BioC 3.4: CHECK report for Chicago on morelia

Package: Chicago

Version: 1.1.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Chicago_1.1.6.tar.gz

StartedAt: 2016-09-20 04:15:41 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:17:25 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 103.4 seconds

RetCode: 0

Status:  OK

CheckDir: Chicago.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 Chicago_1.1.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Chicago.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Chicago/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Chicago’ version ‘1.1.6’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Chicago’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
normaliseOtherEnds 9.229  1.489  24.044
exportResults      8.799  0.237   9.588
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/Chicago.Rcheck/00check.log’
for details.

* installing *source* package ‘Chicago’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Chicago)

name	user	system	elapsed
cdUnitTest	0.043	0.004	0.047
chicagoData	0.001	0.000	0.000
chicagoPipeline	0.056	0.002	0.059
copyCD	0.005	0.000	0.006
defaultSettings	0.001	0.001	0.001
estimateBrownianComponent	0.233	0.003	0.235
estimateDistFun	0.023	0.002	0.024
estimateTechnicalNoise	0.125	0.001	0.127
exportResults	8.799	0.237	9.588
getPvals	0.053	0.001	0.079
getScores	0.029	0.001	0.031
getSkOnly	0.167	0.004	0.171
mergeSamples	0.497	0.005	0.502
modifySettings	0.014	0.001	0.015
normaliseBaits	0.068	0.002	0.070
normaliseOtherEnds	9.229	1.489	24.044
overlapFragWithFeatures	0.068	0.002	0.070
peakEnrichment4Features	2.026	0.375	2.404
plotBaits	0.228	0.003	0.231
plotDistFun	0.008	0.005	0.126
readAndMerge	0.090	0.002	0.092
readSample	0.053	0.002	0.055
setExperiment	0.013	0.001	0.013