Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-12-01 17:17:21 -0500 (Wed, 01 Dec 2021).

CHECK results for CAGEfightR on nebbiolo2

To the developers/maintainers of the CAGEfightR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.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 235/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.14.0  (landing page)
Malte Thodberg
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_14
git_last_commit: 6c27321
git_last_commit_date: 2021-10-26 12:44:41 -0500 (Tue, 26 Oct 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: CAGEfightR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEfightR_1.14.0.tar.gz
StartedAt: 2021-11-30 08:22:16 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 08:27:30 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 314.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings CAGEfightR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/CAGEfightR.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 ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.14.0’
* 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 ‘CAGEfightR’ 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
findLinks 4.367  0.877   4.347
* 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

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘CAGEfightR’ ...
** 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 (CAGEfightR)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID4.0250.0644.089
assignMissingID1.3940.0321.426
assignTxID1.0420.0081.050
assignTxType0.0010.0000.001
balanceBC0.0010.0000.001
balanceD000
bwCommonGenome0.0380.0000.040
bwGenomeCompatibility0.0150.0000.015
bwValid0.0070.0000.007
calcBidirectionality0.6190.0270.647
calcComposition1.5930.0251.617
calcPooled0.1430.0000.142
calcShape3.7200.1873.908
calcSupport0.1510.0010.152
calcTPM0.1910.0080.199
calcTotalTags0.0870.0080.094
checkCTSSs0.2960.0000.297
checkPeaked0.0730.0030.077
checkPooled0.0730.0160.089
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally1.3610.0151.377
combineClusters1.0840.0161.101
convertBAM2BigWig0.0010.0000.000
convertBED2BigWig000
convertGRanges2GPos0.0900.0000.091
exampleDesign0.0040.0000.004
findLinks4.3670.8774.347
findStretches0.4700.0810.551
quantifyCTSSs0.0010.0000.000
quantifyCTSSs2000
quantifyClusters0.5400.0240.564
quantifyGenes1.3320.0601.393
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.000
shapeIQR0.0010.0000.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.4730.0160.489
subsetByComposition2.5150.1122.627
subsetBySupport0.1320.0160.148
swapRanges0.2820.0040.287
swapScores0.1350.0040.139
trackBalance000
trackCTSS2.8500.0282.879
trackClusters2.0850.0122.098
trackLinks1.0140.6311.056
trimToPeak0.9200.0720.993
trimToPercentiles2.5300.0442.575
tuneTagClustering0.0000.0000.001
utilsAggregateRows0.3750.0800.455
utilsDeStrand0.1320.0000.132
utilsScoreOverlaps0.0670.0000.068
utilsSimplifyTxDb000