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CHECK report for plyranges on malbec2

This page was generated on 2019-04-09 11:50:23 -0400 (Tue, 09 Apr 2019).

Package 1202/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyranges 1.3.4
Stuart Lee
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/plyranges
Branch: master
Last Commit: d88cca8
Last Changed Date: 2019-03-09 21:03:53 -0400 (Sat, 09 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: plyranges
Version: 1.3.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plyranges_1.3.4.tar.gz
StartedAt: 2019-04-09 02:45:27 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:49:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 253.3 seconds
RetCode: 0
Status:  OK 
CheckDir: plyranges.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings plyranges_1.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/plyranges.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyranges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plyranges’ version ‘1.3.4’
* 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 ‘plyranges’ 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 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: OK


Installation output

plyranges.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL plyranges
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘plyranges’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (plyranges)

Tests output

plyranges.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(plyranges)
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, 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: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'plyranges'

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

    filter

> 
> test_check("plyranges")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 313 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 40.389   0.651  41.093 

Example timings

plyranges.Rcheck/plyranges-Ex.timings

nameusersystemelapsed
as_ranges0.0930.0010.094
compute_coverage0.0260.0000.026
element-setops0.1650.0040.169
filter-ranges1.5570.0311.590
flank-ranges0.0920.0000.092
group_by-ranges0.5340.0550.595
io-bam-read0.7150.0320.746
io-bed-read3.2320.0753.333
io-bed-write000
io-bigwig-read0.1140.0000.120
io-bigwig-write000
io-gff-read0.3750.0050.379
io-gff-write000
io-wig-read0.3810.0040.393
mutate-ranges0.9770.0160.993
n0.490.000.49
n_distinct0.0430.0000.043
overlap-joins0.0820.0000.082
ranges-anchor0.1340.0040.138
ranges-arrange0.0760.0000.076
ranges-bind0.2520.0000.252
ranges-chop0.5760.0200.600
ranges-construct0.0370.0000.036
ranges-count-overlaps0.0970.0000.098
ranges-disjoin0.7470.0030.751
ranges-filter-overlaps0.0990.0010.099
ranges-follow0.1490.0000.150
ranges-info0.0430.0000.043
ranges-interweave0.2110.0030.215
ranges-nearest0.5050.0030.510
ranges-overlaps-self0.1310.0040.136
ranges-overlaps0.1600.0010.160
ranges-pairs0.2540.0000.255
ranges-precede0.0870.0000.088
ranges-reduce0.5150.0000.515
ranges-select0.0560.0000.056
ranges-setops0.7390.0000.740
ranges-summarise0.150.000.15
ranges-tile0.0790.0000.079
ranges-unnest0.2360.0000.236
shift-ranges0.1420.0000.142
stretch0.240.000.24