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This page was generated on 2024-05-04 11:36:36 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 831/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.12.0  (landing page)
Kristyna Kupkova
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: RELEASE_3_19
git_last_commit: 05ffed2
git_last_commit_date: 2024-04-30 11:30:16 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for GenomicDistributions on nebbiolo1


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: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicDistributions_1.12.0.tar.gz
StartedAt: 2024-05-03 23:34:05 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:37:41 -0400 (Fri, 03 May 2024)
EllapsedTime: 215.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicDistributions_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomicDistributions.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK
* this is package ‘GenomicDistributions’ version ‘1.12.0’
* 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 ‘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 7.511  0.352   7.865
* 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-3.19-bioc/R/bin/R CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘GenomicDistributions’ ...
** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: GenomeInfoDb
> 
> 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 
 24.395   0.884  25.007 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.0110.0040.015
binRegion0.0010.0000.001
calcChromBins1.8480.0431.858
calcChromBinsRef0.0320.0000.017
calcChromBinsRefSlow0.0290.0000.016
calcCumulativePartitions2.5020.0962.593
calcCumulativePartitionsRef1.8990.0481.947
calcDinuclFreq000
calcDinuclFreqRef0.0010.0000.001
calcExpectedPartitions1.3920.0321.424
calcExpectedPartitionsRef1.380.041.42
calcFeatureDist0.0900.0040.094
calcFeatureDistRefTSS0.2010.0160.164
calcGCContent000
calcGCContentRef0.0000.0000.001
calcNearestNeighbors0.0260.0040.030
calcNeighborDist0.0270.0000.027
calcPartitions1.6570.0361.693
calcPartitionsRef1.3190.0201.339
calcSummarySignal0.0460.0000.030
calcWidth0.0010.0000.001
dot-validateInputs0.0000.0000.001
dtToGr0.010.000.01
genomePartitionList1.2020.0201.221
getChromSizes0.0040.0000.005
getChromSizesFromFasta0.0250.0000.025
getGeneModels0.0700.0000.071
getGeneModelsFromGTF7.5110.3527.865
getGenomeBins0.9960.0241.015
getTssFromGTF0.1180.0030.121
loadBSgenome000
loadEnsDb0.0010.0000.000
nlist0.0010.0000.001
plotChromBins0.0510.0030.055
plotCumulativePartitions2.6140.0922.696
plotDinuclFreq0.0170.0000.017
plotExpectedPartitions1.4580.0361.494
plotFeatureDist0.2910.0000.239
plotGCContent0.0310.0000.031
plotNeighborDist0.0110.0000.011
plotPartitions2.1590.0762.235
plotQTHist0.0340.0000.035
plotSummarySignal0.1010.0000.085
retrieveFile0.0020.0000.001