Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 622/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DuplexDiscovereR 1.3.1 (landing page) Egor Semenchenko
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.3.1 |
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_1.3.1.tar.gz |
StartedAt: 2025-08-08 20:45:07 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 20:53:44 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 516.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DuplexDiscovereR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DuplexDiscovereR.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 ‘DuplexDiscovereR/DESCRIPTION’ ... OK * this is package ‘DuplexDiscovereR’ version ‘1.3.1’ * 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 ... NOTE .filterAlignmentLength: no visible binding for global variable 'aln_lenA' .filterAlignmentLength: no visible binding for global variable 'aln_lenB' .filterAlignmentLength: no visible binding for global variable 'len_not_ok' collapseSimilarChimeras: no visible binding for global variable 'n_seqnames' preproc_chim_junction_out_pe: no visible binding for global variable 'lA' preproc_chim_junction_out_pe: no visible binding for global variable 'lB' runDuplexDiscoPreproc: no visible binding for global variable 'aln_lenA' runDuplexDiscoPreproc: no visible binding for global variable 'aln_lenB' runDuplexDiscoverer: no visible binding for global variable 'n_seqnames' trimAroundJunction: no visible binding for global variable 'jA' trimAroundJunction: no visible binding for global variable 'jB' trimAroundJunction: no visible binding for global variable 't1' trimAroundJunction: no visible binding for global variable 't2' trimAroundJunction: no visible binding for global variable 't3' trimAroundJunction: no visible binding for global variable 't4' trimAroundJunction: no visible binding for global variable 'value' trimAroundJunction: no visible binding for global variable 'aln_lenA' trimAroundJunction: no visible binding for global variable 'aln_lenB' Undefined global functions or variables: aln_lenA aln_lenB jA jB lA lB len_not_ok n_seqnames t1 t2 t3 t4 value * 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 ... WARNING Undocumented arguments in Rd file 'collapseSimilarChimeras.Rd' ‘min_nodes’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'trimAroundJunction.Rd': ‘extract_len’ * 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 9.156 0.057 9.251 DuplexDiscovererResults 7.389 0.176 7.612 dd_get_duplex_groups 6.729 0.030 6.781 dd_get_reads_classes 6.665 0.030 6.718 dd_get_run_stats 6.637 0.031 6.694 dd_get_chimeric_reads 6.633 0.034 6.697 dd_get_chimeric_reads_stats 6.530 0.030 6.586 compareMultipleInteractions 6.353 0.028 6.408 * 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 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-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 ‘1.3.1’ ** 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 (2025-06-13) -- "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: Seqinfo 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 47.004 1.570 48.819
DuplexDiscovereR.Rcheck/DuplexDiscovereR-Ex.timings
name | user | system | elapsed | |
DuplexDiscovererResults | 7.389 | 0.176 | 7.612 | |
DuplexTrack | 3.154 | 0.050 | 3.223 | |
annotateGI | 0.307 | 0.007 | 0.314 | |
availableDisplayPars | 0.305 | 0.004 | 0.312 | |
calculateLigationPvalues | 0.638 | 0.008 | 0.649 | |
classifyTwoArmChimeras | 0.571 | 0.010 | 0.585 | |
clusterDuplexGroups | 2.398 | 0.030 | 2.435 | |
collapseIdenticalReads | 0.121 | 0.002 | 0.123 | |
collapse_duplex_groups | 2.385 | 0.021 | 2.415 | |
compareMultipleInteractions | 6.353 | 0.028 | 6.408 | |
computeGISelfOverlaps | 0.257 | 0.003 | 0.262 | |
convert_gi_to_ranges | 0.096 | 0.003 | 0.099 | |
dd_get_chimeric_reads | 6.633 | 0.034 | 6.697 | |
dd_get_chimeric_reads_stats | 6.530 | 0.030 | 6.586 | |
dd_get_duplex_groups | 6.729 | 0.030 | 6.781 | |
dd_get_reads_classes | 6.665 | 0.030 | 6.718 | |
dd_get_run_stats | 6.637 | 0.031 | 6.694 | |
getChimericJunctionTypes | 0.370 | 0.005 | 0.376 | |
getRNAHybrids | 0.061 | 0.001 | 0.063 | |
getSpliceJunctionChimeras | 0.367 | 0.005 | 0.374 | |
get_char_count_cigar | 0.016 | 0.002 | 0.018 | |
makeDfFromGi | 0.103 | 0.003 | 0.106 | |
makeGiFromDf | 0.104 | 0.002 | 0.107 | |
runDuplexDiscoPreproc | 0.213 | 0.005 | 0.219 | |
runDuplexDiscoverer | 9.156 | 0.057 | 9.251 | |
show-DuplexTrack-method | 0.322 | 0.006 | 0.329 | |
trimAroundJunction | 0.233 | 0.005 | 0.239 | |
writeGiToSAMfile | 0.552 | 0.009 | 0.562 | |