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: 2019-04-08 23:37:52 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:46:41 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 528.8 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_1.25.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CAGEr.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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           43.203 10.516  40.915
cumulativeCTSSdistribution 27.919  8.682  32.877
quantilePositions          27.242  1.373  27.789
aggregateTagClusters       14.373  3.746  11.784
distclu-functions          10.396  5.051   7.334
clusterCTSS                11.308  2.410   9.657
coverage-functions          4.960  0.627   5.621
scoreShift                  5.205  0.088   5.345
mergeCAGEsets               3.955  1.295   3.448
* 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’ ...
** 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	4.317	0.260	4.631
CAGEr_Multicore	0.034	0.007	0.043
CAGEset-class	0.003	0.000	0.004
CTSS-class	0.025	0.002	0.027
CTSSclusteringMethod	0.012	0.001	0.013
CTSScoordinates	0.055	0.000	0.056
CTSSnormalizedTpm	2.334	1.548	0.964
CTSStagCount	0.371	0.036	0.412
CTSStagCountTable	0.009	0.001	0.010
CTSStoGenes	0.604	0.026	0.636
CustomConsensusClusters	1.090	0.010	1.113
GeneExpDESeq2	1.553	0.034	1.604
GeneExpSE	0.003	0.001	0.004
QuantileWidthFunctions	0	0	0
aggregateTagClusters	14.373	3.746	11.784
annotateCTSS	2.040	0.016	2.073
byCtss	0.013	0.002	0.011
clusterCTSS	11.308	2.410	9.657
consensusClusterConvertors	0.132	0.116	0.036
consensusClusters	3.702	0.524	4.197
consensusClustersDESeq2	0.150	0.001	0.151
consensusClustersTpm	0.004	0.001	0.005
coverage-functions	4.960	0.627	5.621
cumulativeCTSSdistribution	27.919	8.682	32.877
distclu-functions	10.396	5.051	7.334
exampleCAGEexp	0.002	0.003	0.001
exampleCAGEset	0.080	0.078	0.021
exportCTSStoBedGraph	2.157	0.054	2.218
exportToBed	3.839	0.042	3.896
expressionClasses	0.002	0.000	0.003
extractExpressionClass	0.008	0.001	0.009
genomeName	0.001	0.000	0.001
getCTSS	0.554	0.251	0.311
getExpressionProfiles	1.146	0.575	0.654
getShiftingPromoters	0.004	0.000	0.005
hanabi	0.252	0.009	0.265
hanabiPlot	0.389	0.025	0.419
import.CAGEscanMolecule	0	0	0
import.CTSS	0.067	0.001	0.068
import.bam	0.001	0.000	0.000
import.bedCTSS	0.000	0.000	0.001
import.bedScore	0	0	0
import.bedmolecule	0	0	0
importPublicData	43.203	10.516	40.915
inputFiles	0.002	0.001	0.000
inputFilesType	0.001	0.001	0.001
librarySizes	0.002	0.001	0.001
mapStats	0.824	0.641	0.342
mergeCAGEsets	3.955	1.295	3.448
mergeSamples	0.430	0.002	0.435
moleculesGR2CTSS	0.114	0.001	0.116
normalizeTagCount	2.223	1.676	0.856
parseCAGEscanBlocksToGrangeTSS	0.018	0.001	0.018
plotAnnot	3.376	0.014	3.431
plotCorrelation	0.624	0.002	0.632
plotExpressionProfiles	0.210	0.003	0.213
plotInterquantileWidth	0.337	0.004	0.345
plotReverseCumulatives	2.327	1.663	0.788
quantilePositions	27.242	1.373	27.789
ranges2annot	0.319	0.005	0.328
ranges2genes	0.057	0.001	0.059
ranges2names	0.045	0.001	0.045
sampleLabels	0.000	0.000	0.001
scoreShift	5.205	0.088	5.345
seqNameTotalsSE	0.003	0.001	0.004
setColors	0.417	0.009	0.431
strandInvaders	1.961	2.266	1.102
summariseChrExpr	0.623	0.035	0.674
tagClusterConvertors	0.290	0.048	0.339
tagClusters	0.042	0.001	0.044