Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 330/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPanalyser 1.27.0 (landing page) Patrick C.N. Martin
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | 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. |
Package: ChIPanalyser |
Version: 1.27.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPanalyser_1.27.0.tar.gz |
StartedAt: 2024-08-26 20:10:07 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:12:23 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 135.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPanalyser.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPanalyser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPanalyser_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPanalyser.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ChIPanalyser/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPanalyser’ version ‘1.27.0’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/ChIPanalyser.Rcheck/00check.log’ for details.
ChIPanalyser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPanalyser ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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-apple-darwin20 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, 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 -- Mon Aug 26 20:12:17 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 23.691 10.132 33.943
ChIPanalyser.Rcheck/ChIPanalyser-Ex.timings
name | user | system | elapsed | |
BPFrequency | 0.049 | 0.002 | 0.051 | |
BPFrequency_- | 0.001 | 0.001 | 0.002 | |
ChIPScore-class | 0.001 | 0.000 | 0.001 | |
ChIPanalyser-package | 0 | 0 | 0 | |
DNASequenceLength | 0.001 | 0.001 | 0.001 | |
GRList-class | 0 | 0 | 0 | |
PFMFormat | 0.050 | 0.006 | 0.056 | |
PFMFormat_ | 0.014 | 0.003 | 0.017 | |
PWMThreshold | 0.003 | 0.001 | 0.004 | |
PWMThreshold_- | 0.003 | 0.001 | 0.004 | |
PWMpseudocount | 0.003 | 0.001 | 0.004 | |
PWMpseudocount_- | 0.003 | 0.002 | 0.004 | |
PositionFrequencyMatrix | 0.015 | 0.003 | 0.017 | |
PositionFrequencyMatrix_- | 0.007 | 0.002 | 0.009 | |
PositionWeightMatrix | 0.014 | 0.003 | 0.018 | |
PositionWeightMatrix_- | 0.005 | 0.001 | 0.005 | |
averageExpPWMScore | 0.014 | 0.003 | 0.017 | |
backgroundSignal | 0.003 | 0.000 | 0.003 | |
backgroundSignal_- | 0.003 | 0.002 | 0.006 | |
boundMolecules | 0.002 | 0.001 | 0.003 | |
boundMolecules_- | 0.003 | 0.002 | 0.005 | |
chipMean | 0.003 | 0.000 | 0.003 | |
chipMean_- | 0.002 | 0.001 | 0.003 | |
chipSd | 0.002 | 0.000 | 0.003 | |
chipSd_- | 0.003 | 0.000 | 0.003 | |
chipSmooth | 0.002 | 0.000 | 0.003 | |
chipSmooth_- | 0.003 | 0.000 | 0.003 | |
computeChIPProfile | 0.001 | 0.001 | 0.002 | |
computeGenomeWideScores | 0 | 0 | 0 | |
computeOccupancy | 0.001 | 0.001 | 0.001 | |
computeOptimal | 0.000 | 0.001 | 0.001 | |
computePWMScore | 0.001 | 0.001 | 0.002 | |
data | 0.000 | 0.001 | 0.001 | |
drop | 0.019 | 0.002 | 0.021 | |
evolve | 0.001 | 0.001 | 0.001 | |
generateStartingPopulation | 0.007 | 0.000 | 0.008 | |
genomicProfiles-class | 0 | 0 | 0 | |
genomicProfiles | 0.017 | 0.002 | 0.019 | |
genomicProfilesInternal-class | 0.001 | 0.000 | 0.001 | |
getHighestFitnessSolutions | 0.000 | 0.001 | 0.001 | |
getTestingData | 1.639 | 0.041 | 1.679 | |
getTrainingData | 0.451 | 0.036 | 0.488 | |
lambdaPWM | 0.003 | 0.001 | 0.003 | |
lambdaPWM_ | 0.002 | 0.001 | 0.003 | |
loci-class | 0 | 0 | 0 | |
loci | 0.468 | 0.078 | 0.551 | |
lociWidth | 0.003 | 0.001 | 0.004 | |
lociWidth_ | 0.002 | 0.001 | 0.003 | |
maxPWMScore | 0.000 | 0.001 | 0.002 | |
maxSignal | 0.002 | 0.000 | 0.002 | |
maxSignal_- | 0.002 | 0.000 | 0.003 | |
minPWMScore | 0.000 | 0.001 | 0.001 | |
naturalLog | 0.002 | 0.001 | 0.004 | |
naturalLog_- | 0.002 | 0.001 | 0.003 | |
noOfSites | 0.002 | 0.001 | 0.003 | |
noOfSites_- | 0.003 | 0.001 | 0.003 | |
noiseFilter | 0.002 | 0.001 | 0.003 | |
noiseFilter_ | 0.003 | 0.001 | 0.003 | |
nos-class | 0.000 | 0.000 | 0.001 | |
parameterOptions-class | 0.000 | 0.001 | 0.000 | |
parameterOptions | 0.003 | 0.001 | 0.005 | |
ploidy | 0.002 | 0.000 | 0.002 | |
ploidy_- | 0.003 | 0.000 | 0.002 | |
plotOccupancyProfile | 0.000 | 0.001 | 0.001 | |
plotOptimalHeatMaps | 0.001 | 0.001 | 0.001 | |
processingChIP | 0.472 | 0.040 | 0.512 | |
profileAccuracyEstimate | 0.001 | 0.001 | 0.002 | |
removeBackground | 0.002 | 0.000 | 0.003 | |
removeBackground_- | 0.002 | 0.000 | 0.002 | |
scores | 0.463 | 0.047 | 0.510 | |
searchSites | 0.000 | 0.001 | 0.002 | |
setChromatinStates | 0.426 | 0.009 | 0.434 | |
singleRun | 0.000 | 0.001 | 0.001 | |
splitData | 0.479 | 0.054 | 0.533 | |
stepSize | 0.002 | 0.000 | 0.002 | |
stepSize_- | 0.003 | 0.000 | 0.003 | |
strandRule | 0.002 | 0.001 | 0.003 | |
strandRule_- | 0.003 | 0.001 | 0.003 | |
whichstrand | 0.003 | 0.001 | 0.003 | |
whichstrand_- | 0.003 | 0.001 | 0.004 | |