BioC 3.6: CHECK report for diffloop on veracruz1

Package: diffloop

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.5.0.tar.gz

StartedAt: 2017-08-16 02:17:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:21:24 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 259.0 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.5.0’
* 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-3.6-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	0.842	0.017	0.884
annotateAnchors	0.407	0.022	0.436
annotateAnchors.bed	0.115	0.003	0.118
annotateAnchors.bigwig	0.053	0.002	0.065
annotateLoops	1.412	0.015	1.466
annotateLoops.dge	0.353	0.005	0.371
bedToGRanges	0.106	0.001	0.107
calcLDSizeFactors	0.002	0.000	0.003
callCCDs	0.001	0.001	0.002
computeBoundaryScores	0.002	0.000	0.001
featureTest	0.001	0.000	0.002
filterLoops	0.131	0.001	0.133
filterSpanningLoops	0.018	0.000	0.020
getHumanGenes	0.067	0.002	0.070
getHumanTSS	0.162	0.005	0.176
getMouseGenes	0.086	0.001	0.087
getMouseTSS	0.570	0.006	0.596
interchromosomal	0.019	0.000	0.020
intrachromosomal	0.02	0.00	0.02
keepCTCFloops	0.129	0.002	0.132
keepEPloops	0.361	0.005	0.373
loopAssoc	0.001	0.000	0.002
loopDistancePlot	0.096	0.001	0.101
loopGenes	0.104	0.001	0.104
loopMetrics	0.004	0.000	0.004
loopPlot	1.290	0.033	1.376
loopWidth	0.012	0.000	0.013
loopsMake	0.001	0.000	0.002
loopsMake.mango	0.002	0.000	0.002
loopsSubset	0.444	0.002	0.464
mangoCorrection	0.135	0.000	0.136
manyLoopPlots	0.273	0.002	0.279
mergeAnchors	0.277	0.001	0.281
numAnchors	0.011	0.000	0.011
numLoops	0.004	0.000	0.005
padGRanges	0.143	0.004	0.147
pcaPlot	0.105	0.001	0.107
plotTopLoops	2.155	0.013	2.233
quickAssoc	0.055	0.001	0.057
quickAssocVoom	0.308	0.002	0.313
removeRegion	0.189	0.004	0.196
removeSelfLoops	0.006	0.001	0.007
rmchr	0.163	0.004	0.168
sampleNames-loops-method	0.003	0.000	0.003
slidingWindowTest	0.002	0.001	0.002
splitSamples	0.095	0.000	0.101
subsetLoops	0.028	0.001	0.029
subsetRegion	0.474	0.004	0.480
subsetRegionAB	0.265	0.004	0.275
summary-loops-method	0.096	0.000	0.096
topLoops	0.058	0.001	0.059
union-loops-loops-method	0.162	0.001	0.165
updateLDGroups	0.002	0.000	0.002