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This page was generated on 2023-02-07 11:05:14 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

CHECK results for GenomicDistributions on nebbiolo1


To the developers/maintainers of the GenomicDistributions package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 773/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.7.0  (landing page)
Kristyna Kupkova
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: master
git_last_commit: 134b183
git_last_commit_date: 2022-11-01 11:23:45 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicDistributions
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicDistributions_1.7.0.tar.gz
StartedAt: 2023-02-06 20:53:58 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 20:57:33 -0500 (Mon, 06 Feb 2023)
EllapsedTime: 214.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenomicDistributions_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenomicDistributions.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK
* this is package ‘GenomicDistributions’ version ‘1.7.0’
* 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 R 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 ... 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 6.748   0.34   7.089
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘full-power.Rmd’ using ‘UTF-8’... OK
  ‘intro.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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 ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 23.241   0.705  23.659 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.0170.0000.017
binRegion0.0010.0000.001
calcChromBins1.8200.0241.807
calcChromBinsRef0.0290.0040.019
calcChromBinsRefSlow0.0250.0000.014
calcCumulativePartitions2.5610.0922.650
calcCumulativePartitionsRef1.590.041.63
calcDinuclFreq000
calcDinuclFreqRef0.0010.0000.000
calcExpectedPartitions1.8860.0481.935
calcExpectedPartitionsRef1.4410.0001.442
calcFeatureDist0.0990.0120.112
calcFeatureDistRefTSS0.2360.0200.206
calcGCContent0.0010.0000.000
calcGCContentRef0.0000.0000.001
calcNearestNeighbors0.0320.0000.032
calcNeighborDist0.030.000.03
calcPartitions1.3390.0201.359
calcPartitionsRef1.4070.0121.418
calcSummarySignal0.0430.0000.030
calcWidth0.0040.0000.001
dot-validateInputs0.0010.0000.001
dtToGr0.0110.0000.010
genomePartitionList1.6830.0601.743
getChromSizes0.0040.0000.004
getChromSizesFromFasta0.0240.0000.024
getGeneModels0.0830.0000.083
getGeneModelsFromGTF6.7480.3407.089
getGenomeBins1.1300.0521.177
getTssFromGTF0.1130.0000.114
loadBSgenome000
loadEnsDb0.0010.0000.001
nlist0.0010.0000.001
plotChromBins0.0380.0000.038
plotCumulativePartitions2.9450.1163.052
plotDinuclFreq0.0170.0000.016
plotExpectedPartitions2.4830.0402.523
plotFeatureDist0.2830.0080.237
plotGCContent0.0330.0000.033
plotNeighborDist0.0090.0000.010
plotPartitions1.3910.0081.400
plotQTHist0.0360.0000.035
plotSummarySignal0.0870.0000.074
retrieveFile0.0010.0000.001