BioC 2.12: CHECK report for macat on george2

Package: macat

Version: 1.34.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings macat_1.34.0.tar.gz

StartedAt: 2013-10-09 02:59:45 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:04:13 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 267.4 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 3.0.1 (2013-05-16)
* 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 ‘1.34.0’
* 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/18s] 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 ... [108s/110s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 53.843  0.084  55.045
get_results        24.129  0.000  24.323
evalScoring         7.573  0.060   7.659
* 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
** testing if installed package can be loaded
* DONE (macat)

name	user	system	elapsed
buildMACAT	3.464	0.052	3.524
compute_sliding	4.077	0.028	4.105
discreteKernelize	3.096	0.016	3.115
discretizeAll	0.036	0.000	0.036
discretize_tscores	53.843	0.084	55.045
evalScoring	7.573	0.060	7.659
evaluateParameters	1.096	0.016	1.115
get_results	24.129	0.000	24.323
kernelize	1.140	0.000	1.142
kernelizeAll	0.008	0.000	0.008
kernelizeToPython	0.02	0.00	0.02
kernels	0.056	0.000	0.055
loaddatapkg	0.004	0.000	0.004
plot_MACATevalScoring	0.020	0.000	0.017
preprocessedLoader	0.024	0.000	0.021
pythondata	0.024	0.000	0.021
scoring	0.068	0.000	0.070
stjd	0.040	0.000	0.038