Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-17 11:06:53 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 biscuiteer on riesling1


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 195/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biscuiteer 1.9.2  (landing page)
"Jacob Morrison"
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/biscuiteer
git_branch: master
git_last_commit: a17221f
git_last_commit_date: 2021-11-20 23:10:29 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'bsseq' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: biscuiteer
Version: 1.9.2
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biscuiteer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biscuiteer_1.9.2.tar.gz
StartedAt: 2022-01-16 18:27:12 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 18:34:57 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 465.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biscuiteer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biscuiteer.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biscuiteer_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biscuiteer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biscuiteer' version '1.9.2'
* 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 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 'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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      14.14   2.06   17.29
WGBSage        9.42   0.64   11.39
byExtremality  7.55   0.59    9.53
unionize       6.78   0.45    8.64
filterLoci     6.61   0.61    8.57
RRBSeq         5.67   0.47    6.14
WGBSeq         5.55   0.20    5.94
binCoverage    4.58   0.20    5.48
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/biscuiteer.Rcheck/00check.log'
for details.



Installation output

biscuiteer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL biscuiteer
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'biscuiteer'
    finding HTML links ... done
    CpGindex                                html  
    ENSR_subset.hg19                        html  
    ENSR_subset.hg38                        html  
    GRCh37.chromArm                         html  
    GRCh38.chromArm                         html  
    H9state23unmeth.hg19                    html  
    H9state23unmeth.hg38                    html  
    HMM_CpG_islands.hg19                    html  
    HMM_CpG_islands.hg38                    html  
    RRBSeq                                  html  
    WGBSage                                 html  
    WGBSeq                                  html  
    atRegions                               html  
    binCoverage                             html  
    biscuitMetadata                         html  
    biscuiteer-methods                      html  
    biscuiteer-package                      html  
    byChromArm                              html  
    byExtremality                           html  
    checkBiscuitBED                         html  
    clocks                                  html  
    condenseSampleNames                     html  
    extremality                             html  
    fexpit                                  html  
    filterLoci                              html  
    fixAge                                  html  
    fixNAs                                  html  
    flogit                                  html  
    getClock                                html  
    getLogitFracMeth                        html  
    grToSeg                                 html  
    hg19.chromArm                           html  
    hg38.chromArm                           html  
    makeBSseq                               html  
    readBiscuit                             html  
    segToGr                                 html  
    seqinfo.hg19                            html  
    seqinfo.hg38                            html  
    seqinfo.mm10                            html  
    simplifySampleNames                     html  
    summarizeBsSeqOver                      html  
    unionize                                html  
** building package indices
** installing vignettes
** 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)
Making 'packages.html' ... done

Tests output

biscuiteer.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 message:
replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer' 
> 
> test_check("biscuiteer")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  22.45    1.87   25.75 

Example timings

biscuiteer.Rcheck/biscuiteer-Ex.timings

nameusersystemelapsed
CpGindex14.14 2.0617.29
RRBSeq5.670.476.14
WGBSage 9.42 0.6411.39
WGBSeq5.550.205.94
atRegions2.830.223.72
binCoverage4.580.205.48
biscuitMetadata2.680.213.59
biscuiteer-package2.580.153.38
byChromArm3.170.244.08
byExtremality7.550.599.53
checkBiscuitBED0.220.020.23
condenseSampleNames0.080.010.10
extremality000
fexpit0.010.000.01
filterLoci6.610.618.57
fixAge0.060.000.06
fixNAs000
flogit000
getClock0.050.020.06
getLogitFracMeth4.020.184.88
grToSeg0.060.020.07
makeBSseq2.140.142.97
readBiscuit2.480.173.31
segToGr0.080.000.08
simplifySampleNames3.130.194.08
summarizeBsSeqOver2.200.173.03
unionize6.780.458.64