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This page was generated on 2022-01-21 11:05:57 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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? 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 747/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDistributions 1.3.1  (landing page)
Kristyna Kupkova
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GenomicDistributions.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GenomicDistributions_1.3.1.tar.gz
StartedAt: 2022-01-20 19:17:43 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:24:38 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 414.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicDistributions.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GenomicDistributions.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.3.1’
* 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 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   15.088  1.121  64.675
getTssFromGTF           6.258  0.292   6.551
getChromSizesFromFasta  2.074  0.354 191.802
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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) (2022-01-05 r81451) -- "Unsuffered Consequences"
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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2652 ]
> 
> proc.time()
   user  system elapsed 
 28.114   0.963  28.751 

Example timings

GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings

nameusersystemelapsed
binBSGenome000
binChroms0.0050.0070.013
binRegion0.0010.0000.001
calcChromBins1.6820.0371.652
calcChromBinsRef1.3000.0351.307
calcCumulativePartitions2.2370.0812.312
calcCumulativePartitionsRef2.0210.0632.085
calcDinuclFreq000
calcDinuclFreqRef000
calcExpectedPartitions1.6880.0721.760
calcExpectedPartitionsRef2.1290.0792.209
calcFeatureDist0.0940.0090.102
calcFeatureDistRefTSS0.2080.0070.164
calcGCContent000
calcGCContentRef0.0010.0000.001
calcNeighborDist0.0310.0000.031
calcOpenSignal0.0410.0000.027
calcPartitions1.3340.0841.415
calcPartitionsRef1.2840.0281.312
calcWidth0.4610.0080.412
dot-validateInputs0.0010.0000.000
dtToGr0.0070.0040.010
genomePartitionList1.5610.0041.565
getChromSizes0.0000.0040.004
getChromSizesFromFasta 2.074 0.354191.802
getGeneModels0.0670.0000.068
getGeneModelsFromGTF15.088 1.12164.675
getGenomeBins0.9430.1201.053
getTssFromGTF6.2580.2926.551
loadBSgenome0.0000.0000.001
loadEnsDb000
nlist0.0000.0000.001
plotChromBins0.0160.0000.016
plotCumulativePartitions1.6490.0561.693
plotDinuclFreq0.0140.0000.014
plotExpectedPartitions1.2600.0241.283
plotFeatureDist0.2410.0000.190
plotGCContent0.0170.0040.020
plotNeighborDist0.0070.0000.007
plotOpenSignal0.0730.0000.059
plotPartitions1.2790.0121.290
plotQTHist0.3290.0000.328
retrieveFile0.0010.0000.001