Back to Multiple platform build/check report for BioC 3.19:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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

Package 262/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.24.0  (landing page)
Malte Thodberg
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_19
git_last_commit: e83345a
git_last_commit_date: 2024-04-30 11:06:32 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CAGEfightR on nebbiolo1

To the developers/maintainers of the CAGEfightR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CAGEfightR
Version: 1.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEfightR_1.24.0.tar.gz
StartedAt: 2024-06-09 21:10:17 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 21:18:57 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 520.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CAGEfightR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.24.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 5.42  0.805   5.726
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
assignGeneID3.2210.0683.289
assignMissingID0.9180.0160.934
assignTxID0.7970.0000.797
assignTxType000
balanceBC000
balanceD000
bwCommonGenome0.0300.0040.037
bwGenomeCompatibility0.0150.0000.015
bwValid0.0070.0000.007
calcBidirectionality0.3700.0030.373
calcComposition1.2080.0281.236
calcPooled0.0830.0000.083
calcShape2.0610.2202.281
calcSupport0.0990.0000.099
calcTPM0.1020.0120.114
calcTotalTags0.0740.0040.078
checkCTSSs0.2070.0000.207
checkPeaked0.0540.0000.054
checkPooled0.0430.0080.051
clusterBidirectionally000
clusterUnidirectionally2.2460.1322.377
combineClusters0.6460.0040.650
convertBAM2BigWig0.0000.0010.000
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.0630.0020.065
exampleDesign0.0050.0000.004
findLinks5.4200.8055.726
findStretches0.3190.0280.347
quantifyCTSSs0.0000.0000.001
quantifyCTSSs20.0000.0000.001
quantifyClusters0.3280.0480.376
quantifyGenes1.0680.0721.140
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0000.001
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.3500.0160.366
subsetByComposition1.0600.0241.084
subsetBySupport0.0610.0000.061
swapRanges0.1480.0000.148
swapScores0.0740.0040.078
trackBalance000
trackCTSS2.7670.1722.939
trackClusters1.8510.0441.895
trackLinks0.7530.3980.916
trimToPeak0.6240.0740.698
trimToPercentiles1.5750.0721.647
tuneTagClustering0.0000.0010.000
utilsAggregateRows0.2860.4550.739
utilsDeStrand0.1030.0000.103
utilsScoreOverlaps0.0540.0000.054
utilsSimplifyTxDb000