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CHECK report for CAGEr on merida2

This page was generated on 2019-04-09 13:27:54 -0400 (Tue, 09 Apr 2019).

Package 198/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.25.1
Vanja Haberle , Charles Plessy
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: master
Last Commit: d93551e
Last Changed Date: 2018-12-12 00:42:09 -0400 (Wed, 12 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

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

Command output

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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


Installation output

CAGEr.Rcheck/00install.out

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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)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class4.3170.2604.631
CAGEr_Multicore0.0340.0070.043
CAGEset-class0.0030.0000.004
CTSS-class0.0250.0020.027
CTSSclusteringMethod0.0120.0010.013
CTSScoordinates0.0550.0000.056
CTSSnormalizedTpm2.3341.5480.964
CTSStagCount0.3710.0360.412
CTSStagCountTable0.0090.0010.010
CTSStoGenes0.6040.0260.636
CustomConsensusClusters1.0900.0101.113
GeneExpDESeq21.5530.0341.604
GeneExpSE0.0030.0010.004
QuantileWidthFunctions000
aggregateTagClusters14.373 3.74611.784
annotateCTSS2.0400.0162.073
byCtss0.0130.0020.011
clusterCTSS11.308 2.410 9.657
consensusClusterConvertors0.1320.1160.036
consensusClusters3.7020.5244.197
consensusClustersDESeq20.1500.0010.151
consensusClustersTpm0.0040.0010.005
coverage-functions4.9600.6275.621
cumulativeCTSSdistribution27.919 8.68232.877
distclu-functions10.396 5.051 7.334
exampleCAGEexp0.0020.0030.001
exampleCAGEset0.0800.0780.021
exportCTSStoBedGraph2.1570.0542.218
exportToBed3.8390.0423.896
expressionClasses0.0020.0000.003
extractExpressionClass0.0080.0010.009
genomeName0.0010.0000.001
getCTSS0.5540.2510.311
getExpressionProfiles1.1460.5750.654
getShiftingPromoters0.0040.0000.005
hanabi0.2520.0090.265
hanabiPlot0.3890.0250.419
import.CAGEscanMolecule000
import.CTSS0.0670.0010.068
import.bam0.0010.0000.000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule000
importPublicData43.20310.51640.915
inputFiles0.0020.0010.000
inputFilesType0.0010.0010.001
librarySizes0.0020.0010.001
mapStats0.8240.6410.342
mergeCAGEsets3.9551.2953.448
mergeSamples0.4300.0020.435
moleculesGR2CTSS0.1140.0010.116
normalizeTagCount2.2231.6760.856
parseCAGEscanBlocksToGrangeTSS0.0180.0010.018
plotAnnot3.3760.0143.431
plotCorrelation0.6240.0020.632
plotExpressionProfiles0.2100.0030.213
plotInterquantileWidth0.3370.0040.345
plotReverseCumulatives2.3271.6630.788
quantilePositions27.242 1.37327.789
ranges2annot0.3190.0050.328
ranges2genes0.0570.0010.059
ranges2names0.0450.0010.045
sampleLabels0.0000.0000.001
scoreShift5.2050.0885.345
seqNameTotalsSE0.0030.0010.004
setColors0.4170.0090.431
strandInvaders1.9612.2661.102
summariseChrExpr0.6230.0350.674
tagClusterConvertors0.2900.0480.339
tagClusters0.0420.0010.044