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This page was generated on 2022-01-20 11:07:22 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 riesling1


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? here 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 747/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.3.1  (landing page)
Kristyna Kupkova
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicDistributions
git_branch: master
git_last_commit: bebda48
git_last_commit_date: 2021-11-20 04:03:57 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'IRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicDistributions
Version: 1.3.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicDistributions_1.3.1.tar.gz
StartedAt: 2022-01-19 18:58:46 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 19:02:21 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 215.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicDistributions_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicDistributions.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicDistributions/DESCRIPTION' ... OK
* this is package 'GenomicDistributions' version '1.3.1'
* 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 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   17.98   1.05   27.28
getTssFromGTF           9.32   0.36    9.69
getChromSizesFromFasta  1.95   0.16   26.57
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'GenomicDistributions'
    finding HTML links ... done
    BSdtToGRanges                           html  
    GenomicDistributions                    html  
    TSS_hg19                                html  
    binBSGenome                             html  
    binChroms                               html  
    binRegion                               html  
    calcChromBins                           html  
    calcChromBinsRef                        html  
    calcCumulativePartitions                html  
    calcCumulativePartitionsRef             html  
    calcDinuclFreq                          html  
    calcDinuclFreqRef                       html  
    calcExpectedPartitions                  html  
    calcExpectedPartitionsRef               html  
    calcFeatureDist                         html  
    calcFeatureDistRefTSS                   html  
    calcGCContent                           html  
    calcGCContentRef                        html  
    calcNeighborDist                        html  
    calcOpenSignal                          html  
    calcPartitions                          html  
    calcPartitionsRef                       html  
    calcWidth                               html  
    cellTypeMetadata                        html  
    chromSizes_hg19                         html  
    dot-requireAndReturn                    html  
    dot-validateInputs                      html  
    dtToGr                                  html  
    dtToGrInternal                          html  
    exampleOpenSignalMatrix_hg19            html  
    geneModels_hg19                         html  
    genomePartitionList                     html  
    getChromSizes                           html  
    getChromSizesFromFasta                  html  
    getGeneModels                           html  
    getGeneModelsFromGTF                    html  
    getGenomeBins                           html  
    getReferenceData                        html  
    getTssFromGTF                           html  
    grToDt                                  html  
    labelCuts                               html  
    loadBSgenome                            html  
    loadEnsDb                               html  
    neighbordt                              html  
    nlist                                   html  
    plotChromBins                           html  
    plotCumulativePartitions                html  
    plotDinuclFreq                          html  
    plotExpectedPartitions                  html  
    plotFeatureDist                         html  
    plotGCContent                           html  
    plotNeighborDist                        html  
    plotOpenSignal                          html  
    plotPartitions                          html  
    plotQTHist                              html  
    retrieveFile                            html  
    setB_100                                html  
    splitDataTable                          html  
    theme_blank_facet_label                 html  
    vistaEnhancers                          html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ggmanh' is missing or broken
 done

Tests output

GenomicDistributions.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> 
> test_check("GenomicDistributions")
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]
> 
> proc.time()
   user  system elapsed 
  23.25    1.87   25.11 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.000.010.02
binRegion000
calcChromBins2.020.022.39
calcChromBinsRef1.420.001.45
calcCumulativePartitions2.050.142.25
calcCumulativePartitionsRef2.110.142.26
calcDinuclFreq000
calcDinuclFreqRef000
calcExpectedPartitions1.000.171.18
calcExpectedPartitionsRef1.390.251.64
calcFeatureDist0.080.000.08
calcFeatureDistRefTSS0.150.000.14
calcGCContent000
calcGCContentRef000
calcNeighborDist0.030.000.03
calcOpenSignal0.020.000.01
calcPartitions0.980.161.14
calcPartitionsRef0.970.151.13
calcWidth0.310.000.31
dot-validateInputs000
dtToGr0.020.000.02
genomePartitionList1.270.241.50
getChromSizes000
getChromSizesFromFasta 1.95 0.1626.57
getGeneModels0.080.000.08
getGeneModelsFromGTF17.98 1.0527.28
getGenomeBins0.880.080.95
getTssFromGTF9.320.369.69
loadBSgenome0.020.000.02
loadEnsDb000
nlist000
plotChromBins0.020.000.01
plotCumulativePartitions2.010.262.28
plotDinuclFreq0.020.000.02
plotExpectedPartitions1.070.251.33
plotFeatureDist0.160.000.16
plotGCContent0.030.000.03
plotNeighborDist0.010.000.02
plotOpenSignal0.080.000.07
plotPartitions1.200.151.36
plotQTHist0.290.000.28
retrieveFile000