
getPradaPar	0.008	0.002	0.011
plotNorm2	0.321	0.016	0.357
plotPlate	1.755	0.057	1.825
readCytoSet	0.009	0.001	0.009
readFCS	0.095	0.011	0.106
removeCensored	0.025	0.005	0.030
tcltkProgress	0.012	0.001	0.013
threePanelPlot	0.662	0.032	0.704
thresholds	0.006	0.001	0.007
vpLocation	0.008	0.001	0.009