BioC 3.4: CHECK report for diffloop on morelia

Package: diffloop

Version: 1.1.99

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.1.99.tar.gz

StartedAt: 2016-09-20 05:38:49 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:42:20 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 210.8 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_1.1.99.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/diffloop.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.99’
* 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 ... OK
* 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: OK

* installing *source* package ‘diffloop’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘diffloop’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘diffloop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffloop)

name	user	system	elapsed
addchr	0.186	0.004	0.191
annotateAnchors	0.426	0.003	0.429
annotateAnchors.bed	0.038	0.002	0.039
annotateAnchors.bigwig	0.061	0.002	0.063
annotateLoops	1.156	0.020	1.177
annotateLoops.dge	0.759	0.014	0.838
bedToGRanges	0.170	0.002	0.196
calcLDSizeFactors	0.003	0.001	0.003
callCCDs	0.531	0.002	0.556
computeBoundaryScores	0.524	0.039	0.586
featureTest	3.260	0.041	3.366
filterLoops	0.125	0.000	0.128
filterSpanningLoops	0.033	0.000	0.037
getHumanGenes	0.096	0.004	0.101
getHumanTSS	0.284	0.004	0.294
getMouseGenes	0.156	0.003	0.160
getMouseTSS	0.879	0.014	0.900
interchromosomal	0.040	0.001	0.040
intrachromosomal	0.031	0.001	0.032
keepCTCFloops	0.387	0.007	0.400
keepEPloops	0.852	0.005	0.864
loopFit	0.389	0.001	0.419
loopGenes	0.173	0.001	0.175
loopMetrics	0.004	0.000	0.005
loopPlot	1.052	0.024	1.085
loopTest	0.415	0.006	0.422
loopWidth	0.039	0.000	0.040
loopsMake	0.001	0.000	0.002
loopsMake.mango	0.002	0.001	0.002
loopsSubset	0.292	0.004	0.323
mangoCorrection	0.153	0.001	0.174
manyLoopPlots	0.426	0.002	0.535
mergeAnchors	0.177	0.001	0.197
numAnchors	0.013	0.000	0.013
numLoops	0.003	0.000	0.003
padGRanges	0.181	0.006	0.199
pcaPlot	0.011	0.000	0.012
plotTopLoops	1.136	0.011	1.151
quickAssoc	0.119	0.001	0.119
quickAssocVoom	0.151	0.002	0.156
removeRegion	0.225	0.005	0.231
removeSelfLoops	0.014	0.000	0.016
rmchr	0.208	0.005	0.216
sampleNames-loops-method	0.004	0.000	0.004
slidingWindowTest	0.363	0.002	0.370
splitSamples	0.158	0.001	0.159
subsetLoops	0.043	0.000	0.043
subsetRegion	0.521	0.006	0.536
subsetRegionAB	0.258	0.004	0.261
summary-loops-method	0.122	0.000	0.122
topLoops	0.103	0.001	0.104
union-loops-loops-method	0.178	0.001	0.179
updateLDGroups	0.001	0.001	0.002