BioC 3.5: CHECK report for diffloop on veracruz2

Package: diffloop

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.4.0.tar.gz

StartedAt: 2017-08-16 02:02:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:06:54 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 258.3 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/diffloop.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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:
  .travis.yml
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 ‘diffloop’ 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 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
* 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-3.5-bioc/meat/diffloop.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
addchr	0.583	0.045	0.653
annotateAnchors	0.913	0.006	0.955
annotateAnchors.bed	0.110	0.002	0.114
annotateAnchors.bigwig	0.052	0.002	0.056
annotateLoops	1.496	0.016	1.568
annotateLoops.dge	0.327	0.008	0.346
bedToGRanges	0.112	0.001	0.120
calcLDSizeFactors	0.003	0.000	0.003
callCCDs	0.002	0.000	0.002
computeBoundaryScores	0.002	0.000	0.003
featureTest	0.001	0.001	0.002
filterLoops	0.138	0.000	0.140
filterSpanningLoops	0.021	0.001	0.023
getHumanGenes	0.044	0.001	0.045
getHumanTSS	0.610	0.003	0.622
getMouseGenes	0.085	0.003	0.088
getMouseTSS	0.141	0.003	0.145
interchromosomal	0.019	0.000	0.021
intrachromosomal	0.014	0.001	0.016
keepCTCFloops	0.134	0.002	0.137
keepEPloops	0.343	0.010	0.358
loopAssoc	0.001	0.001	0.002
loopDistancePlot	0.113	0.000	0.116
loopGenes	0.124	0.001	0.133
loopMetrics	0.004	0.000	0.004
loopPlot	1.405	0.038	1.467
loopWidth	0.018	0.001	0.017
loopsMake	0.001	0.000	0.002
loopsMake.mango	0.001	0.001	0.001
loopsSubset	0.528	0.005	0.543
mangoCorrection	0.143	0.001	0.147
manyLoopPlots	0.291	0.004	0.305
mergeAnchors	0.255	0.008	0.273
numAnchors	0.011	0.001	0.011
numLoops	0.004	0.000	0.004
padGRanges	0.142	0.006	0.156
pcaPlot	0.118	0.000	0.123
plotTopLoops	2.242	0.013	2.313
quickAssoc	0.055	0.001	0.055
quickAssocVoom	0.300	0.001	0.313
removeRegion	0.194	0.004	0.202
removeSelfLoops	0.008	0.000	0.009
rmchr	0.167	0.005	0.177
sampleNames-loops-method	0.003	0.000	0.003
slidingWindowTest	0.002	0.001	0.002
splitSamples	0.097	0.000	0.097
subsetLoops	0.031	0.000	0.031
subsetRegion	0.502	0.005	0.513
subsetRegionAB	0.246	0.004	0.250
summary-loops-method	0.106	0.000	0.112
topLoops	0.055	0.001	0.057
union-loops-loops-method	0.152	0.001	0.155
updateLDGroups	0.002	0.000	0.003