Package: macat

Version: 1.31.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.31.0.tar.gz

StartedAt: 2012-06-21 01:21:03 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:24:49 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 225.2 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/macat.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.31.0'
* 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 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 ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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
** installing vignettes
   'macat.Rnw' 
** testing if installed package can be loaded

* DONE (macat)

name	user	system	elapsed
buildMACAT	3.107	0.112	3.308
compute_sliding	4.029	0.019	4.254
discreteKernelize	3.659	0.017	3.809
discretizeAll	0.000	0.000	0.001
discretize_tscores	54.955	0.401	56.649
evalScoring	5.629	0.332	6.029
evaluateParameters	1.187	0.053	1.249
get_results	24.064	0.096	24.385
kernelize	1.125	0.007	1.140
kernelizeAll	0.001	0.000	0.000
kernelizeToPython	0.000	0.000	0.001
kernels	0.036	0.004	0.040
loaddatapkg	0	0	0
plot_MACATevalScoring	0.000	0.000	0.001
preprocessedLoader	0.000	0.001	0.000
pythondata	0.000	0.000	0.001
scoring	0.033	0.007	0.041
stjd	0.030	0.003	0.034