Package: CAGEr

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2020-04-15 00:53:56 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:04:17 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 621.3 seconds

RetCode: 0

Status:  OK

CheckDir: CAGEr.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CAGEr.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.28.0’
* 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           44.412 10.617  46.208
cumulativeCTSSdistribution 33.975  9.198  38.850
quantilePositions          28.362  1.884  29.248
aggregateTagClusters       17.703  4.218  15.749
distclu-functions          11.842  5.880   9.468
clusterCTSS                12.227  4.068   8.974
mergeCAGEsets               4.697  1.427   4.176
scoreShift                  5.859  0.145   6.027
plotReverseCumulatives      3.774  1.734   0.909
coverage-functions          4.759  0.619   5.414
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* 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	4.570	0.344	4.935
CAGEr_Multicore	0.901	0.015	0.927
CAGEset-class	0.004	0.001	0.005
CTSS-class	0.047	0.001	0.049
CTSSclusteringMethod	0.012	0.001	0.014
CTSScoordinates	0.150	0.001	0.151
CTSSnormalizedTpm	2.519	1.788	1.576
CTSStagCount	0.412	0.048	0.467
CTSStagCountTable	0.007	0.001	0.008
CTSStoGenes	0.714	0.031	0.747
CustomConsensusClusters	1.349	0.008	1.362
GeneExpDESeq2	1.951	0.051	2.013
GeneExpSE	0.005	0.000	0.006
QuantileWidthFunctions	0	0	0
aggregateTagClusters	17.703	4.218	15.749
annotateCTSS	1.938	0.012	1.954
byCtss	0.013	0.015	0.006
clusterCTSS	12.227	4.068	8.974
consensusClusterConvertors	0.048	0.013	0.044
consensusClusters	4.193	0.485	4.717
consensusClustersDESeq2	0.200	0.009	0.212
consensusClustersTpm	0.011	0.001	0.012
coverage-functions	4.759	0.619	5.414
cumulativeCTSSdistribution	33.975	9.198	38.850
distclu-functions	11.842	5.880	9.468
exampleCAGEexp	0.000	0.001	0.001
exampleCAGEset	0.020	0.000	0.021
exportCTSStoBedGraph	4.113	0.098	4.238
exportToBed	4.147	0.013	4.188
expressionClasses	0.003	0.000	0.004
extractExpressionClass	0.010	0.001	0.010
genomeName	0.000	0.000	0.001
getCTSS	0.455	0.397	0.250
getExpressionProfiles	0.980	0.596	0.661
getShiftingPromoters	0.008	0.000	0.009
hanabi	0.377	0.008	0.387
hanabiPlot	0.405	0.022	0.428
import.CAGEscanMolecule	0	0	0
import.CTSS	0.116	0.002	0.117
import.bam	0	0	0
import.bedCTSS	0	0	0
import.bedScore	0.000	0.000	0.001
import.bedmolecule	0	0	0
importPublicData	44.412	10.617	46.208
inputFiles	0.001	0.001	0.001
inputFilesType	0.001	0.001	0.001
librarySizes	0.001	0.001	0.000
mapStats	0.310	0.377	0.107
mergeCAGEsets	4.697	1.427	4.176
mergeSamples	0.641	0.002	0.646
moleculesGR2CTSS	0.218	0.001	0.221
normalizeTagCount	2.239	1.444	1.295
parseCAGEscanBlocksToGrangeTSS	0.034	0.001	0.034
plotAnnot	3.929	0.019	3.974
plotCorrelation	0.604	0.002	0.607
plotExpressionProfiles	0.173	0.003	0.176
plotInterquantileWidth	0.469	0.005	0.481
plotReverseCumulatives	3.774	1.734	0.909
quantilePositions	28.362	1.884	29.248
ranges2annot	0.597	0.033	0.634
ranges2genes	0.094	0.001	0.095
ranges2names	0.077	0.001	0.078
sampleLabels	0.001	0.000	0.000
scoreShift	5.859	0.145	6.027
seqNameTotalsSE	0.006	0.001	0.006
setColors	0.500	0.005	0.507
strandInvaders	2.099	1.512	1.295
summariseChrExpr	0.844	0.053	0.902
tagClusterConvertors	0.488	0.003	0.492
tagClusters	0.061	0.001	0.062