Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:04 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 666/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epigenomix 1.49.0 (landing page) Hans-Ulrich Klein
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the epigenomix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epigenomix.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: epigenomix |
Version: 1.49.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epigenomix_1.49.0.tar.gz |
StartedAt: 2025-08-31 20:38:51 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 20:43:57 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 305.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: epigenomix.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epigenomix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epigenomix_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/epigenomix.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘epigenomix/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘epigenomix’ version ‘1.49.0’ * 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 ‘epigenomix’ 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) MixModel-class.Rd:77-81: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:85-86: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:87: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModel-class.Rd:88-89: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:55: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:56-58: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:59-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:65-66: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:67-68: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:69-70: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelBayes-class.Rd:71-72: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:51-53: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:58: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:59-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) MixModelML-class.Rd:61: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:50-55: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:56-60: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:61-63: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalize.Rd:64-72: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:35-38: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:39-46: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:47-51: Lost braces in \enumerate; meant \describe ? checkRd: (-1) normalizeChIP.Rd:52-53: Lost braces in \enumerate; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: ChIPseqSet-class.Rd: RangedSummarizedExperiment-class calculateCrossCorrelation.Rd: GRanges, GRanges-class eSet.Rd: ExpressionSet-class integrateData.Rd: ExpressionSet mappedReads.Rd: GRangesList-class, GRanges-class normalize.Rd: ExpressionSet-class summarizeReads.Rd: countOverlaps Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotChains 23.977 0.313 24.386 bayesMixModel 20.635 0.213 20.981 mlMixModel 9.317 0.194 9.603 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/epigenomix.Rcheck/00check.log’ for details.
epigenomix.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL epigenomix ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘epigenomix’ ... ** this is package ‘epigenomix’ version ‘1.49.0’ ** using staged installation ** R ** data ** 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 (epigenomix)
epigenomix.Rcheck/epigenomix-Ex.timings
name | user | system | elapsed | |
ChIPseqSet-class | 0.001 | 0.000 | 0.002 | |
MixModel-class | 0.001 | 0.000 | 0.001 | |
MixModelBayes-class | 0.000 | 0.001 | 0.001 | |
MixModelML-class | 0.001 | 0.001 | 0.002 | |
MixtureComponent-class | 0.000 | 0.001 | 0.000 | |
bayesMixModel | 20.635 | 0.213 | 20.981 | |
calculateCrossCorrelation | 0.785 | 0.011 | 0.800 | |
eSet | 0.013 | 0.003 | 0.017 | |
fpkm | 0.029 | 0.002 | 0.031 | |
getAlignmentQuality | 0 | 0 | 0 | |
integrateData | 0.196 | 0.005 | 0.202 | |
mappedReads | 0.030 | 0.002 | 0.033 | |
matchProbeToPromoter | 0.366 | 0.013 | 0.381 | |
mlMixModel | 9.317 | 0.194 | 9.603 | |
normalize | 0.167 | 0.002 | 0.170 | |
normalizeChIP | 0.109 | 0.001 | 0.111 | |
plotChains | 23.977 | 0.313 | 24.386 | |
plotClassification | 0.026 | 0.001 | 0.029 | |
plotComponents | 0.037 | 0.002 | 0.040 | |
summarizeReads | 0.332 | 0.003 | 0.335 | |
transToTSS | 0.004 | 0.003 | 0.006 | |