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

This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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: 2024-06-26 14:00 -0400 (Wed, 26 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


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: 2024-06-26 21:16:14 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 21:25:01 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 527.0 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 6.012  0.908   6.323
* 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
assignGeneID3.4630.1353.599
assignMissingID0.9900.0291.018
assignTxID0.8570.0350.892
assignTxType0.0000.0000.001
balanceBC0.0000.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0430.0030.052
bwGenomeCompatibility0.0180.0070.025
bwValid0.0090.0010.009
calcBidirectionality0.3870.0070.395
calcComposition1.3080.0081.316
calcPooled0.0880.0000.088
calcShape2.1100.1682.278
calcSupport0.0970.0040.101
calcTPM0.1200.0070.128
calcTotalTags0.0800.0080.087
checkCTSSs0.2350.0030.239
checkPeaked0.0540.0040.057
checkPooled0.0550.0010.055
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally2.8060.1352.942
combineClusters0.6600.0160.676
convertBAM2BigWig000
convertBED2BigWig0.0000.0000.001
convertGRanges2GPos0.0620.0060.069
exampleDesign0.0050.0000.005
findLinks6.0120.9086.323
findStretches0.3280.0360.363
quantifyCTSSs0.0000.0010.001
quantifyCTSSs20.0000.0010.000
quantifyClusters0.3610.0380.398
quantifyGenes1.1330.0641.196
quickEnhancers000
quickGenes0.0000.0010.000
quickTSSs000
shapeEntropy0.0000.0000.001
shapeIQR0.0000.0000.001
shapeMean0.0000.0000.001
shapeMultimodality000
subsetByBidirectionality0.3520.0100.362
subsetByComposition1.1420.0161.157
subsetBySupport0.0600.0040.065
swapRanges0.1730.0000.172
swapScores0.0870.0080.095
trackBalance0.0000.0000.001
trackCTSS3.3440.2043.548
trackClusters2.1960.0442.240
trackLinks0.7800.4400.941
trimToPeak0.6900.0560.746
trimToPercentiles1.6750.0241.698
tuneTagClustering0.0010.0000.000
utilsAggregateRows0.3330.4280.761
utilsDeStrand0.1180.0080.126
utilsScoreOverlaps0.0610.0000.061
utilsSimplifyTxDb0.0010.0000.000