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: 2017-10-18 02:47:37 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:52:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 278.1 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 3.4.2 (2017-09-28)
* 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	0.540	0.027	0.583
annotateAnchors	0.433	0.005	0.454
annotateAnchors.bed	0.482	0.007	0.511
annotateAnchors.bigwig	0.049	0.002	0.051
annotateLoops	1.451	0.033	1.535
annotateLoops.dge	0.368	0.006	0.389
bedToGRanges	0.097	0.002	0.102
calcLDSizeFactors	0.003	0.000	0.003
callCCDs	0.001	0.001	0.001
computeBoundaryScores	0.002	0.000	0.002
featureTest	0.002	0.000	0.002
filterLoops	0.141	0.000	0.146
filterSpanningLoops	0.018	0.001	0.018
getHumanGenes	0.065	0.001	0.068
getHumanTSS	0.189	0.004	0.200
getMouseGenes	0.115	0.003	0.123
getMouseTSS	0.581	0.006	0.619
interchromosomal	0.017	0.001	0.019
intrachromosomal	0.017	0.000	0.017
keepCTCFloops	0.130	0.003	0.136
keepEPloops	0.295	0.007	0.307
loopAssoc	0.001	0.001	0.001
loopDistancePlot	0.101	0.001	0.104
loopGenes	0.088	0.001	0.091
loopMetrics	0.003	0.000	0.004
loopPlot	1.454	0.036	1.526
loopWidth	0.018	0.000	0.018
loopsMake	0.001	0.001	0.001
loopsMake.mango	0.001	0.000	0.001
loopsSubset	0.512	0.013	0.550
mangoCorrection	0.142	0.001	0.144
manyLoopPlots	0.296	0.002	0.305
mergeAnchors	0.225	0.002	0.230
numAnchors	0.011	0.000	0.011
numLoops	0.004	0.000	0.004
padGRanges	0.133	0.003	0.138
pcaPlot	0.108	0.001	0.111
plotTopLoops	2.270	0.018	2.350
quickAssoc	0.070	0.002	0.071
quickAssocVoom	0.298	0.001	0.306
removeRegion	0.186	0.005	0.195
removeSelfLoops	0.006	0.000	0.007
rmchr	0.163	0.005	0.173
sampleNames-loops-method	0.003	0.000	0.004
slidingWindowTest	0.002	0.001	0.002
splitSamples	0.100	0.000	0.109
subsetLoops	0.023	0.000	0.024
subsetRegion	0.483	0.006	0.497
subsetRegionAB	0.296	0.007	0.309
summary-loops-method	0.121	0.000	0.140
topLoops	0.074	0.001	0.094
union-loops-loops-method	0.175	0.001	0.186
updateLDGroups	0.002	0.000	0.002