Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 333/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPanalyser 1.28.0 (landing page) Patrick C.N. Martin
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the ChIPanalyser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPanalyser.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: ChIPanalyser |
Version: 1.28.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPanalyser_1.28.0.tar.gz |
StartedAt: 2024-11-20 06:10:35 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 06:17:34 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 418.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPanalyser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ChIPanalyser_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPanalyser.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘ChIPanalyser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPanalyser’ version ‘1.28.0’ * 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 ‘ChIPanalyser’ 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 ... NOTE checkRd: (-1) data.Rd:24-25: Lost braces in \enumerate; meant \describe ? checkRd: (-1) data.Rd:26-27: Lost braces in \enumerate; meant \describe ? checkRd: (-1) data.Rd:28-31: Lost braces in \enumerate; meant \describe ? checkRd: (-1) data.Rd:32-33: Lost braces in \enumerate; meant \describe ? checkRd: (-1) data.Rd:34-35: Lost braces in \enumerate; meant \describe ? checkRd: (-1) evolve.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evolve.Rd:93-94: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evolve.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) generateStartingPopulation.Rd:31-39: Lost braces in \enumerate; meant \describe ? checkRd: (-1) generateStartingPopulation.Rd:40-44: Lost braces in \enumerate; meant \describe ? * 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 getTestingData 4.851 0.128 5.037 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ChIPanalyser.Rcheck/00check.log’ for details.
ChIPanalyser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ChIPanalyser ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘ChIPanalyser’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘drop’ in package ‘ChIPanalyser’ ** 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 (ChIPanalyser)
ChIPanalyser.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("ChIPanalyser") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat Attaching package: 'ChIPanalyser' The following object is masked from 'package:IRanges': drop The following object is masked from 'package:base': drop Loading required package: BSgenome.Dmelanogaster.UCSC.dm6 RUNIT TEST PROTOCOL -- Wed Nov 20 06:17:27 2024 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : ChIPanalyser RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 77.349 6.523 84.013
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
name | user | system | elapsed | |
BPFrequency | 0.206 | 0.004 | 0.211 | |
BPFrequency_- | 0.003 | 0.000 | 0.002 | |
ChIPScore-class | 0.001 | 0.000 | 0.001 | |
ChIPanalyser-package | 0 | 0 | 0 | |
DNASequenceLength | 0.003 | 0.000 | 0.002 | |
GRList-class | 0.001 | 0.000 | 0.000 | |
PFMFormat | 1.201 | 0.052 | 1.256 | |
PFMFormat_ | 0.063 | 0.000 | 0.063 | |
PWMThreshold | 0.012 | 0.000 | 0.012 | |
PWMThreshold_- | 0.013 | 0.000 | 0.013 | |
PWMpseudocount | 0.009 | 0.004 | 0.013 | |
PWMpseudocount_- | 0.013 | 0.000 | 0.012 | |
PositionFrequencyMatrix | 0.062 | 0.000 | 0.062 | |
PositionFrequencyMatrix_- | 0.032 | 0.000 | 0.033 | |
PositionWeightMatrix | 0.061 | 0.001 | 0.062 | |
PositionWeightMatrix_- | 0.012 | 0.006 | 0.018 | |
averageExpPWMScore | 0.055 | 0.012 | 0.066 | |
backgroundSignal | 0.008 | 0.004 | 0.012 | |
backgroundSignal_- | 0.016 | 0.000 | 0.015 | |
boundMolecules | 0.012 | 0.000 | 0.012 | |
boundMolecules_- | 0.015 | 0.000 | 0.015 | |
chipMean | 0.008 | 0.004 | 0.011 | |
chipMean_- | 0.008 | 0.004 | 0.012 | |
chipSd | 0.008 | 0.004 | 0.012 | |
chipSd_- | 0.011 | 0.000 | 0.012 | |
chipSmooth | 0.008 | 0.004 | 0.012 | |
chipSmooth_- | 0.004 | 0.008 | 0.012 | |
computeChIPProfile | 0.002 | 0.000 | 0.002 | |
computeGenomeWideScores | 0 | 0 | 0 | |
computeOccupancy | 0.002 | 0.000 | 0.002 | |
computeOptimal | 0.002 | 0.000 | 0.002 | |
computePWMScore | 0.002 | 0.000 | 0.002 | |
data | 0.001 | 0.000 | 0.001 | |
drop | 0.065 | 0.000 | 0.066 | |
evolve | 0.002 | 0.000 | 0.002 | |
generateStartingPopulation | 0.028 | 0.000 | 0.029 | |
genomicProfiles-class | 0.001 | 0.000 | 0.001 | |
genomicProfiles | 0.059 | 0.024 | 0.083 | |
genomicProfilesInternal-class | 0.001 | 0.000 | 0.000 | |
getHighestFitnessSolutions | 0.001 | 0.000 | 0.001 | |
getTestingData | 4.851 | 0.128 | 5.037 | |
getTrainingData | 1.636 | 0.028 | 1.667 | |
lambdaPWM | 0.012 | 0.000 | 0.012 | |
lambdaPWM_ | 0.013 | 0.000 | 0.013 | |
loci-class | 0.000 | 0.000 | 0.001 | |
loci | 1.622 | 0.075 | 1.703 | |
lociWidth | 0.013 | 0.000 | 0.012 | |
lociWidth_ | 0.012 | 0.000 | 0.012 | |
maxPWMScore | 0.002 | 0.000 | 0.002 | |
maxSignal | 0.011 | 0.000 | 0.011 | |
maxSignal_- | 0.011 | 0.000 | 0.011 | |
minPWMScore | 0.000 | 0.002 | 0.002 | |
naturalLog | 0.011 | 0.001 | 0.012 | |
naturalLog_- | 0.008 | 0.004 | 0.013 | |
noOfSites | 0.012 | 0.000 | 0.013 | |
noOfSites_- | 0.013 | 0.000 | 0.012 | |
noiseFilter | 0.013 | 0.000 | 0.012 | |
noiseFilter_ | 0.012 | 0.000 | 0.013 | |
nos-class | 0.001 | 0.000 | 0.000 | |
parameterOptions-class | 0.001 | 0.000 | 0.001 | |
parameterOptions | 0.014 | 0.000 | 0.014 | |
ploidy | 0.012 | 0.000 | 0.012 | |
ploidy_- | 0.011 | 0.000 | 0.012 | |
plotOccupancyProfile | 0.002 | 0.000 | 0.003 | |
plotOptimalHeatMaps | 0.002 | 0.000 | 0.002 | |
processingChIP | 1.625 | 0.044 | 1.672 | |
profileAccuracyEstimate | 0.002 | 0.000 | 0.002 | |
removeBackground | 0.011 | 0.000 | 0.012 | |
removeBackground_- | 0.009 | 0.003 | 0.012 | |
scores | 1.594 | 0.092 | 1.689 | |
searchSites | 0.002 | 0.000 | 0.002 | |
setChromatinStates | 2.292 | 0.040 | 2.338 | |
singleRun | 0.002 | 0.000 | 0.001 | |
splitData | 1.675 | 0.056 | 1.734 | |
stepSize | 0.012 | 0.000 | 0.012 | |
stepSize_- | 0.012 | 0.000 | 0.011 | |
strandRule | 0.013 | 0.000 | 0.013 | |
strandRule_- | 0.013 | 0.000 | 0.013 | |
whichstrand | 0.013 | 0.000 | 0.012 | |
whichstrand_- | 0.012 | 0.000 | 0.013 | |