Back to Multiple platform build/check report for BioC 3.7
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GenomicInteractions on malbec2

This page was generated on 2018-10-17 08:26:42 -0400 (Wed, 17 Oct 2018).

Package 596/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.14.0
Liz Ing-Simmons
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GenomicInteractions
Branch: RELEASE_3_7
Last Commit: 9856ce2
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicInteractions
Version: 1.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicInteractions_1.14.0.tar.gz
StartedAt: 2018-10-16 00:45:12 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:49:27 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 254.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicInteractions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings GenomicInteractions_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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  9.3Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
* 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 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.



Installation output

GenomicInteractions.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL GenomicInteractions
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘GenomicInteractions’ ...
** 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
* DONE (GenomicInteractions)

Tests output

GenomicInteractions.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

> 
> test_check("GenomicInteractions")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 48 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.28    0.54   18.86 

Example timings

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings

nameusersystemelapsed
GInteractions-subsetByFeatures-methods0.3680.0000.371
GenomicInteractions-class0.0920.0000.092
GenomicInteractions-package0.0000.0000.001
GenomicInteractions0.0720.0000.072
InteractionHelpers0.0480.0000.045
InteractionTrack1.2640.0201.287
annotateInteractions0.1000.0000.098
annotateRegions0.040.000.04
asBED-GInteractions-method0.2440.0000.243
availableDisplayPars0.0160.0000.016
calculateDistances0.0440.0000.044
categoriseInteractions0.1400.0000.142
export.bed122.6360.0762.714
export.bedpe0.1200.0040.122
export.chiasig0.0880.0000.090
export.igraph0.0560.0000.057
getters0.0560.0040.058
makeGenomicInteractionsFromFile0.6200.0240.656
plotAvgViewpoint0.2040.0000.204
plotCisTrans0.4640.0000.464
plotCounts0.3000.0000.299
plotDists0.1800.0000.181
plotInteractionAnnotations0.2480.0000.250
plotSummaryStats0.6640.0000.666
plotViewpoint0.2840.0000.287
resetAnnotations0.0280.0000.027
setters0.0440.0000.044
summariseByFeaturePairs0.6480.0000.651
summariseByFeatures0.2600.0080.268
viewPoint0.1600.0000.158