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This page was generated on 2025-08-04 11:44 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 628/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DuplexDiscovereR 1.2.0  (landing page)
Egor Semenchenko
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/DuplexDiscovereR
git_branch: RELEASE_3_21
git_last_commit: e0f306d
git_last_commit_date: 2025-04-15 13:42:20 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DuplexDiscovereR on merida1

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.

raw results


Summary

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

Command output

##############################################################################
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###
### 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.


Installation output

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)

Tests output

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 

Example timings

DuplexDiscovereR.Rcheck/DuplexDiscovereR-Ex.timings

nameusersystemelapsed
DuplexDiscovererResults10.070 0.33610.613
DuplexTrack6.0750.0916.199
annotateGI0.5690.0160.584
availableDisplayPars0.5880.0050.595
calculateLigationPvalues1.2720.0141.308
classifyTwoArmChimeras1.0960.0201.121
clusterDuplexGroups3.6370.0443.705
collapseIdenticalReads0.2590.0040.264
collapse_duplex_groups3.6790.0323.724
compareMultipleInteractions8.8510.0279.009
computeGISelfOverlaps0.4840.0060.511
convert_gi_to_ranges0.1620.0070.169
dd_get_chimeric_reads8.6940.0348.759
dd_get_chimeric_reads_stats8.9030.0419.002
dd_get_duplex_groups8.7470.0398.820
dd_get_reads_classes8.8500.0418.976
dd_get_run_stats8.9190.0469.324
getChimericJunctionTypes0.7780.0130.798
getRNAHybrids0.1200.0020.123
getSpliceJunctionChimeras0.7080.0140.729
get_char_count_cigar0.0230.0020.024
makeDfFromGi0.2050.0040.210
makeGiFromDf0.2040.0050.209
runDuplexDiscoPreproc0.3900.0190.410
runDuplexDiscoverer12.883 0.07513.098
show-DuplexTrack-method0.6530.0080.662
writeGiToSAMfile1.0800.0141.097