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Package 373/658HostnameOS / ArchBUILDCHECKBUILD BIN
macat 1.33.0
Joern Toedling
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/macat
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: macat
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch macat_1.33.0.tar.gz
StartedAt: 2013-03-24 07:16:03 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 07:19:59 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 236.1 seconds
RetCode: 0
Status:  OK 
CheckDir: macat.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/macat.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [14s/15s] 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 ... [103s/105s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
discretize_tscores 53.305  0.293  54.018
get_results        22.710  0.100  22.898
evalScoring         5.578  0.245   5.851
* 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-2.12-bioc/meat/macat.Rcheck/00check.log'
for details.

macat.Rcheck/00install.out:

* 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)

macat.Rcheck/macat-Ex.timings:

nameusersystemelapsed
buildMACAT4.3020.1194.490
compute_sliding3.9790.0224.107
discreteKernelize3.1320.0193.239
discretizeAll0.0220.0020.024
discretize_tscores53.305 0.29354.018
evalScoring5.5780.2455.851
evaluateParameters0.9820.0651.061
get_results22.710 0.10022.898
kernelize1.0240.0091.034
kernelizeAll0.0110.0060.017
kernelizeToPython0.0100.0040.015
kernels0.0490.0090.060
loaddatapkg0.0090.0020.012
plot_MACATevalScoring0.0030.0020.005
preprocessedLoader0.0190.0050.023
pythondata0.0100.0030.013
scoring0.0450.0070.052
stjd0.0430.0060.049