BioC 3.5: CHECK report for Chicago on malbec2

Package: Chicago

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.4.0.tar.gz

StartedAt: 2017-08-15 21:49:12 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:50:58 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 106.0 seconds

RetCode: 0

Status:  OK

CheckDir: Chicago.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Chicago.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 ... 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 13.052  2.608  13.139
exportResults      10.644  0.160  11.523
* 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
  ‘/home/biocbuild/bbs-3.5-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	0.044	0.000	0.044
chicagoData	0.000	0.000	0.001
chicagoPipeline	0.316	0.000	0.176
copyCD	0.008	0.000	0.009
defaultSettings	0.000	0.000	0.002
estimateBrownianComponent	0.960	0.020	0.741
estimateDistFun	0.272	0.000	0.094
estimateTechnicalNoise	0.568	0.000	0.160
exportResults	10.644	0.160	11.523
getPvals	0.184	0.000	0.052
getScores	0.060	0.000	0.045
getSkOnly	0.704	0.012	0.452
mergeSamples	0.404	0.024	0.157
modifySettings	0.02	0.00	0.02
normaliseBaits	1.172	0.000	0.808
normaliseOtherEnds	13.052	2.608	13.139
overlapFragWithFeatures	0.140	0.000	0.085
peakEnrichment4Features	0.924	0.000	0.898
plotBaits	0.124	0.004	0.131
plotDistFun	0.004	0.004	0.010
readAndMerge	1.140	0.024	0.825
readSample	0.228	0.000	0.092
setExperiment	0.008	0.000	0.011