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This page was generated on 2021-12-03 13:04:44 -0500 (Fri, 03 Dec 2021).

CHECK results for CAGEr on nebbiolo2

To the developers/maintainers of the CAGEr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 237/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.0.2  (landing page)
Charles Plessy
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_14
git_last_commit: 9218aa9
git_last_commit_date: 2021-11-16 19:37:08 -0500 (Tue, 16 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CAGEr
Version: 2.0.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEr_2.0.2.tar.gz
StartedAt: 2021-12-02 06:28:02 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:35:00 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 417.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEr_2.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CAGEr.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘2.0.2’
* 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 LazyData ... 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
clusterCTSS                29.622  1.076  30.686
exportToTrack              29.850  0.100  29.950
cumulativeCTSSdistribution 23.066  6.591  29.639
quantilePositions          17.959  0.168  18.127
aggregateTagClusters        8.342  0.037   8.350
* 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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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CAGEr
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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-class4.2760.2564.534
CAGEr_Multicore1.0830.0071.111
CTSS-class0.3670.0000.367
CTSSclusteringMethod0.0010.0000.001
CTSScoordinates0.0910.0000.091
CTSSnormalizedTpm0.7950.0280.822
CTSStagCount0.9180.0961.014
CTSStoGenes0.5410.0310.572
CustomConsensusClusters1.2390.2601.499
GeneExpDESeq21.1870.2761.463
GeneExpSE0.0110.0000.011
QuantileWidthFunctions0.1410.0280.169
aggregateTagClusters8.3420.0378.350
annotateCTSS1.7470.0041.751
byCtss0.0050.0000.005
clusterCTSS29.622 1.07630.686
consensusClusters0.1670.0000.167
consensusClustersDESeq20.270.000.27
consensusClustersTpm0.0080.0000.007
coverage-functions3.4060.4403.846
cumulativeCTSSdistribution23.066 6.59129.639
distclu-functions4.0750.6354.648
exampleCAGEexp000
exportToTrack29.85 0.1029.95
expressionClasses0.020.000.02
genomeName000
getCTSS1.2270.0201.247
getExpressionProfiles2.0200.0122.032
getShiftingPromoters000
hanabi0.2340.0040.238
hanabiPlot0.3030.0120.315
import.CAGEscanMolecule000
import.CTSS0.0960.0000.096
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
inputFiles0.0010.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.001
mapStats0.0350.0040.039
mergeCAGEsets2.8210.0122.833
mergeSamples0.7210.0000.720
moleculesGR2CTSS0.1510.0000.151
normalizeTagCount0.7800.0000.758
parseCAGEscanBlocksToGrangeTSS0.0620.0000.063
plotAnnot1.7780.0161.794
plotCorrelation0.4760.0000.476
plotExpressionProfiles4.1150.1004.215
plotInterquantileWidth2.6410.0042.645
plotReverseCumulatives0.4170.0000.368
quantilePositions17.959 0.16818.127
ranges2annot0.4610.0040.465
ranges2genes0.0600.0000.061
ranges2names0.0680.0000.068
sampleLabels0.0020.0000.001
scoreShift000
seqNameTotalsSE0.0150.0000.015
setColors0.5340.0000.535
strandInvaders0.9780.0280.993
summariseChrExpr0.7120.0080.720
tagClusters0.1580.0000.159