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This page was generated on 2025-10-22 12:07 -0400 (Wed, 22 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4890
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4680
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4625
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 272/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.2  (landing page)
Charles Plessy
Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 Oct 2025)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: 679bef9
git_last_commit_date: 2025-10-14 05:35:27 -0400 (Tue, 14 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CAGEr on taishan

To the developers/maintainers of the CAGEr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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: CAGEr
Version: 2.15.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEr_2.15.2.tar.gz
StartedAt: 2025-10-21 06:10:21 -0000 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 06:24:26 -0000 (Tue, 21 Oct 2025)
EllapsedTime: 844.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEr_2.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.15.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘CAGEr’ 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 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
paraclu                    73.817  0.387  74.425
exportToTrack              61.027  0.291  61.508
aggregateTagClusters       34.120  0.626  34.853
scoreShift                 34.229  0.335  34.675
annotateCTSS               20.559  0.275  20.900
quantilePositions          20.132  0.060  20.256
distclu                    16.037  0.203  16.291
plotExpressionProfiles     12.464  0.071  12.572
getExpressionProfiles       8.201  0.028   8.258
CustomConsensusClusters     7.857  0.291   8.170
cumulativeCTSSdistribution  5.871  0.080   5.970
plotAnnot                   5.065  0.064   5.145
* 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

CAGEr.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘CAGEr’ ...
** this is package ‘CAGEr’ version ‘2.15.2’
** 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class3.7020.3154.057
CAGEr_Multicore3.2300.2073.446
CTSS-class0.3810.0040.386
CTSScoordinates0.1260.0000.125
CTSSnormalizedTpm1.1300.0471.181
CTSStagCount1.0640.1521.219
CTSStoGenes0.5660.0760.643
CustomConsensusClusters7.8570.2918.170
GeneExpDESeq20.7520.0200.774
GeneExpSE0.0060.0000.007
QuantileWidthFunctions0.2030.0040.207
TSSlogo4.4240.1164.572
aggregateTagClusters34.120 0.62634.853
annotateCTSS20.559 0.27520.900
byCtss0.0440.0000.044
consensusClusters0.2360.0000.237
consensusClustersDESeq23.4700.0043.486
consensusClustersTpm0.0080.0000.009
cumulativeCTSSdistribution5.8710.0805.970
distclu16.037 0.20316.291
dot-ctss_summary_for_clusters1.4350.0081.447
exampleCAGEexp000
exportToTrack61.027 0.29161.508
expressionClasses3.2110.0003.221
filteredCTSSidx0.0160.0000.015
flagLowExpCTSS0.0550.0000.056
genomeName0.0000.0000.001
getCTSS1.4430.0041.452
getExpressionProfiles8.2010.0288.258
getShiftingPromoters3.1780.0283.217
hanabi0.3460.0040.351
hanabiPlot0.4050.0240.430
import.CAGEscanMolecule000
import.CTSS0.1190.0000.119
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
import.bigwig0.4850.0000.489
importPublicData0.0000.0000.001
inputFiles0.0020.0000.002
inputFilesType0.0010.0000.002
librarySizes0.0010.0000.001
mapStats0.0710.0000.071
mergeCAGEsets3.0930.0163.118
mergeSamples0.6820.0320.717
moleculesGR2CTSS0.1960.0000.197
normalizeTagCount0.7810.0120.792
paraclu73.817 0.38774.425
parseCAGEscanBlocksToGrangeTSS0.0310.0000.032
plotAnnot5.0650.0645.145
plotCorrelation0.4060.0040.411
plotExpressionProfiles12.464 0.07112.572
plotInterquantileWidth3.4350.0203.463
plotReverseCumulatives4.1180.0084.127
quantilePositions20.132 0.06020.256
quickEnhancers000
ranges2annot0.5050.0000.506
ranges2genes0.0850.0000.085
ranges2names0.0840.0000.085
resetCAGEexp0.5110.0000.513
rowSums.RleDataFrame0.0320.0000.032
rowsum.RleDataFrame0.0350.0000.036
sampleLabels0.0060.0000.006
scoreShift34.229 0.33534.675
seqNameTotalsSE0.0050.0000.005
setColors0.4310.0000.432
strandInvaders0.8440.0400.883
summariseChrExpr0.5690.0000.570
tagClusters0.5690.0040.575