Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-20 11:07:02 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
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 CopyNumberPlots on riesling1


To the developers/maintainers of the CopyNumberPlots package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CopyNumberPlots.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 396/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.11.0  (landing page)
Bernat Gel
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/CopyNumberPlots
git_branch: master
git_last_commit: 9f4d690
git_last_commit_date: 2021-10-26 12:51:20 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'karyoploteR' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CopyNumberPlots
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CopyNumberPlots.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CopyNumberPlots_1.11.0.tar.gz
StartedAt: 2022-01-19 18:35:53 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 18:40:20 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 266.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CopyNumberPlots.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CopyNumberPlots_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CopyNumberPlots.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 'CopyNumberPlots/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CopyNumberPlots' version '1.11.0'
* 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 'CopyNumberPlots' 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

CopyNumberPlots.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CopyNumberPlots' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CopyNumberPlots'
    finding HTML links ... done
    EnsemblStyle                            html  
    UCSCStyle                               html  
    Ztree2Hclust                            html  
    colByCopyNumber                         html  
    computeHclustPlotOrder                  html  
    getBAFColumn                            html  
    getChrColumn                            html  
    getColumn                               html  
    getCopyNumberColors                     html  
    getCopyNumberColumn                     html  
    getEndColumn                            html  
    getIDColumn                             html  
    getLOHColumn                            html  
    getLRRColumn                            html  
    getPosColumn                            html  
    getSegmentValueColumn                   html  
    getStartColumn                          html  
    loadCopyNumberCalls                     html  
    loadCopyNumberCallsCNVkit               html  
    loadCopyNumberCallsCnmops               html  
    loadCopyNumberCallsDECoN                html  
    loadCopyNumberCallsDNAcopy              html  
    loadCopyNumberCallsPanelcnmops          html  
    loadCopyNumberCallsSeg                  html  
    loadCopyNumberCallspennCNV              html  
    loadSNPData                             html  
    loadSNPDataDNAcopy                      html  
    loadSNPDataFromVCF                      html  
    plotBAF                                 html  
    finding level-2 HTML links ... done

    plotCopyNumberCalls                     html  
    plotCopyNumberCallsAsLines              html  
    plotCopyNumberSummary                   html  
    plotLRR                                 html  
    plotSingleCellCopyNumberCalls           html  
    plotSingleCellCopyNumberSummary         html  
    prepareLabels                           html  
    readHDF5Ztree                           html  
    removeNAs                               html  
    transformChr                            html  
** 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 (CopyNumberPlots)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ideal' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'VariantFiltering' is missing or broken
 done

Tests output

CopyNumberPlots.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(CopyNumberPlots)
Loading required package: karyoploteR
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
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: 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
> 
> test_check("CopyNumberPlots")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  11.34    1.12   12.43 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.340.040.39
UCSCStyle0.220.020.24
Ztree2Hclust000
colByCopyNumber0.280.160.44
computeHclustPlotOrder0.030.000.03
getBAFColumn000
getChrColumn000
getColumn000
getCopyNumberColors000
getCopyNumberColumn000
getEndColumn000
getIDColumn0.000.020.02
getLOHColumn000
getLRRColumn000
getPosColumn000
getSegmentValueColumn000
getStartColumn000
loadCopyNumberCalls0.030.000.03
loadCopyNumberCallsCNVkit0.020.000.02
loadCopyNumberCallsCnmops0.140.030.17
loadCopyNumberCallsDECoN0.030.030.06
loadCopyNumberCallsDNAcopy0.640.000.64
loadCopyNumberCallsPanelcnmops0.220.000.21
loadCopyNumberCallsSeg0.020.000.02
loadCopyNumberCallspennCNV0.030.000.03
loadSNPData0.050.000.05
loadSNPDataDNAcopy0.560.010.58
loadSNPDataFromVCF000
plotBAF0.710.020.72
plotCopyNumberCalls0.140.000.14
plotCopyNumberCallsAsLines0.110.000.11
plotCopyNumberSummary0.130.020.14
plotLRR0.280.090.38
plotSingleCellCopyNumberCalls0.050.000.04
plotSingleCellCopyNumberSummary0.030.000.04
prepareLabels0.040.000.04
readHDF5Ztree000
removeNAs0.160.000.16
transformChr000