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This page was generated on 2022-08-12 13:20:17 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 GenomicInteractions on nebbiolo1


To the developers/maintainers of the GenomicInteractions package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicInteractions.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 776/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.30.0  (landing page)
Liz Ing-Simmons
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/GenomicInteractions
git_branch: RELEASE_3_15
git_last_commit: cc79eb1
git_last_commit_date: 2022-04-26 11:21:41 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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: GenomicInteractions
Version: 1.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GenomicInteractions_1.30.0.tar.gz
StartedAt: 2022-08-11 20:15:44 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 20:21:27 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 343.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomicInteractions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GenomicInteractions_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/GenomicInteractions.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.30.0’
* 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 ‘GenomicInteractions’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
* 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 ... NOTE
plotCisTrans: no visible global function definition for 'head'
plotInteractionAnnotations: no visible global function definition for
  'head'
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.



Installation output

GenomicInteractions.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GenomicInteractions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GenomicInteractions’ ...
** using staged installation
** R
** data
** 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 (GenomicInteractions)

Tests output

GenomicInteractions.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(GenomicInteractions)
Loading required package: InteractionSet
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("GenomicInteractions")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 57 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 57 ]
> 
> proc.time()
   user  system elapsed 
 23.197   1.126  24.310 

Example timings

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings

nameusersystemelapsed
GInteractions-subsetByFeatures-methods0.1330.0080.140
GenomicInteractions-class0.1160.0000.116
GenomicInteractions0.0680.0000.068
InteractionHelpers0.0410.0000.040
InteractionTrack0.5780.0800.657
annotateInteractions0.3930.0000.392
annotateRegions0.0530.0040.058
asBED-GInteractions-method0.2620.0120.273
availableDisplayPars0.0140.0040.019
calculateDistances0.0530.0000.053
categoriseInteractions1.3970.0001.397
export.bed120.3870.0000.387
export.bedpe0.0990.0000.100
export.chiasig0.0690.0000.069
export.igraph0.0970.0000.097
getters0.0570.0000.058
makeGenomicInteractionsFromFile0.6420.0400.683
plotAvgViewpoint0.2480.0000.248
plotCisTrans0.1980.0040.201
plotCounts0.2270.0000.228
plotDists0.130.000.13
plotInteractionAnnotations0.2460.0040.250
plotSummaryStats0.5030.0200.523
plotViewpoint0.3260.0040.331
resetAnnotations0.0340.0000.033
setters0.0890.0000.089
summariseByFeaturePairs0.7490.0840.832
summariseByFeatures0.3470.0080.354
viewPoint0.1710.0000.171