Package: macat

Version: 1.27.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.27.1.tar.gz

StartedAt: 2011-06-22 03:53:07 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 03:56:10 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 182.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: macat.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/macat.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.27.1’
* checking package name space 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 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 ... 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-2.9-bioc/meat/macat.Rcheck/00check.log’
for details

* installing *source* package ‘macat’ ...
** R
** data
** demo
** 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: AnnotationDbi
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘macat.Rnw’ 
** 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	2.893	0.093	3.033
compute_sliding	4.525	0.016	4.599
discreteKernelize	4.359	0.020	4.472
discretizeAll	0.001	0.000	0.001
discretize_tscores	61.844	0.427	63.998
evalScoring	6.532	0.360	7.209
evaluateParameters	1.322	0.055	1.391
get_results	28.525	0.135	29.033
kernelize	1.435	0.011	1.454
kernelizeAll	0.000	0.001	0.000
kernelizeToPython	0.001	0.000	0.001
kernels	0.055	0.003	0.059
loaddatapkg	0	0	0
plot_MACATevalScoring	0.000	0.001	0.001
preprocessedLoader	0.000	0.000	0.001
pythondata	0	0	0
scoring	0.056	0.007	0.065
stjd	0.047	0.003	0.051