Package: CAGEr

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.24.0.tar.gz

StartedAt: 2019-04-15 22:43:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:51:19 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 472.1 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/CAGEr.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.24.0’
* package encoding: UTF-8
* 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 ‘CAGEr’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
importPublicData           41.706 10.947  41.454
cumulativeCTSSdistribution 29.247  9.301  35.319
quantilePositions          30.192  0.831  29.919
distclu-functions          11.027  6.221   7.541
aggregateTagClusters       14.560  2.171  10.381
clusterCTSS                12.659  3.311  10.499
mergeCAGEsets               4.687  1.875   3.527
scoreShift                  5.488  0.035   5.561
coverage-functions          4.581  0.618   5.227
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CAGEr’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CAGEr)

name	user	system	elapsed
CAGEexp-class	4.503	0.284	4.837
CAGEr_Multicore	0.032	0.005	0.038
CAGEset-class	0.005	0.001	0.006
CTSS-class	0.038	0.004	0.042
CTSSclusteringMethod	0.013	0.002	0.015
CTSScoordinates	0.058	0.002	0.061
CTSSnormalizedTpm	2.109	1.951	1.056
CTSStagCount	0.312	0.005	0.324
CTSStagCountTable	0.009	0.001	0.009
CTSStoGenes	0.531	0.010	0.551
CustomConsensusClusters	1.096	0.035	1.139
GeneExpDESeq2	1.702	0.048	1.776
GeneExpSE	0.006	0.000	0.006
QuantileWidthFunctions	0	0	0
aggregateTagClusters	14.560	2.171	10.381
annotateCTSS	1.620	0.024	1.653
byCtss	0.014	0.009	0.009
clusterCTSS	12.659	3.311	10.499
consensusClusterConvertors	0.377	0.001	0.044
consensusClusters	4.073	0.555	4.662
consensusClustersDESeq2	0.178	0.006	0.185
consensusClustersTpm	0.008	0.001	0.008
coverage-functions	4.581	0.618	5.227
cumulativeCTSSdistribution	29.247	9.301	35.319
distclu-functions	11.027	6.221	7.541
exampleCAGEexp	0.002	0.003	0.000
exampleCAGEset	0.070	0.100	0.022
exportCTSStoBedGraph	2.052	0.035	2.131
exportToBed	4.323	0.013	4.378
expressionClasses	0.003	0.000	0.004
extractExpressionClass	0.011	0.001	0.012
genomeName	0.001	0.000	0.001
getCTSS	0.537	0.344	0.359
getExpressionProfiles	1.04	0.64	0.67
getShiftingPromoters	0.007	0.000	0.008
hanabi	0.264	0.008	0.274
hanabiPlot	0.367	0.107	0.483
import.CAGEscanMolecule	0	0	0
import.CTSS	0.057	0.001	0.058
import.bam	0	0	0
import.bedCTSS	0.000	0.000	0.001
import.bedScore	0	0	0
import.bedmolecule	0	0	0
importPublicData	41.706	10.947	41.454
inputFiles	0.002	0.002	0.000
inputFilesType	0.001	0.001	0.001
librarySizes	0.002	0.002	0.000
mapStats	0.697	0.680	0.357
mergeCAGEsets	4.687	1.875	3.527
mergeSamples	0.428	0.003	0.436
moleculesGR2CTSS	0.137	0.001	0.137
normalizeTagCount	3.260	1.327	0.757
parseCAGEscanBlocksToGrangeTSS	0.016	0.001	0.017
plotAnnot	3.314	0.016	3.351
plotCorrelation	1.527	0.003	1.539
plotExpressionProfiles	0.177	0.002	0.180
plotInterquantileWidth	0.326	0.004	0.333
plotReverseCumulatives	1.767	1.266	0.812
quantilePositions	30.192	0.831	29.919
ranges2annot	0.390	0.001	0.392
ranges2genes	0.077	0.001	0.077
ranges2names	0.079	0.031	0.111
sampleLabels	0.000	0.001	0.001
scoreShift	5.488	0.035	5.561
seqNameTotalsSE	0.005	0.000	0.005
setColors	0.337	0.003	0.342
strandInvaders	1.820	1.439	1.077
summariseChrExpr	0.661	0.005	0.672
tagClusterConvertors	0.335	0.003	0.339
tagClusters	0.051	0.001	0.055