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This page was generated on 2021-10-21 12:04:13 -0400 (Thu, 21 Oct 2021).

CHECK results for biscuiteer on nebbiolo2

To the developers/maintainers of the biscuiteer package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biscuiteer.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 196/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biscuiteer 1.7.2  (landing page)
"Jacob Morrison"
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/biscuiteer
git_branch: master
git_last_commit: 979bd5b
git_last_commit_date: 2021-06-30 15:03:49 -0400 (Wed, 30 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: biscuiteer
Version: 1.7.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biscuiteer.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biscuiteer_1.7.2.tar.gz
StartedAt: 2021-10-20 19:19:45 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 19:30:32 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 647.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biscuiteer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:biscuiteer.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings biscuiteer_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/biscuiteer.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.7.2’
* 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-3.14-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      17.730  2.664  20.691
WGBSage        8.615  0.312   8.851
RRBSeq         6.608  0.530   7.164
byExtremality  5.811  0.112   5.854
filterLoci     5.517  0.048   5.491
unionize       5.536  0.027   5.491
* 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-3.14-bioc/meat/biscuiteer.Rcheck/00check.log’
for details.



Installation output

biscuiteer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL biscuiteer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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’
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** 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’
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
Warning: replacing previous import ‘AnnotationHub::hubUrl’ by ‘rtracklayer::hubUrl’ when loading ‘annotatr’
** testing if installed package keeps a record of temporary installation path
* DONE (biscuiteer)

Tests output

biscuiteer.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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

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: 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 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

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

    cache

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

    cache




Warning messages:
1: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer' 
2: replacing previous import 'AnnotationHub::hubUrl' by 'rtracklayer::hubUrl' when loading 'annotatr' 
> 
> test_check("biscuiteer")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 30.503   1.534  32.732 

Example timings

biscuiteer.Rcheck/biscuiteer-Ex.timings

nameusersystemelapsed
CpGindex17.730 2.66420.691
RRBSeq6.6080.5307.164
WGBSage8.6150.3128.851
WGBSeq3.1510.2203.372
atRegions3.6560.1723.789
binCoverage4.1420.1244.228
biscuitMetadata2.1420.0242.126
biscuiteer-package1.9020.0081.872
byChromArm3.9580.1524.067
byExtremality5.8110.1125.854
checkBiscuitBED0.1530.0000.153
condenseSampleNames0.0640.0000.065
extremality0.0010.0000.001
fexpit0.0030.0000.003
filterLoci5.5170.0485.491
fixAge0.0610.0000.062
fixNAs0.0020.0000.002
flogit0.0010.0000.001
getClock0.0570.0000.057
getLogitFracMeth3.7610.1363.858
grToSeg0.070.000.07
makeBSseq2.5960.0162.578
readBiscuit2.2500.0202.237
segToGr0.0840.0000.084
simplifySampleNames3.4740.0453.480
summarizeBsSeqOver2.2850.0242.268
unionize5.5360.0275.491