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This page was generated on 2024-06-11 14:40 -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 palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEfightR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CAGEfightR_1.24.0.tar.gz
StartedAt: 2024-06-10 01:21:53 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:30:35 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 522.1 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEfightR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CAGEfightR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CAGEfightR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CAGEfightR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CAGEfightR' version '1.24.0'
* 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 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 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    6.14   0.19   53.92
assignGeneID 3.91   0.28   11.03
trackLinks   2.06   0.14   25.69
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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
assignGeneID 3.91 0.2811.03
assignMissingID0.980.061.04
assignTxID0.780.080.86
assignTxType000
balanceBC000
balanceD000
bwCommonGenome000
bwGenomeCompatibility000
bwValid0.030.000.03
calcBidirectionality0.470.000.47
calcComposition1.430.121.56
calcPooled0.130.000.13
calcShape2.440.252.68
calcSupport0.080.020.10
calcTPM0.140.000.14
calcTotalTags0.060.030.10
checkCTSSs000
checkPeaked0.050.010.06
checkPooled0.060.000.06
clusterBidirectionally000
clusterUnidirectionally2.620.032.66
combineClusters0.750.000.75
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.080.000.08
exampleDesign0.000.050.05
findLinks 6.14 0.1953.92
findStretches0.500.010.52
quantifyCTSSs0.020.000.01
quantifyCTSSs2000
quantifyClusters0.510.040.55
quantifyGenes1.190.061.26
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR000
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.420.080.49
subsetByComposition1.220.111.33
subsetBySupport0.090.000.09
swapRanges0.180.010.19
swapScores0.110.020.12
trackBalance000
trackCTSS3.530.113.67
trackClusters2.050.012.08
trackLinks 2.06 0.1425.69
trimToPeak0.830.050.87
trimToPercentiles2.190.062.25
tuneTagClustering000
utilsAggregateRows0.530.280.81
utilsDeStrand0.110.000.11
utilsScoreOverlaps0.070.000.06
utilsSimplifyTxDb000