Package: prada

Version: 1.29.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings prada_1.29.0.tar.gz

StartedAt: 2011-05-09 13:46:45 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:47:41 -0700 (Mon, 09 May 2011)

EllapsedTime: 56.0 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/prada.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.29.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
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 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o prada.so inPolygon.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/prada.Rcheck/prada/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)
Creating a new generic function for "split" in "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 1.3-00)

* DONE (prada)

name	user	system	elapsed
analysePlate	0	0	0
as.all	0.004	0.000	0.000
barploterrbar	0.004	0.000	0.004
combineFrames	0.220	0.000	0.224
csApply	0.124	0.004	0.128
cytoFrame-class	0.108	0.008	0.118
cytoSet-class	0.060	0.004	0.062
data-cytoFrame	0.02	0.00	0.02
data-cytoSet	0.008	0.000	0.005
devDims	0	0	0
devRes	0.004	0.000	0.002
fitNorm2	0.224	0.008	0.232
gate-class	0.020	0.000	0.021
gateSet-class	0.028	0.000	0.025
getPradaPar	0.000	0.000	0.001
plotNorm2	0.204	0.000	0.258
plotPlate	1.540	0.024	1.563
readCytoSet	0	0	0
readFCS	0.072	0.000	0.069
removeCensored	0.008	0.000	0.007
tcltkProgress	0	0	0
threePanelPlot	0.580	0.020	0.598
thresholds	0	0	0
vpLocation	0.004	0.000	0.003