Package: CAGEr

Version: 1.26.0

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_1.26.0.tar.gz

StartedAt: 2019-10-16 01:05:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:15:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 631.8 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_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEr.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.26.0’
* 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           43.654  9.612  44.024
cumulativeCTSSdistribution 32.284 13.677  43.660
quantilePositions          37.526  2.355  38.750
aggregateTagClusters       15.294  1.773  13.801
clusterCTSS                14.687  2.126  11.550
distclu-functions          11.633  3.734   8.363
coverage-functions          6.402  1.157   7.563
scoreShift                  7.229  0.228   7.461
CAGEexp-class               5.623  0.526   6.172
consensusClusters           5.239  0.753   6.016
* 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	5.623	0.526	6.172
CAGEr_Multicore	0.988	0.015	1.003
CAGEset-class	0.003	0.001	0.005
CTSS-class	0.028	0.005	0.033
CTSSclusteringMethod	0.010	0.003	0.014
CTSScoordinates	0.066	0.001	0.068
CTSSnormalizedTpm	3.295	0.583	1.215
CTSStagCount	0.497	0.088	0.585
CTSStagCountTable	0.011	0.002	0.013
CTSStoGenes	0.777	0.045	0.822
CustomConsensusClusters	1.490	0.021	1.511
GeneExpDESeq2	2.249	0.083	2.333
GeneExpSE	0.006	0.000	0.007
QuantileWidthFunctions	0	0	0
aggregateTagClusters	15.294	1.773	13.801
annotateCTSS	2.064	0.020	2.085
byCtss	0.015	0.007	0.009
clusterCTSS	14.687	2.126	11.550
consensusClusterConvertors	0.042	0.002	0.044
consensusClusters	5.239	0.753	6.016
consensusClustersDESeq2	0.201	0.005	0.206
consensusClustersTpm	0.009	0.000	0.009
coverage-functions	6.402	1.157	7.563
cumulativeCTSSdistribution	32.284	13.677	43.660
distclu-functions	11.633	3.734	8.363
exampleCAGEexp	0.001	0.000	0.001
exampleCAGEset	0.021	0.001	0.022
exportCTSStoBedGraph	2.406	0.059	2.465
exportToBed	4.783	0.063	4.847
expressionClasses	0.002	0.001	0.002
extractExpressionClass	0.011	0.001	0.011
genomeName	0.001	0.000	0.001
getCTSS	0.693	0.210	0.531
getExpressionProfiles	0.984	0.344	0.674
getShiftingPromoters	0.008	0.001	0.009
hanabi	0.354	0.157	0.512
hanabiPlot	0.468	0.028	0.502
import.CAGEscanMolecule	0	0	0
import.CTSS	0.067	0.001	0.069
import.bam	0.001	0.000	0.000
import.bedCTSS	0.000	0.001	0.000
import.bedScore	0	0	0
import.bedmolecule	0.000	0.000	0.001
importPublicData	43.654	9.612	44.024
inputFiles	0.002	0.002	0.001
inputFilesType	0.001	0.002	0.001
librarySizes	0.001	0.002	0.001
mapStats	0.847	0.338	0.541
mergeCAGEsets	3.625	0.649	3.253
mergeSamples	0.532	0.009	0.541
moleculesGR2CTSS	0.160	0.001	0.161
normalizeTagCount	1.768	0.854	0.941
parseCAGEscanBlocksToGrangeTSS	0.019	0.000	0.020
plotAnnot	4.503	0.022	4.527
plotCorrelation	0.672	0.003	0.674
plotExpressionProfiles	0.203	0.008	0.212
plotInterquantileWidth	0.406	0.007	0.416
plotReverseCumulatives	2.182	1.367	0.909
quantilePositions	37.526	2.355	38.750
ranges2annot	0.460	0.064	0.524
ranges2genes	0.046	0.000	0.047
ranges2names	0.073	0.001	0.074
sampleLabels	0.001	0.000	0.001
scoreShift	7.229	0.228	7.461
seqNameTotalsSE	0.004	0.000	0.004
setColors	0.494	0.003	0.497
strandInvaders	3.282	0.817	1.573
summariseChrExpr	0.767	0.036	0.803
tagClusterConvertors	0.455	0.034	0.489
tagClusters	0.063	0.003	0.066