Package: CAGEr

Version: 1.25.1

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_1.25.1.tar.gz

StartedAt: 2019-04-09 00:20:49 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:30:53 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 603.9 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_1.25.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.25.1’
* 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           48.765  9.820  45.057
cumulativeCTSSdistribution 35.526 13.277  45.042
quantilePositions          34.810  2.245  36.518
aggregateTagClusters       15.852  2.487  13.887
distclu-functions          11.663  5.044   7.858
clusterCTSS                12.714  2.747  10.094
coverage-functions          6.361  1.144   7.507
scoreShift                  6.888  0.116   7.005
CAGEexp-class               5.450  0.477   5.944
* 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/3.6/Resources/library’
* installing *source* package ‘CAGEr’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CAGEr)

name	user	system	elapsed
CAGEexp-class	5.450	0.477	5.944
CAGEr_Multicore	0.041	0.009	0.050
CAGEset-class	0.004	0.001	0.005
CTSS-class	0.027	0.003	0.030
CTSSclusteringMethod	0.010	0.002	0.012
CTSScoordinates	0.049	0.003	0.052
CTSSnormalizedTpm	2.335	1.541	1.024
CTSStagCount	0.414	0.008	0.423
CTSStagCountTable	0.011	0.001	0.012
CTSStoGenes	0.852	0.078	0.931
CustomConsensusClusters	1.032	0.013	1.045
GeneExpDESeq2	2.090	0.076	2.167
GeneExpSE	0.004	0.000	0.004
QuantileWidthFunctions	0.000	0.000	0.001
aggregateTagClusters	15.852	2.487	13.887
annotateCTSS	2.035	0.024	2.060
byCtss	0.018	0.010	0.010
clusterCTSS	12.714	2.747	10.094
consensusClusterConvertors	0.027	0.001	0.028
consensusClusters	4.121	0.688	4.812
consensusClustersDESeq2	0.232	0.017	0.248
consensusClustersTpm	0.008	0.001	0.009
coverage-functions	6.361	1.144	7.507
cumulativeCTSSdistribution	35.526	13.277	45.042
distclu-functions	11.663	5.044	7.858
exampleCAGEexp	0.000	0.000	0.001
exampleCAGEset	0.017	0.001	0.018
exportCTSStoBedGraph	2.652	0.081	2.737
exportToBed	4.334	0.016	4.351
expressionClasses	0.003	0.001	0.004
extractExpressionClass	0.013	0.001	0.014
genomeName	0	0	0
getCTSS	0.707	0.271	0.509
getExpressionProfiles	1.086	0.437	0.680
getShiftingPromoters	0.009	0.001	0.010
hanabi	0.286	0.034	0.321
hanabiPlot	0.463	0.059	0.523
import.CAGEscanMolecule	0.001	0.000	0.000
import.CTSS	0.052	0.001	0.054
import.bam	0	0	0
import.bedCTSS	0	0	0
import.bedScore	0	0	0
import.bedmolecule	0.000	0.000	0.001
importPublicData	48.765	9.820	45.057
inputFiles	0.002	0.002	0.000
inputFilesType	0.002	0.002	0.001
librarySizes	0.002	0.002	0.001
mapStats	1.207	0.285	0.492
mergeCAGEsets	3.547	0.508	3.402
mergeSamples	0.603	0.004	0.608
moleculesGR2CTSS	0.151	0.001	0.151
normalizeTagCount	1.958	1.179	0.953
parseCAGEscanBlocksToGrangeTSS	0.020	0.001	0.021
plotAnnot	3.847	0.021	3.873
plotCorrelation	0.923	0.004	0.974
plotExpressionProfiles	0.224	0.004	0.228
plotInterquantileWidth	0.408	0.008	0.423
plotReverseCumulatives	2.164	1.418	0.845
quantilePositions	34.810	2.245	36.518
ranges2annot	0.438	0.001	0.440
ranges2genes	0.074	0.001	0.074
ranges2names	0.076	0.001	0.078
sampleLabels	0.000	0.001	0.001
scoreShift	6.888	0.116	7.005
seqNameTotalsSE	0.005	0.001	0.005
setColors	0.528	0.005	0.533
strandInvaders	2.167	0.630	1.697
summariseChrExpr	0.525	0.002	0.526
tagClusterConvertors	0.383	0.006	0.388
tagClusters	0.058	0.004	0.062