BioC 3.5: CHECK report for diffloop on malbec2

Package: diffloop

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings diffloop_1.4.0.tar.gz

StartedAt: 2017-10-17 22:41:50 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:45:33 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 223.2 seconds

RetCode: 0

Status:  OK

CheckDir: diffloop.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings diffloop_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/diffloop.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/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	0.432	0.028	0.462
annotateAnchors	0.328	0.000	0.332
annotateAnchors.bed	0.084	0.000	0.082
annotateAnchors.bigwig	0.036	0.004	0.039
annotateLoops	1.188	0.008	1.196
annotateLoops.dge	0.332	0.000	0.333
bedToGRanges	0.064	0.000	0.066
calcLDSizeFactors	0.004	0.000	0.002
callCCDs	0.000	0.000	0.002
computeBoundaryScores	0.004	0.000	0.001
featureTest	0.000	0.000	0.001
filterLoops	0.124	0.000	0.121
filterSpanningLoops	0.012	0.000	0.013
getHumanGenes	0.044	0.000	0.044
getHumanTSS	0.184	0.000	0.185
getMouseGenes	0.144	0.000	0.143
getMouseTSS	0.252	0.000	0.251
interchromosomal	0.024	0.004	0.026
intrachromosomal	0.024	0.000	0.025
keepCTCFloops	0.164	0.000	0.166
keepEPloops	0.416	0.000	0.418
loopAssoc	0.000	0.000	0.002
loopDistancePlot	0.136	0.000	0.137
loopGenes	0.120	0.000	0.118
loopMetrics	0.004	0.000	0.002
loopPlot	1.496	0.000	1.498
loopWidth	0.016	0.000	0.016
loopsMake	0.000	0.000	0.032
loopsMake.mango	0.000	0.004	0.001
loopsSubset	0.404	0.000	0.423
mangoCorrection	0.128	0.000	0.128
manyLoopPlots	0.432	0.000	0.434
mergeAnchors	0.244	0.000	0.245
numAnchors	0.008	0.000	0.009
numLoops	0.004	0.000	0.004
padGRanges	0.116	0.000	0.117
pcaPlot	0.088	0.000	0.088
plotTopLoops	1.980	0.000	1.978
quickAssoc	0.036	0.000	0.039
quickAssocVoom	0.232	0.000	0.232
removeRegion	0.128	0.004	0.131
removeSelfLoops	0.008	0.000	0.007
rmchr	0.124	0.000	0.123
sampleNames-loops-method	0.004	0.000	0.002
slidingWindowTest	0.000	0.000	0.001
splitSamples	0.084	0.000	0.086
subsetLoops	0.020	0.000	0.019
subsetRegion	0.372	0.000	0.370
subsetRegionAB	0.232	0.004	0.234
summary-loops-method	0.1	0.0	0.1
topLoops	0.044	0.000	0.047
union-loops-loops-method	0.108	0.004	0.115
updateLDGroups	0.000	0.000	0.002