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: 2011-07-07 04:09:14 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:12:29 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 194.8 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) (2011-06-22 r56208)
* 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 '1.27.1'
* 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	3.024	0.090	3.166
compute_sliding	4.879	0.030	5.166
discreteKernelize	4.598	0.021	4.717
discretizeAll	0	0	0
discretize_tscores	66.175	0.473	68.761
evalScoring	6.869	0.362	7.327
evaluateParameters	1.345	0.057	1.409
get_results	30.046	0.144	30.522
kernelize	1.498	0.013	1.532
kernelizeAll	0	0	0
kernelizeToPython	0.001	0.000	0.000
kernels	0.056	0.003	0.060
loaddatapkg	0	0	0
plot_MACATevalScoring	0.001	0.000	0.000
preprocessedLoader	0	0	0
pythondata	0.000	0.000	0.001
scoring	0.056	0.007	0.064
stjd	0.047	0.002	0.050