Package: macat

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.30.0.tar.gz

StartedAt: 2012-09-24 00:47:06 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:50:26 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 199.8 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/macat.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.30.0'
* 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-2.10-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	3.073	0.103	3.182
compute_sliding	3.094	0.008	3.103
discreteKernelize	2.648	0.009	2.657
discretizeAll	0	0	0
discretize_tscores	44.614	0.229	44.851
evalScoring	5.921	0.249	6.174
evaluateParameters	1.296	0.047	1.343
get_results	23.065	0.050	23.116
kernelize	0.741	0.003	0.745
kernelizeAll	0	0	0
kernelizeToPython	0.000	0.001	0.000
kernels	0.025	0.002	0.028
loaddatapkg	0	0	0
plot_MACATevalScoring	0	0	0
preprocessedLoader	0.001	0.000	0.001
pythondata	0	0	0
scoring	0.025	0.006	0.030
stjd	0.019	0.002	0.020