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CHECK report for biscuiteer on malbec1

This page was generated on 2020-08-06 11:46:40 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biscuiteer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 182/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biscuiteer 1.3.0
"Jacob Morrison"
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/biscuiteer
Branch: master
Last Commit: 35ac8d6
Last Changed Date: 2020-04-27 15:31:52 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biscuiteer
Version: 1.3.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biscuiteer.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biscuiteer_1.3.0.tar.gz
StartedAt: 2020-08-06 05:05:55 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 05:16:00 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 604.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: biscuiteer.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biscuiteer.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biscuiteer_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/biscuiteer.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biscuiteer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biscuiteer’ version ‘1.3.0’
* 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 ‘biscuiteer’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
See ‘/home/biocbuild/bbs-3.12-bioc/meat/biscuiteer.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.4Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’
  See the note in ?`:::` about the use of this operator.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
CpGindex      17.348  0.380  17.851
RRBSeq        10.468  0.884  11.576
WGBSage       11.260  0.036  10.909
filterLoci     9.880  0.052   9.575
byExtremality  8.336  0.032   8.008
unionize       7.348  0.040   6.997
WGBSeq         6.872  0.076   6.954
binCoverage    5.752  0.040   5.596
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/biscuiteer.Rcheck/00check.log’
for details.



Installation output

biscuiteer.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL biscuiteer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘biscuiteer’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘biscuiteer.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
** testing if installed package keeps a record of temporary installation path
* DONE (biscuiteer)

Tests output

biscuiteer.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(biscuiteer)
Loading required package: biscuiteerData
Loading required package: ExperimentHub
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, 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: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading biscuiteerData.
Loading required package: bsseq
Loading required package: GenomicRanges
Loading required package: stats4
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")'.


Attaching package: 'Biobase'

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

    cache

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

    cache

Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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, rowsum




Warning message:
replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer' 
> 
> test_check("biscuiteer")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.084   0.512  28.994 

Example timings

biscuiteer.Rcheck/biscuiteer-Ex.timings

nameusersystemelapsed
CpGindex17.348 0.38017.851
RRBSeq10.468 0.88411.576
WGBSage11.260 0.03610.909
WGBSeq6.8720.0766.954
atRegions2.9960.0562.844
binCoverage5.7520.0405.596
biscuitMetadata4.2400.0084.057
biscuiteer-package2.9040.0082.765
byChromArm3.8960.0283.711
byExtremality8.3360.0328.008
checkBiscuitBED0.2360.0000.236
condenseSampleNames0.0720.0000.072
extremality0.0000.0000.001
filterLoci9.8800.0529.575
fixAge0.0480.0000.049
fixNAs0.0000.0000.002
getClock0.0480.0000.046
getLogitFracMeth3.7520.0283.582
grToSeg0.0920.0000.095
makeBSseq3.7760.0163.595
readBiscuit3.6600.0123.485
segToGr0.1280.0000.131
simplifySampleNames3.9120.0123.715
summarizeBsSeqOver4.9880.0124.800
unionize7.3480.0406.997