Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:05:11 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
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 20.04.4 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: 2022-01-18 06:35:08 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 06:40:14 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 305.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

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###
### 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 4.788  1.503   5.292
* 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

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###
### 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
assignGeneID3.8630.0803.947
assignMissingID1.1840.0241.207
assignTxID0.9490.0000.949
assignTxType0.0000.0000.001
balanceBC000
balanceD000
bwCommonGenome0.0360.0000.037
bwGenomeCompatibility0.0140.0000.014
bwValid0.0070.0000.006
calcBidirectionality0.5960.0160.611
calcComposition1.5620.0201.583
calcPooled0.1550.0000.155
calcShape4.0950.5124.608
calcSupport0.1760.0120.189
calcTPM0.2450.0080.253
calcTotalTags0.1130.0040.117
checkCTSSs0.3710.0160.387
checkPeaked0.0880.0080.096
checkPooled0.0790.0640.142
clusterBidirectionally000
clusterUnidirectionally1.4760.0721.548
combineClusters1.1260.2081.334
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0910.0000.091
exampleDesign0.0020.0020.004
findLinks4.7881.5035.292
findStretches0.4930.0400.533
quantifyCTSSs000
quantifyCTSSs20.0010.0000.001
quantifyClusters0.5370.0560.593
quantifyGenes1.4250.0361.461
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0000.0000.001
shapeIQR000
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.5050.0000.505
subsetByComposition2.6860.1192.805
subsetBySupport0.1440.0000.144
swapRanges0.3020.0200.322
swapScores0.1390.0030.143
trackBalance000
trackCTSS3.0520.0043.056
trackClusters2.3520.0162.368
trackLinks1.0240.6321.067
trimToPeak0.9920.0641.057
trimToPercentiles2.4130.0042.418
tuneTagClustering0.0000.0010.000
utilsAggregateRows0.3440.1090.452
utilsDeStrand0.1250.0050.130
utilsScoreOverlaps0.0710.0000.071
utilsSimplifyTxDb000