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This page was generated on 2024-05-15 13:46:28 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 257/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.25.0  (landing page)
Malte Thodberg
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: devel
git_last_commit: 28828d6
git_last_commit_date: 2024-04-30 11:06:32 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for CAGEfightR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CAGEfightR
Version: 1.24.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CAGEfightR_1.24.0.tar.gz
StartedAt: 2024-05-09 05:30:39 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 05:38:47 -0000 (Thu, 09 May 2024)
EllapsedTime: 487.8 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings CAGEfightR_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 7.459  1.106   7.839
* 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

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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
assignGeneID4.6930.0834.806
assignMissingID1.3800.0041.387
assignTxID1.1510.0001.153
assignTxType000
balanceBC000
balanceD0.0000.0000.001
bwCommonGenome0.0480.0030.055
bwGenomeCompatibility0.0240.0000.024
bwValid0.0110.0000.011
calcBidirectionality0.6180.0030.621
calcComposition3.1080.0123.126
calcPooled0.1240.0000.124
calcShape3.3730.0563.436
calcSupport0.1420.0000.142
calcTPM0.1650.0040.169
calcTotalTags0.0800.0040.083
checkCTSSs0.3350.0000.340
checkPeaked0.0790.0070.086
checkPooled0.0770.0080.085
clusterBidirectionally000
clusterUnidirectionally1.8950.0161.915
combineClusters1.0260.0041.031
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.1020.0000.103
exampleDesign0.0020.0030.005
findLinks7.4591.1067.839
findStretches0.5060.0790.586
quantifyCTSSs0.0010.0000.001
quantifyCTSSs20.0010.0000.001
quantifyClusters0.5080.0640.574
quantifyGenes1.5820.1161.702
quickEnhancers000
quickGenes000
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0000.001
shapeIQR0.0010.0000.001
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.5760.0070.585
subsetByComposition1.6790.0091.690
subsetBySupport0.0830.0150.099
swapRanges0.2160.0000.216
swapScores0.1230.0000.123
trackBalance000
trackCTSS4.0320.5474.588
trackClusters2.7120.1602.877
trackLinks1.1360.6311.441
trimToPeak0.9380.2041.145
trimToPercentiles2.6470.1682.820
tuneTagClustering000
utilsAggregateRows0.3650.0990.465
utilsDeStrand0.1680.0040.175
utilsScoreOverlaps0.0870.0080.095
utilsSimplifyTxDb000