Package: macat

Version: 1.33.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings macat_1.33.0.tar.gz

StartedAt: 2013-03-25 02:49:11 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:53:40 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 269.1 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/macat.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.33.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘macat’ can be installed ... [18s/19s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 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 ... [111s/114s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 57.395  0.116  59.087
get_results        23.189  0.152  23.961
evalScoring         7.597  0.072   7.689
* 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
  ‘/home/biocbuild/bbs-2.12-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	3.840	0.084	4.221
compute_sliding	4.269	0.008	4.277
discreteKernelize	3.220	0.016	3.270
discretizeAll	0.04	0.00	0.04
discretize_tscores	57.395	0.116	59.087
evalScoring	7.597	0.072	7.689
evaluateParameters	1.044	0.016	1.063
get_results	23.189	0.152	23.961
kernelize	1.048	0.000	1.044
kernelizeAll	0.02	0.00	0.02
kernelizeToPython	0.024	0.000	0.022
kernels	0.060	0.000	0.059
loaddatapkg	0.016	0.000	0.016
plot_MACATevalScoring	0.004	0.000	0.005
preprocessedLoader	0.036	0.000	0.034
pythondata	0.016	0.000	0.017
scoring	0.056	0.004	0.060
stjd	0.060	0.004	0.064