BioC 3.5: CHECK report for diffloop on toluca2

Package: diffloop

Version: 1.3.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.3.4.tar.gz

StartedAt: 2017-04-23 03:01:43 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 03:06:37 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 293.8 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_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/diffloop.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.3.4’
* 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	1.075	0.021	1.107
annotateAnchors	0.546	0.033	0.585
annotateAnchors.bed	0.144	0.004	0.152
annotateAnchors.bigwig	0.067	0.003	0.071
annotateLoops	1.871	0.020	1.898
annotateLoops.dge	0.509	0.011	0.521
bedToGRanges	0.152	0.001	0.156
calcLDSizeFactors	0.002	0.001	0.003
callCCDs	0.001	0.000	0.002
computeBoundaryScores	0.001	0.000	0.002
featureTest	0.001	0.000	0.002
filterLoops	0.165	0.001	0.166
filterSpanningLoops	0.022	0.000	0.022
getHumanGenes	0.078	0.001	0.080
getHumanTSS	0.234	0.010	0.245
getMouseGenes	0.116	0.002	0.120
getMouseTSS	0.212	0.002	0.219
interchromosomal	0.024	0.001	0.025
intrachromosomal	0.024	0.001	0.025
keepCTCFloops	0.211	0.004	0.219
keepEPloops	0.891	0.014	0.907
loopAssoc	0.001	0.000	0.002
loopDistancePlot	0.138	0.001	0.139
loopGenes	0.134	0.001	0.139
loopMetrics	0.003	0.000	0.004
loopPlot	1.867	0.042	2.004
loopWidth	0.023	0.000	0.023
loopsMake	0.001	0.000	0.001
loopsMake.mango	0.001	0.000	0.001
loopsSubset	0.594	0.003	0.607
mangoCorrection	0.173	0.001	0.175
manyLoopPlots	0.401	0.002	0.410
mergeAnchors	0.311	0.002	0.313
numAnchors	0.013	0.000	0.013
numLoops	0.004	0.001	0.005
padGRanges	0.204	0.003	0.209
pcaPlot	0.144	0.001	0.145
plotTopLoops	2.935	0.019	2.981
quickAssoc	0.061	0.001	0.061
quickAssocVoom	0.379	0.001	0.381
removeRegion	0.232	0.007	0.241
removeSelfLoops	0.012	0.000	0.012
rmchr	0.190	0.004	0.195
sampleNames-loops-method	0.003	0.001	0.003
slidingWindowTest	0.002	0.000	0.002
splitSamples	0.109	0.001	0.109
subsetLoops	0.029	0.000	0.029
subsetRegion	0.593	0.007	0.602
subsetRegionAB	0.319	0.006	0.327
summary-loops-method	0.124	0.001	0.124
topLoops	0.061	0.000	0.062
union-loops-loops-method	0.172	0.000	0.175
updateLDGroups	0.002	0.000	0.002