BioC 3.3: CHECK report for diffloop on oaxaca

Package: diffloop

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.0.2.tar.gz

StartedAt: 2016-06-24 01:05:32 -0700 (Fri, 24 Jun 2016)

EndedAt: 2016-06-24 01:08:30 -0700 (Fri, 24 Jun 2016)

EllapsedTime: 177.4 seconds

RetCode: 0

Status:  OK

CheckDir: diffloop.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 diffloop_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/diffloop.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘diffloop/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffloop’ version ‘1.0.2’
* 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 ‘diffloop’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    rda   4.5Mb
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
loopGenes    6.513  0.016   6.955
loopsMake    4.216  0.189   5.851
plotTopLoops 4.108  0.066   5.842
* 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-3.3-bioc/meat/diffloop.Rcheck/00check.log’
for details.

* installing *source* package ‘diffloop’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘diffloop’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘diffloop’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘diffloop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffloop)

name	user	system	elapsed
addchr	0.163	0.005	0.168
annotateAnchors	0.132	0.003	0.135
annotateLoops	1.256	0.024	1.286
bedToGRanges	0.168	0.002	0.170
calcLDSizeFactors	0.002	0.001	0.002
featureTest	2.351	0.012	2.376
filterLoops	0.173	0.001	0.174
getHumanGenes	0.072	0.001	0.073
getHumanTSS	0.291	0.005	0.297
interchromosomal	0.015	0.000	0.016
intrachromosomal	0.018	0.001	0.019
loopFit	0.260	0.001	0.262
loopGenes	6.513	0.016	6.955
loopMetrics	0.004	0.001	0.004
loopPlot	0.245	0.005	0.333
loopTest	0.360	0.002	0.481
loopWidth	0.016	0.001	0.022
loopsMake	4.216	0.189	5.851
loopsSubset	0.332	0.005	0.425
mergeAnchors	0.383	0.021	0.529
numAnchors	0.015	0.000	0.020
numLoops	0.005	0.001	0.005
padGRanges	0.207	0.008	0.276
pcaPlot	0.025	0.001	0.031
plotTopLoops	4.108	0.066	5.842
quickAssoc	0.180	0.000	0.181
removeSelfLoops	0.053	0.001	0.053
rmchr	0.123	0.004	0.128
sampleNames-loops-method	0.003	0.000	0.003
slidingWindowTest	0.286	0.001	0.288
splitSamples	0.659	0.001	0.802
subsetLoops	0.082	0.001	0.101
subsetRegion	0.528	0.006	0.673
summary-loops-method	0.354	0.001	0.397
topLoops	0.235	0.001	0.237
union-loops-loops-method	0.259	0.001	0.262
updateLDGroups	0.002	0.001	0.002