Package: macat

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.26.0.tar.gz

StartedAt: 2011-10-20 15:46:06 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:49:09 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 182.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: macat.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/macat.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'macat/DESCRIPTION' ... OK
* this is package 'macat' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'macat' 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 ... OK
* 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 sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   macat.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/macat.Rcheck/00check.log'
for details

* installing *source* package 'macat' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Loading MicroArray Chromosome Analysis Tool...
Loading required packages...
Type 'demo(macatdemo)' for a quick tour...

* DONE (macat)

name	user	system	elapsed
buildMACAT	2.860	0.090	2.978
compute_sliding	4.563	0.014	4.621
discreteKernelize	4.393	0.021	4.516
discretizeAll	0.001	0.000	0.000
discretize_tscores	62.400	0.412	64.858
evalScoring	6.592	0.364	7.029
evaluateParameters	1.393	0.062	1.468
get_results	28.464	0.117	28.887
kernelize	1.378	0.009	1.398
kernelizeAll	0.000	0.000	0.001
kernelizeToPython	0.001	0.000	0.001
kernels	0.055	0.003	0.059
loaddatapkg	0.000	0.000	0.001
plot_MACATevalScoring	0	0	0
preprocessedLoader	0.000	0.001	0.000
pythondata	0	0	0
scoring	0.055	0.008	0.063
stjd	0.046	0.003	0.049