Package: CAGEr

Version: 1.29.0

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_1.29.0.tar.gz

StartedAt: 2020-01-16 02:25:42 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:38:26 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 764.1 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_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.29.0’
* 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 (user + system) or elapsed time > 5s
                             user system elapsed
cumulativeCTSSdistribution 47.066 14.732  57.132
importPublicData           47.426  8.493  71.907
quantilePositions          44.612  2.208  46.358
aggregateTagClusters       24.524  1.756  22.335
distclu-functions          15.124  2.446  12.406
clusterCTSS                13.340  2.792  10.575
scoreShift                  8.384  0.241   8.628
CAGEexp-class               7.293  0.715   8.268
consensusClusters           7.168  0.785   7.987
coverage-functions          6.531  1.241   7.775
mergeCAGEsets               5.482  0.611   5.437
exportCTSStoBedGraph        5.840  0.073   6.000
exportToBed                 5.824  0.036   5.863
* 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/4.0/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	7.293	0.715	8.268
CAGEr_Multicore	1.170	0.051	1.226
CAGEset-class	0.006	0.001	0.007
CTSS-class	0.064	0.004	0.069
CTSSclusteringMethod	0.013	0.003	0.016
CTSScoordinates	0.221	0.003	0.223
CTSSnormalizedTpm	2.536	0.775	1.994
CTSStagCount	0.607	0.080	0.688
CTSStagCountTable	0.010	0.001	0.012
CTSStoGenes	1.124	0.102	1.227
CustomConsensusClusters	2.002	0.017	2.020
GeneExpDESeq2	2.216	0.073	2.296
GeneExpSE	0.005	0.000	0.005
QuantileWidthFunctions	0.000	0.000	0.001
aggregateTagClusters	24.524	1.756	22.335
annotateCTSS	3.167	0.017	3.185
byCtss	0.018	0.006	0.013
clusterCTSS	13.340	2.792	10.575
consensusClusterConvertors	0.074	0.002	0.077
consensusClusters	7.168	0.785	7.987
consensusClustersDESeq2	0.270	0.009	0.280
consensusClustersTpm	0.011	0.001	0.012
coverage-functions	6.531	1.241	7.775
cumulativeCTSSdistribution	47.066	14.732	57.132
distclu-functions	15.124	2.446	12.406
exampleCAGEexp	0.001	0.000	0.001
exampleCAGEset	0.024	0.001	0.026
exportCTSStoBedGraph	5.840	0.073	6.000
exportToBed	5.824	0.036	5.863
expressionClasses	0.004	0.000	0.004
extractExpressionClass	0.013	0.000	0.013
genomeName	0.000	0.000	0.001
getCTSS	1.418	0.074	0.415
getExpressionProfiles	1.185	0.207	0.648
getShiftingPromoters	0.009	0.001	0.010
hanabi	0.453	0.029	0.482
hanabiPlot	0.582	0.049	0.632
import.CAGEscanMolecule	0.000	0.000	0.001
import.CTSS	0.205	0.002	0.206
import.bam	0.001	0.000	0.000
import.bedCTSS	0.000	0.000	0.001
import.bedScore	0.000	0.001	0.000
import.bedmolecule	0.001	0.000	0.000
importPublicData	47.426	8.493	71.907
inputFiles	0.001	0.002	0.001
inputFilesType	0.002	0.002	0.001
librarySizes	0.002	0.002	0.001
mapStats	0.331	0.211	0.122
mergeCAGEsets	5.482	0.611	5.437
mergeSamples	0.904	0.006	0.910
moleculesGR2CTSS	0.330	0.004	0.335
normalizeTagCount	2.860	0.649	1.520
parseCAGEscanBlocksToGrangeTSS	0.046	0.001	0.047
plotAnnot	4.740	0.031	4.851
plotCorrelation	1.052	0.004	1.087
plotExpressionProfiles	0.222	0.005	0.231
plotInterquantileWidth	0.689	0.008	0.703
plotReverseCumulatives	2.173	0.948	1.213
quantilePositions	44.612	2.208	46.358
ranges2annot	0.703	0.003	0.705
ranges2genes	0.090	0.001	0.090
ranges2names	0.125	0.001	0.126
sampleLabels	0.000	0.000	0.001
scoreShift	8.384	0.241	8.628
seqNameTotalsSE	0.005	0.001	0.005
setColors	0.572	0.006	0.578
strandInvaders	3.170	0.669	3.805
summariseChrExpr	1.206	0.090	1.297
tagClusterConvertors	0.633	0.007	0.639
tagClusters	0.099	0.003	0.102