BioC 2.13: CHECK report for macat on perceval

Package: macat

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.36.0.tar.gz

StartedAt: 2014-04-05 02:23:23 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:27:00 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 216.6 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/macat.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.36.0’
* 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 ... [13s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘annotate’ ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ‘:::’ call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘macat.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [89s/91s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 45.212  0.258  46.878
get_results        19.197  0.108  19.742
evalScoring         5.514  0.173   5.879
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	3.671	0.081	3.840
compute_sliding	3.340	0.028	3.404
discreteKernelize	2.645	0.017	2.693
discretizeAll	0.028	0.001	0.035
discretize_tscores	45.212	0.258	46.878
evalScoring	5.514	0.173	5.879
evaluateParameters	0.793	0.017	0.818
get_results	19.197	0.108	19.742
kernelize	0.888	0.011	0.912
kernelizeAll	0.018	0.004	0.022
kernelizeToPython	0.012	0.003	0.016
kernels	0.040	0.005	0.045
loaddatapkg	0.013	0.003	0.016
plot_MACATevalScoring	0.012	0.003	0.016
preprocessedLoader	0.013	0.004	0.017
pythondata	0.013	0.004	0.017
scoring	0.048	0.010	0.058
stjd	0.041	0.004	0.046