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This page was generated on 2025-07-25 12:05 -0400 (Fri, 25 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4793
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4531
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4574
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4515
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4512
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 827/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.17.1  (landing page)
Kristyna Kupkova
Snapshot Date: 2025-07-24 13:25 -0400 (Thu, 24 Jul 2025)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: devel
git_last_commit: 981f02c
git_last_commit_date: 2025-04-23 16:47:28 -0400 (Wed, 23 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GenomicDistributions on nebbiolo2

To the developers/maintainers of the GenomicDistributions package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.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: GenomicDistributions
Version: 1.17.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicDistributions_1.17.1.tar.gz
StartedAt: 2025-07-24 22:44:55 -0400 (Thu, 24 Jul 2025)
EndedAt: 2025-07-24 22:48:20 -0400 (Thu, 24 Jul 2025)
EllapsedTime: 205.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GenomicDistributions_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GenomicDistributions.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK
* this is package ‘GenomicDistributions’ version ‘1.17.1’
* 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 ‘GenomicDistributions’ 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 loading without being on the library search path ... 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 ... OK
* 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 LazyData ... 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
getGeneModelsFromGTF 7.243  0.261   7.505
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GenomicDistributions.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GenomicDistributions’ ...
** this is package ‘GenomicDistributions’ version ‘1.17.1’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (GenomicDistributions)

Tests output

GenomicDistributions.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-pc-linux-gnu

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.

> library(testthat)
> library("GenomicDistributions")
Loading required package: IRanges
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
Loading required package: stats4

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: GenomicRanges
Loading required package: Seqinfo
> 
> test_check("GenomicDistributions")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_all.R:139:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 23.651   0.724  24.063 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.0120.0000.012
binRegion0.0010.0000.001
calcChromBins1.8820.0011.832
calcChromBinsRef0.0330.0000.018
calcChromBinsRefSlow0.0310.0000.015
calcCumulativePartitions2.2000.0312.222
calcCumulativePartitionsRef1.6940.0251.719
calcDinuclFreq000
calcDinuclFreqRef0.0000.0000.001
calcExpectedPartitions1.8010.0071.808
calcExpectedPartitionsRef1.4210.0061.427
calcFeatureDist0.0920.0010.093
calcFeatureDistRefTSS0.4770.0010.428
calcGCContent000
calcGCContentRef000
calcNearestNeighbors0.0330.0000.034
calcNeighborDist0.0300.0000.032
calcPartitions1.3150.0261.341
calcPartitionsRef1.3220.0021.323
calcSummarySignal0.0370.0000.024
calcWidth0.0000.0000.001
dot-validateInputs000
dtToGr0.0100.0000.009
genomePartitionList1.1920.0051.197
getChromSizes0.0030.0000.002
getChromSizesFromFasta0.0170.0010.018
getGeneModels0.0650.0000.065
getGeneModelsFromGTF7.2430.2617.505
getGenomeBins1.1560.0031.152
getTssFromGTF0.1370.0010.136
loadBSgenome000
loadEnsDb000
nlist0.0010.0000.000
plotChromBins0.0480.0010.051
plotCumulativePartitions2.5990.0422.633
plotDinuclFreq0.0150.0000.015
plotExpectedPartitions1.3870.0021.390
plotFeatureDist0.2810.0010.232
plotGCContent0.0320.0000.033
plotNeighborDist0.0110.0000.011
plotPartitions2.0760.0152.092
plotQTHist0.0370.0000.037
plotSummarySignal0.1010.0010.088
retrieveFile0.0010.0000.001