Back to Multiple platform build/check report for BioC 3.10
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CAGEr on malbec1

This page was generated on 2020-04-15 12:07:30 -0400 (Wed, 15 Apr 2020).

Package 214/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.28.0
Vanja Haberle , Charles Plessy , Damir Baranasic , Sarvesh Nikumbh
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: RELEASE_3_10
Last Commit: de5899e
Last Changed Date: 2019-10-29 13:08:37 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.28.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEr_1.28.0.tar.gz
StartedAt: 2020-04-15 01:37:28 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:45:55 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 506.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings CAGEr_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/CAGEr.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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
cumulativeCTSSdistribution 34.296  4.800  37.053
importPublicData           38.336  0.472  43.187
quantilePositions          25.268  0.704  26.009
aggregateTagClusters       18.020  0.052  15.159
clusterCTSS                13.844  0.376  11.573
distclu-functions          11.004  0.656   9.087
plotReverseCumulatives      9.384  0.048   2.330
scoreShift                  6.296  0.064   6.397
CTSSnormalizedTpm           5.956  0.076   2.014
coverage-functions          5.172  0.476   5.668
normalizeTagCount           5.460  0.032   2.116
mergeCAGEsets               5.360  0.016   4.444
CAGEexp-class               4.864  0.172   5.276
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-class4.8640.1725.276
CAGEr_Multicore0.9200.1921.118
CAGEset-class0.0040.0000.004
CTSS-class0.0600.0040.061
CTSSclusteringMethod0.0120.0000.013
CTSScoordinates0.1920.0040.193
CTSSnormalizedTpm5.9560.0762.014
CTSStagCount0.3920.0200.415
CTSStagCountTable0.0040.0000.007
CTSStoGenes0.6040.0480.654
CustomConsensusClusters1.5880.0001.595
GeneExpDESeq21.8280.0161.847
GeneExpSE0.0040.0000.004
QuantileWidthFunctions000
aggregateTagClusters18.020 0.05215.159
annotateCTSS1.8040.0001.806
byCtss0.2880.0040.108
clusterCTSS13.844 0.37611.573
consensusClusterConvertors0.0520.0000.058
consensusClusters3.8480.5324.410
consensusClustersDESeq20.1400.0000.141
consensusClustersTpm0.0120.0000.012
coverage-functions5.1720.4765.668
cumulativeCTSSdistribution34.296 4.80037.053
distclu-functions11.004 0.656 9.087
exampleCAGEexp000
exampleCAGEset0.0160.0000.017
exportCTSStoBedGraph3.4680.0123.489
exportToBed4.6200.0084.662
expressionClasses0.0040.0000.002
extractExpressionClass0.0040.0000.006
genomeName000
getCTSS2.1320.0160.675
getExpressionProfiles0.1480.0040.154
getShiftingPromoters0.0000.0000.004
hanabi0.2640.0240.291
hanabiPlot0.3200.0200.336
import.CAGEscanMolecule000
import.CTSS0.1360.0000.133
import.bam0.0000.0000.001
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData38.336 0.47243.187
inputFiles000
inputFilesType000
librarySizes000
mapStats0.0800.0000.079
mergeCAGEsets5.3600.0164.444
mergeSamples0.6840.0000.685
moleculesGR2CTSS0.2240.0000.228
normalizeTagCount5.4600.0322.116
parseCAGEscanBlocksToGrangeTSS0.0360.0000.035
plotAnnot3.2840.0043.294
plotCorrelation0.4720.0000.472
plotExpressionProfiles0.1560.0000.156
plotInterquantileWidth0.3520.0000.352
plotReverseCumulatives9.3840.0482.330
quantilePositions25.268 0.70426.009
ranges2annot0.4520.0000.452
ranges2genes0.0880.0000.086
ranges2names0.0840.0000.087
sampleLabels000
scoreShift6.2960.0646.397
seqNameTotalsSE0.0040.0000.004
setColors0.3800.0000.381
strandInvaders1.2720.0361.212
summariseChrExpr0.9640.0000.964
tagClusterConvertors0.5240.0040.530
tagClusters0.0720.0000.074