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This page was generated on 2022-01-20 11:07:22 -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 genotypeeval on riesling1


To the developers/maintainers of the genotypeeval package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genotypeeval.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 757/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genotypeeval 1.27.0  (landing page)
Jennifer Tom
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/genotypeeval
git_branch: master
git_last_commit: 4ce3be2
git_last_commit_date: 2021-10-26 12:21:35 -0500 (Tue, 26 Oct 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 'VariantAnnotation' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: genotypeeval
Version: 1.27.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genotypeeval.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genotypeeval_1.27.0.tar.gz
StartedAt: 2022-01-19 18:59:22 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 19:04:35 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 313.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genotypeeval.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genotypeeval.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genotypeeval_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/genotypeeval.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 'genotypeeval/DESCRIPTION' ... OK
* this is package 'genotypeeval' version '1.27.0'
* 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 'genotypeeval' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Missing or unexported object: 'GenomicRanges::subset'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'D:/biocbuild/bbs-3.15-bioc/meat/genotypeeval.Rcheck/00check.log'
for details.



Installation output

genotypeeval.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'genotypeeval' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genotypeeval'
    finding HTML links ... done
    GoldData-class                          html  
    GoldDataFromGRanges                     html  
    GoldDataParam-class                     html  
    GoldDataParam                           html  
    ReadGoldData                            html  
    ReadVCFData                             html  
    ReadVCFDataChunk                        html  
    VCFData-class                           html  
    VCFEvaluate                             html  
    VCFQAParam-class                        html  
    VCFQAParam                              html  
    VCFQAReport-class                       html  
    XHeterozygosity                         html  
    admixture                               html  
    callbyChrPlot                           html  
    calltypePlot                            html  
    chunkData                               html  
    computeTiTv                             html  
    didSamplePass                           html  
    didSamplePassOverall                    html  
    genotypeQualityPlot                     html  
    getCoefs                                html  
    getDescriptors                          html  
    getName                                 html  
    getPlots                                html  
    getResults                              html  
    getVR                                   html  
    goldCompare                             html  
    hetGap                                  html  
    hetsMasked                              html  
    homrefPlot                              html  
    meanGQ                                  html  
    myf                                     html  
    numberCalls                             html  
    numberOfHets                            html  
    numberOfHomRefs                         html  
    numberOfHomVars                         html  
    percentHets                             html  
    percentInTarget                         html  
    rareCompare                             html  
    readDepth                               html  
    readVcfGold                             html  
    readdepthPlot                           html  
    reformatData                            html  
    titv                                    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 (genotypeeval)
Making 'packages.html' ... done

Tests output

genotypeeval.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(genotypeeval)
Loading required package: VariantAnnotation
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: 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: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

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: GenomicRanges
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:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate

> 
> test_check("genotypeeval")
Reading VCF ... 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
  68.45    3.28   71.67 
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"
[W::bcf_hdr_register_hrec] The type "NULL" is not supported, assuming "String"

Example timings

genotypeeval.Rcheck/genotypeeval-Ex.timings

nameusersystemelapsed
GoldDataFromGRanges0.070.000.06
GoldDataParam000
ReadGoldData1.110.031.14
ReadVCFData2.830.012.84
ReadVCFDataChunk4.810.054.86
VCFEvaluate2.450.142.60
VCFQAParam000
didSamplePass2.950.083.03
didSamplePassOverall2.600.022.61
getName2.340.002.35
getPlots3.610.013.62
getResults2.770.022.78
getVR1.840.031.88