Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 628/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DuplexDiscovereR 1.2.0 (landing page) Egor Semenchenko
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DuplexDiscovereR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DuplexDiscovereR.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: DuplexDiscovereR |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DuplexDiscovereR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DuplexDiscovereR_1.2.0.tar.gz |
StartedAt: 2025-08-01 02:57:59 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 03:12:32 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 873.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DuplexDiscovereR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DuplexDiscovereR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DuplexDiscovereR_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DuplexDiscovereR.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘DuplexDiscovereR/DESCRIPTION’ ... OK * this is package ‘DuplexDiscovereR’ version ‘1.2.0’ * 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 ‘DuplexDiscovereR’ 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'computeGISelfOverlaps.Rd': ‘[InteractionSet:overlaps]{InteractionSet::findOverlaps()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runDuplexDiscoverer 12.883 0.075 13.098 DuplexDiscovererResults 10.070 0.336 10.613 dd_get_run_stats 8.919 0.046 9.324 dd_get_chimeric_reads_stats 8.903 0.041 9.002 dd_get_reads_classes 8.850 0.041 8.976 compareMultipleInteractions 8.851 0.027 9.009 dd_get_duplex_groups 8.747 0.039 8.820 dd_get_chimeric_reads 8.694 0.034 8.759 DuplexTrack 6.075 0.091 6.199 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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-3.21-bioc/meat/DuplexDiscovereR.Rcheck/00check.log’ for details.
DuplexDiscovereR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DuplexDiscovereR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘DuplexDiscovereR’ ... ** this is package ‘DuplexDiscovereR’ version ‘1.2.0’ ** 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 (DuplexDiscovereR)
DuplexDiscovereR.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(DuplexDiscovereR) Loading required package: InteractionSet Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics 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 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("DuplexDiscovereR") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 24 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 72.382 2.520 75.955
DuplexDiscovereR.Rcheck/DuplexDiscovereR-Ex.timings
name | user | system | elapsed | |
DuplexDiscovererResults | 10.070 | 0.336 | 10.613 | |
DuplexTrack | 6.075 | 0.091 | 6.199 | |
annotateGI | 0.569 | 0.016 | 0.584 | |
availableDisplayPars | 0.588 | 0.005 | 0.595 | |
calculateLigationPvalues | 1.272 | 0.014 | 1.308 | |
classifyTwoArmChimeras | 1.096 | 0.020 | 1.121 | |
clusterDuplexGroups | 3.637 | 0.044 | 3.705 | |
collapseIdenticalReads | 0.259 | 0.004 | 0.264 | |
collapse_duplex_groups | 3.679 | 0.032 | 3.724 | |
compareMultipleInteractions | 8.851 | 0.027 | 9.009 | |
computeGISelfOverlaps | 0.484 | 0.006 | 0.511 | |
convert_gi_to_ranges | 0.162 | 0.007 | 0.169 | |
dd_get_chimeric_reads | 8.694 | 0.034 | 8.759 | |
dd_get_chimeric_reads_stats | 8.903 | 0.041 | 9.002 | |
dd_get_duplex_groups | 8.747 | 0.039 | 8.820 | |
dd_get_reads_classes | 8.850 | 0.041 | 8.976 | |
dd_get_run_stats | 8.919 | 0.046 | 9.324 | |
getChimericJunctionTypes | 0.778 | 0.013 | 0.798 | |
getRNAHybrids | 0.120 | 0.002 | 0.123 | |
getSpliceJunctionChimeras | 0.708 | 0.014 | 0.729 | |
get_char_count_cigar | 0.023 | 0.002 | 0.024 | |
makeDfFromGi | 0.205 | 0.004 | 0.210 | |
makeGiFromDf | 0.204 | 0.005 | 0.209 | |
runDuplexDiscoPreproc | 0.390 | 0.019 | 0.410 | |
runDuplexDiscoverer | 12.883 | 0.075 | 13.098 | |
show-DuplexTrack-method | 0.653 | 0.008 | 0.662 | |
writeGiToSAMfile | 1.080 | 0.014 | 1.097 | |