BioC 2.14: CHECK report for macat on petty

Package: macat

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.38.0.tar.gz

StartedAt: 2014-10-07 22:44:58 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:49:41 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 283.8 seconds

RetCode: 0

Status:  OK

CheckDir: macat.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/macat.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.38.0’
* 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 ... [17s/17s] 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 loading without being on the library search path ... 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [118s/120s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 60.757  0.190  61.692
get_results        26.329  0.083  27.031
buildMACAT          6.169  0.093   6.377
evalScoring         5.586  0.094   5.721
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	6.169	0.093	6.377
compute_sliding	4.295	0.010	4.335
discreteKernelize	3.967	0.020	4.014
discretizeAll	0.001	0.000	0.002
discretize_tscores	60.757	0.190	61.692
evalScoring	5.586	0.094	5.721
evaluateParameters	1.159	0.011	1.181
get_results	26.329	0.083	27.031
kernelize	1.253	0.005	1.270
kernelizeAll	0.001	0.000	0.001
kernelizeToPython	0.001	0.000	0.002
kernels	0.035	0.002	0.038
loaddatapkg	0.001	0.001	0.001
plot_MACATevalScoring	0.001	0.000	0.002
preprocessedLoader	0.001	0.000	0.002
pythondata	0.002	0.000	0.001
scoring	0.034	0.002	0.035
stjd	0.024	0.001	0.026