Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:24 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 750/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.2.0  (landing page)
Kristyna Kupkova
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: RELEASE_3_14
git_last_commit: 2a030e7
git_last_commit_date: 2021-10-26 13:06:06 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicDistributions
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicDistributions_1.2.0.tar.gz
StartedAt: 2022-04-12 07:34:07 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:39:37 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 329.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GenomicDistributions_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GenomicDistributions.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicDistributions/DESCRIPTION’ ... OK
* this is package ‘GenomicDistributions’ 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 ‘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   14.887  1.251  47.675
getTssFromGTF           6.329  0.207   6.537
getChromSizesFromFasta  2.259  0.348 121.506
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GenomicDistributions.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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, 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 2652 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]
> 
> proc.time()
   user  system elapsed 
 30.832   0.776  31.216 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.0140.0000.014
binRegion0.0010.0000.001
calcChromBins2.4250.0402.400
calcChromBinsRef1.9380.0031.907
calcCumulativePartitions2.6830.1282.807
calcCumulativePartitionsRef1.8300.0441.875
calcDinuclFreq000
calcDinuclFreqRef000
calcExpectedPartitions1.8420.0561.898
calcExpectedPartitionsRef1.5890.0041.594
calcFeatureDist0.1120.0040.116
calcFeatureDistRefTSS0.2180.0000.164
calcGCContent000
calcGCContentRef000
calcNeighborDist0.0310.0000.032
calcOpenSignal0.0300.0040.024
calcPartitions1.9700.0522.016
calcPartitionsRef1.5350.0281.562
calcWidth0.4690.0160.437
dot-validateInputs000
dtToGr0.0180.0000.018
genomePartitionList1.4440.0081.452
getChromSizes0.0020.0000.002
getChromSizesFromFasta 2.259 0.348121.506
getGeneModels0.0890.0130.101
getGeneModelsFromGTF14.887 1.25147.675
getGenomeBins1.5900.1361.721
getTssFromGTF6.3290.2076.537
loadBSgenome000
loadEnsDb000
nlist000
plotChromBins0.0150.0030.018
plotCumulativePartitions2.6310.1522.774
plotDinuclFreq0.0110.0000.011
plotExpectedPartitions1.4410.0081.448
plotFeatureDist0.2190.0000.167
plotGCContent0.0210.0000.021
plotNeighborDist0.0070.0000.007
plotOpenSignal0.0800.0000.066
plotPartitions1.4770.0201.497
plotQTHist0.310.000.31
retrieveFile0.0000.0000.001