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CHECK report for biscuiteer on tokay2

This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 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 189/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biscuiteer 1.2.0
"Jacob Morrison"
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/biscuiteer
Branch: RELEASE_3_11
Last Commit: 00c2aca
Last Changed Date: 2020-04-27 15:31:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biscuiteer
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biscuiteer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biscuiteer_1.2.0.tar.gz
StartedAt: 2020-10-17 02:04:37 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:24:01 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 1164.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biscuiteer.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biscuiteer.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings biscuiteer_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/biscuiteer.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.0'
* 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 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 'C:/Users/biocbuild/bbs-3.11-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
CpGindex           16.37   2.81   45.92
WGBSage             9.82   0.47   13.08
unionize            9.14   0.36   11.25
byExtremality       9.14   0.33   16.67
RRBSeq              8.66   0.17   21.17
filterLoci          8.33   0.39   21.76
binCoverage         4.46   0.14    5.54
getLogitFracMeth    4.25   0.14    5.57
readBiscuit         4.25   0.09    5.20
atRegions           4.22   0.07    5.22
byChromArm          3.66   0.15   13.07
summarizeBsSeqOver  3.31   0.07   45.90
makeBSseq           3.13   0.03    5.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CpGindex      20.07   1.55   26.23
WGBSage        9.44   0.22   18.00
unionize       8.65   0.14   10.24
byExtremality  8.33   0.13   26.31
RRBSeq         7.98   0.40   10.00
filterLoci     7.13   0.09   10.05
WGBSeq         5.43   0.13    5.57
binCoverage    4.47   0.23    6.79
atRegions      2.91   0.17    6.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/biscuiteer.Rcheck/00check.log'
for details.



Installation output

biscuiteer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/biscuiteer_1.2.0.tar.gz && rm -rf biscuiteer.buildbin-libdir && mkdir biscuiteer.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biscuiteer.buildbin-libdir biscuiteer_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL biscuiteer_1.2.0.zip && rm biscuiteer_1.2.0.tar.gz biscuiteer_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4608k  100 4608k    0     0  39.7M      0 --:--:-- --:--:-- --:--:-- 42.0M

install for i386

* 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
   '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

install for x64

* installing *source* package 'biscuiteer' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocParallel::bpstart' by 'QDNAseq::bpstart' when loading 'biscuiteer'
* MD5 sums
packaged installation of 'biscuiteer' as biscuiteer_1.2.0.zip
* DONE (biscuiteer)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'biscuiteer' successfully unpacked and MD5 sums checked

Tests output

biscuiteer.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

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: 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 
  27.40    2.56   34.42 

biscuiteer.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
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, 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

Attaching package: 'IRanges'

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

    windows

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: 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 
  32.35    1.26   39.70 

Example timings

biscuiteer.Rcheck/examples_i386/biscuiteer-Ex.timings

nameusersystemelapsed
CpGindex16.37 2.8145.92
RRBSeq 8.66 0.1721.17
WGBSage 9.82 0.4713.08
WGBSeq3.930.204.14
atRegions4.220.075.22
binCoverage4.460.145.54
biscuitMetadata3.030.073.71
biscuiteer-package2.420.153.60
byChromArm 3.66 0.1513.07
byExtremality 9.14 0.3316.67
checkBiscuitBED0.170.000.17
condenseSampleNames0.050.020.06
extremality000
filterLoci 8.33 0.3921.76
fixAge0.060.010.08
fixNAs000
getClock0.10.00.1
getLogitFracMeth4.250.145.57
grToSeg0.040.020.07
makeBSseq3.130.035.59
readBiscuit4.250.095.20
segToGr0.100.021.56
simplifySampleNames2.970.054.06
summarizeBsSeqOver 3.31 0.0745.90
unionize 9.14 0.3611.25

biscuiteer.Rcheck/examples_x64/biscuiteer-Ex.timings

nameusersystemelapsed
CpGindex20.07 1.5526.23
RRBSeq 7.98 0.4010.00
WGBSage 9.44 0.2218.00
WGBSeq5.430.135.57
atRegions2.910.176.21
binCoverage4.470.236.79
biscuitMetadata2.760.073.56
biscuiteer-package2.740.044.83
byChromArm3.140.064.45
byExtremality 8.33 0.1326.31
checkBiscuitBED0.170.000.17
condenseSampleNames0.040.020.06
extremality000
filterLoci 7.13 0.0910.05
fixAge0.060.000.06
fixNAs000
getClock0.060.000.06
getLogitFracMeth2.920.003.82
grToSeg0.070.000.06
makeBSseq3.540.034.36
readBiscuit3.050.063.70
segToGr0.060.020.08
simplifySampleNames3.360.014.09
summarizeBsSeqOver3.910.074.64
unionize 8.65 0.1410.24