| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 343/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChIPpeakAnno 3.42.0 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the ChIPpeakAnno package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPpeakAnno.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. |
| Package: ChIPpeakAnno |
| Version: 3.42.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.42.0.tar.gz |
| StartedAt: 2025-10-14 07:25:26 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 08:05:26 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 2400.6 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: ChIPpeakAnno.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPpeakAnno.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPpeakAnno_3.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ChIPpeakAnno.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPpeakAnno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPpeakAnno’ version ‘3.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 ‘ChIPpeakAnno’ can be installed ... OK
* checking installed package size ... INFO
installed size is 21.1Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 12.6Mb
extdata 7.2Mb
* 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 ...
ChIPpeakAnno.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ChIPpeakAnno ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘ChIPpeakAnno’ ... ** this is package ‘ChIPpeakAnno’ version ‘3.42.0’ ** 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 (ChIPpeakAnno)
ChIPpeakAnno.Rcheck/ChIPpeakAnno-Ex.timings
| name | user | system | elapsed | |
| ChIPpeakAnno-package | 0 | 0 | 0 | |
| ExonPlusUtr.human.GRCh37 | 4.013 | 0.096 | 4.118 | |
| HOT.spots | 0.117 | 0.000 | 0.117 | |
| IDRfilter | 0 | 0 | 0 | |
| Peaks.Ste12.Replicate1 | 0.072 | 0.000 | 0.072 | |
| Peaks.Ste12.Replicate2 | 0.018 | 0.000 | 0.019 | |
| Peaks.Ste12.Replicate3 | 0.018 | 0.000 | 0.019 | |
| TSS.human.GRCh37 | 0.096 | 0.004 | 0.101 | |
| TSS.human.GRCh38 | 0.229 | 0.000 | 0.230 | |
| TSS.human.NCBI36 | 0.093 | 0.008 | 0.101 | |
| TSS.mouse.GRCm38 | 0.097 | 0.000 | 0.098 | |
| TSS.mouse.NCBIM37 | 0.087 | 0.000 | 0.088 | |
| TSS.rat.RGSC3.4 | 0.066 | 0.008 | 0.074 | |
| TSS.rat.Rnor_5.0 | 0.059 | 0.004 | 0.063 | |
| TSS.zebrafish.Zv8 | 0.063 | 0.004 | 0.067 | |
| TSS.zebrafish.Zv9 | 0.083 | 0.000 | 0.083 | |
| addAncestors | 1.215 | 0.032 | 1.255 | |
| addGeneIDs | 0.903 | 0.056 | 0.965 | |
| addMetadata | 1.789 | 0.044 | 1.838 | |
| annoGR | 0 | 0 | 0 | |
| annoPeaks | 3.485 | 0.339 | 10.307 | |
| annotatePeakInBatch | 17.280 | 1.220 | 18.554 | |
| annotatedPeak | 0.059 | 0.000 | 0.059 | |
| assignChromosomeRegion | 0.001 | 0.000 | 0.001 | |
| bdp | 0 | 0 | 0 | |
| binOverFeature | 1.029 | 0.016 | 1.048 | |
| binOverGene | 0.000 | 0.000 | 0.001 | |
| binOverRegions | 0.000 | 0.000 | 0.001 | |
| condenseMatrixByColnames | 0.014 | 0.000 | 0.014 | |
| convert2EntrezID | 0.451 | 0.004 | 0.456 | |
| countPatternInSeqs | 0.210 | 0.008 | 0.219 | |
| cumulativePercentage | 0 | 0 | 0 | |
| downstreams | 0.036 | 0.000 | 0.037 | |
| egOrgMap | 0.001 | 0.000 | 0.000 | |
| enrichedGO | 0.002 | 0.000 | 0.002 | |
| enrichmentPlot | 1.118 | 0.040 | 1.161 | |
| estFragmentLength | 0.001 | 0.000 | 0.000 | |
| estLibSize | 0.001 | 0.000 | 0.000 | |
| featureAlignedDistribution | 0.310 | 0.004 | 0.315 | |
| featureAlignedExtendSignal | 0.001 | 0.000 | 0.001 | |
| featureAlignedHeatmap | 0.455 | 0.012 | 0.468 | |
| featureAlignedSignal | 0.241 | 0.028 | 0.271 | |
| findEnhancers | 34.912 | 0.734 | 35.752 | |
| findMotifsInPromoterSeqs | 20.142 | 0.201 | 21.060 | |
| findOverlappingPeaks | 0.001 | 0.000 | 0.001 | |
| findOverlapsOfPeaks | 2.592 | 0.024 | 2.624 | |
| genomicElementDistribution | 0.001 | 0.000 | 0.000 | |
| genomicElementUpSetR | 0.000 | 0.000 | 0.001 | |
| getAllPeakSequence | 0.692 | 0.027 | 0.734 | |
| getAnnotation | 0.001 | 0.000 | 0.000 | |
| getEnrichedGO | 0.012 | 0.000 | 0.012 | |
| getEnrichedPATH | 0.001 | 0.000 | 0.001 | |
| getGO | 0.000 | 0.000 | 0.001 | |
| getGeneSeq | 0.000 | 0.001 | 0.001 | |
| getUniqueGOidCount | 0.000 | 0.000 | 0.001 | |
| getVennCounts | 0.001 | 0.000 | 0.001 | |
| hyperGtest | 0.001 | 0.000 | 0.001 | |
| makeVennDiagram | 0.003 | 0.000 | 0.002 | |
| mergePlusMinusPeaks | 0.001 | 0.000 | 0.000 | |
| metagenePlot | 3.343 | 0.056 | 3.413 | |
| myPeakList | 0.016 | 0.000 | 0.016 | |
| oligoFrequency | 0.129 | 0.000 | 0.128 | |
| oligoSummary | 0 | 0 | 0 | |
| peakPermTest | 0.001 | 0.000 | 0.001 | |
| peaks1 | 0.012 | 0.000 | 0.011 | |
| peaks2 | 0.012 | 0.000 | 0.012 | |
| peaks3 | 0.01 | 0.00 | 0.01 | |
| peaksNearBDP | 0.001 | 0.000 | 0.000 | |
| pie1 | 0.007 | 0.000 | 0.007 | |
| plotBinOverRegions | 0.001 | 0.000 | 0.001 | |
| preparePool | 0.001 | 0.000 | 0.001 | |
| reCenterPeaks | 0.036 | 0.000 | 0.036 | |
| summarizeOverlapsByBins | 6.843 | 0.526 | 7.022 | |
| summarizePatternInPeaks | 1.967 | 0.526 | 2.505 | |