Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-11 11:42 -0500 (Wed, 11 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4752 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4464 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4414 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4369 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4277 |
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 581/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DMRcaller 1.39.0 (landing page) Nicolae Radu Zabet
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the DMRcaller package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/DMRcaller.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: DMRcaller |
Version: 1.39.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcaller.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DMRcaller_1.39.0.tar.gz |
StartedAt: 2024-12-11 00:50:34 -0500 (Wed, 11 Dec 2024) |
EndedAt: 2024-12-11 00:56:12 -0500 (Wed, 11 Dec 2024) |
EllapsedTime: 337.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DMRcaller.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcaller.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings DMRcaller_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/DMRcaller.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'DMRcaller/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DMRcaller' version '1.39.0' * 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 whether package 'DMRcaller' 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 ... NOTE extractGC: no visible global function definition for 'getSeq' extractGC: no visible global function definition for 'seqlevels' Undefined global functions or variables: getSeq seqlevels * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: DMRcaller.Rd: GRanges DMRsNoiseFilterCG.Rd: GRanges analyseReadsInsideRegionsForCondition.Rd: GRanges computeDMRs.Rd: GRanges computeDMRsReplicates.Rd: GRanges computeMethylationDataCoverage.Rd: GRanges computeMethylationDataSpatialCorrelation.Rd: GRanges computeMethylationProfile.Rd: GRanges computeOverlapProfile.Rd: GRanges extractGC.Rd: GRanges filterDMRs.Rd: GRanges getWholeChromosomes.Rd: GRanges joinReplicates.Rd: GRanges mergeDMRsIteratively.Rd: GRanges plotLocalMethylationProfile.Rd: GRanges, GRangesList plotMethylationDataCoverage.Rd: GRanges plotMethylationDataSpatialCorrelation.Rd: GRanges plotMethylationProfile.Rd: GRanges plotMethylationProfileFromData.Rd: GRanges plotOverlapProfile.Rd: GRanges poolMethylationDatasets.Rd: GRangesList, GRanges poolTwoMethylationDatasets.Rd: GRanges readBismark.Rd: GRanges readBismarkPool.Rd: GRanges saveBismark.Rd: GRanges syntheticDataReplicates.Rd: GRanges 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 readBismarkPool 11.43 0.30 11.72 mergeDMRsIteratively 11.26 0.14 11.41 computeDMRs 10.59 0.19 10.80 readBismark 5.61 0.14 6.02 saveBismark 5.07 0.14 5.22 * 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: 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/DMRcaller.Rcheck/00check.log' for details.
DMRcaller.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL DMRcaller ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'DMRcaller' ... ** 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 (DMRcaller)
DMRcaller.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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("DMRcaller") Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: 'IRanges' The following object is masked from 'package:grDevices': windows Parameters checking ... Extract methylation in the corresponding context Computing DMRs Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Calculating interpolations... Identifying DMRs... Analysed reads inside DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Selecting data... Identifying DMRs... Validating objects Finding overlaps Joining objects Parameters checking ... Extract methylation in the corresponding context Computing DMRs at Chr1:1..4976 Count inside each bin... Filter the bins... Identifying DMRs... Merge adjacent DMRs Merge DMRs iteratively Filter DMRs Parameters checking ... Merge DMRs iteratively ... RUNIT TEST PROTOCOL -- Wed Dec 11 00:56:00 2024 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : DMRcaller RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 Warning message: In fisher.test(matrix(unlist(x), nrow = 2, byrow = TRUE), alternative = alternative) : 'x' has been rounded to integer: Mean relative difference: 0.002857143 > > proc.time() user system elapsed 161.95 1.98 163.92
DMRcaller.Rcheck/DMRcaller-Ex.timings
name | user | system | elapsed | |
DMRcaller | 0.00 | 0.02 | 0.02 | |
analyseReadsInsideRegionsForCondition | 0.89 | 0.06 | 0.95 | |
computeDMRs | 10.59 | 0.19 | 10.80 | |
computeDMRsReplicates | 0 | 0 | 0 | |
computeMethylationDataCoverage | 0.89 | 0.03 | 0.92 | |
computeMethylationDataSpatialCorrelation | 0.58 | 0.01 | 0.60 | |
computeMethylationProfile | 1.33 | 0.04 | 1.36 | |
computeOverlapProfile | 1.41 | 0.01 | 1.42 | |
extractGC | 0 | 0 | 0 | |
filterDMRs | 1.92 | 0.07 | 2.00 | |
getWholeChromosomes | 0.16 | 0.04 | 0.19 | |
joinReplicates | 0 | 0 | 0 | |
mergeDMRsIteratively | 11.26 | 0.14 | 11.41 | |
plotLocalMethylationProfile | 1.34 | 0.07 | 1.42 | |
plotMethylationDataCoverage | 1.16 | 0.16 | 1.31 | |
plotMethylationDataSpatialCorrelation | 0 | 0 | 0 | |
plotMethylationProfile | 1.06 | 0.02 | 1.09 | |
plotMethylationProfileFromData | 2.66 | 0.11 | 2.77 | |
plotOverlapProfile | 2.22 | 0.04 | 2.28 | |
poolMethylationDatasets | 0.90 | 0.05 | 0.95 | |
poolTwoMethylationDatasets | 1.00 | 0.03 | 1.03 | |
readBismark | 5.61 | 0.14 | 6.02 | |
readBismarkPool | 11.43 | 0.30 | 11.72 | |
saveBismark | 5.07 | 0.14 | 5.22 | |