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CHECK report for CAGEr on merida1

This page was generated on 2020-08-11 11:54:49 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAGEr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 214/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.31.4
Vanja Haberle , Charles Plessy , Damir Baranasic , Sarvesh Nikumbh
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: master
Last Commit: f845b5c
Last Changed Date: 2020-07-14 02:01:55 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.31.4
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_1.31.4.tar.gz
StartedAt: 2020-08-11 00:10:41 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 00:20:19 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 577.5 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_1.31.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CAGEr.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘1.31.4’
* 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
importPublicData           40.595  1.284  50.210
cumulativeCTSSdistribution 33.240  1.641  34.929
quantilePositions          30.731  0.506  31.341
aggregateTagClusters       18.885  0.091  19.002
distclu-functions           8.670  0.240   8.920
clusterCTSS                 8.317  0.277   8.621
CAGEexp-class               6.332  0.628   6.972
scoreShift                  6.317  0.100   6.434
consensusClusters           5.446  0.224   5.678
coverage-functions          5.020  0.309   5.336
* 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/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)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class6.3320.6286.972
CAGEr_Multicore0.8640.0090.873
CAGEset-class0.0030.0010.004
CTSS-class0.0360.0000.037
CTSSclusteringMethod0.0090.0000.010
CTSScoordinates0.1570.0020.159
CTSSnormalizedTpm1.2250.0081.235
CTSStagCount0.4210.0070.429
CTSStagCountTable0.0080.0010.010
CTSStoGenes1.0980.0041.104
CustomConsensusClusters1.8120.0081.821
GeneExpDESeq22.1440.0342.181
GeneExpSE0.0060.0010.007
QuantileWidthFunctions0.0000.0010.000
aggregateTagClusters18.885 0.09119.002
annotateCTSS2.6690.0212.699
byCtss0.0070.0010.007
clusterCTSS8.3170.2778.621
consensusClusterConvertors0.0490.0010.051
consensusClusters5.4460.2245.678
consensusClustersDESeq20.4760.0050.482
consensusClustersTpm0.0080.0010.009
coverage-functions5.0200.3095.336
cumulativeCTSSdistribution33.240 1.64134.929
distclu-functions8.670.248.92
exampleCAGEexp0.0000.0010.001
exampleCAGEset0.0200.0020.022
exportCTSStoBedGraph4.5200.0244.551
exportToBed4.8470.0344.959
expressionClasses0.0020.0010.003
extractExpressionClass0.0100.0010.011
genomeName0.0010.0000.001
getCTSS0.2130.0100.223
getExpressionProfiles0.6670.0020.670
getShiftingPromoters0.0050.0010.006
hanabi0.3550.0110.367
hanabiPlot0.3990.0060.407
import.CAGEscanMolecule0.0000.0010.001
import.CTSS0.1500.0030.154
import.bam000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule0.0000.0000.001
importPublicData40.595 1.28450.210
inputFiles0.0000.0000.001
inputFilesType000
librarySizes0.0010.0010.001
mapStats0.1040.0820.186
mergeCAGEsets4.3490.0444.398
mergeSamples1.1580.0051.164
moleculesGR2CTSS0.2290.0010.231
normalizeTagCount1.0080.0031.012
parseCAGEscanBlocksToGrangeTSS0.0360.0010.037
plotAnnot2.9270.0263.003
plotCorrelation0.7060.0040.713
plotExpressionProfiles0.1790.0070.187
plotInterquantileWidth1.1380.0181.201
plotReverseCumulatives0.8160.0140.836
quantilePositions30.731 0.50631.341
ranges2annot0.5740.0040.580
ranges2genes0.0950.0020.097
ranges2names0.0800.0010.082
sampleLabels0.0000.0000.001
scoreShift6.3170.1006.434
seqNameTotalsSE0.0060.0000.007
setColors2.3820.0072.391
strandInvaders1.5940.0801.686
summariseChrExpr0.8320.0020.836
tagClusterConvertors0.4870.0060.493
tagClusters0.0750.0020.076