Package: prada

Version: 1.35.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings prada_1.35.1.tar.gz

StartedAt: 2013-01-16 05:23:22 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:24:34 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 71.5 seconds

RetCode: 0

Status:  OK

CheckDir: prada.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/prada.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.35.1’
* 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 ... 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 ... 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

NOTE: There was 1 note.
See
  ‘/loc/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  -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o prada.so inPolygon.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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
   ‘norm2.Rnw’ 
   ‘prada2cellHTS.Rnw’ 
** testing if installed package can be loaded

* DONE (prada)

name	user	system	elapsed
analysePlate	0.008	0.000	0.009
as.all	0.008	0.000	0.009
barploterrbar	0.020	0.000	0.021
combineFrames	0.300	0.004	0.303
csApply	0.064	0.008	0.073
cytoFrame-class	0.180	0.008	0.190
cytoSet-class	0.096	0.004	0.097
data-cytoFrame	0.036	0.000	0.054
data-cytoSet	0.132	0.000	0.131
devDims	0.008	0.000	0.009
devRes	0.008	0.000	0.009
fitNorm2	0.272	0.020	0.292
gate-class	0.048	0.000	0.049
gateSet-class	0.064	0.000	0.065
getPradaPar	0.012	0.000	0.013
plotNorm2	0.248	0.000	0.251
plotPlate	1.384	0.008	1.393
readCytoSet	0.008	0.000	0.007
readFCS	0.196	0.004	0.198
removeCensored	0.012	0.004	0.016
tcltkProgress	0.008	0.004	0.010
threePanelPlot	0.532	0.016	0.548
thresholds	0.004	0.000	0.006
vpLocation	0.008	0.000	0.009