BioC 2.12: CHECK report for prada on george2

Package: prada

Version: 1.36.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings prada_1.36.1.tar.gz

StartedAt: 2013-10-09 04:08:10 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:09:57 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 106.8 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/prada.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.36.1’
* 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 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 ... [10s/10s] OK
* checking PDF version of manual ... OK

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

* installing *source* package ‘prada’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib -o prada.so inPolygon.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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	0.196	0.000	0.197
as.all	0.028	0.000	0.028
barploterrbar	0.024	0.000	0.024
combineFrames	0.428	0.008	0.439
csApply	0.092	0.008	0.099
cytoFrame-class	0.456	0.020	0.478
cytoSet-class	0.116	0.004	0.119
data-cytoFrame	0.040	0.004	0.057
data-cytoSet	0.020	0.000	0.021
devDims	0.024	0.004	0.026
devRes	0.012	0.004	0.017
fitNorm2	0.384	0.008	0.391
gate-class	0.056	0.012	0.070
gateSet-class	0.088	0.004	0.107
getPradaPar	0.016	0.000	0.013
plotNorm2	0.372	0.012	0.384
plotPlate	1.948	0.052	2.008
readCytoSet	0.012	0.000	0.010
readFCS	0.124	0.004	0.128
removeCensored	0.040	0.004	0.042
tcltkProgress	0.264	0.000	0.264
threePanelPlot	0.784	0.028	0.875
thresholds	0.008	0.000	0.011
vpLocation	0.016	0.000	0.014