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This page was generated on 2021-11-30 13:54:51 -0500 (Tue, 30 Nov 2021).

CHECK results for doppelgangR on riesling1

To the developers/maintainers of the doppelgangR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/doppelgangR.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 532/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doppelgangR 1.23.0  (landing page)
Levi Waldron
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/doppelgangR
git_branch: master
git_last_commit: 8b1f509
git_last_commit_date: 2021-10-26 12:26:10 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: doppelgangR
Version: 1.23.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings doppelgangR_1.23.0.tar.gz
StartedAt: 2021-11-30 01:33:15 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 01:41:56 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 521.3 seconds
RetCode: 0
Status:   OK  
CheckDir: doppelgangR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings doppelgangR_1.23.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/doppelgangR.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 'doppelgangR/DESCRIPTION' ... OK
* this is package 'doppelgangR' version '1.23.0'
* 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 'doppelgangR' 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
plot-methods 6.46   0.57   38.78
doppelgangR  2.89   0.30   23.33
* 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

doppelgangR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/doppelgangR_1.23.0.tar.gz && rm -rf doppelgangR.buildbin-libdir && mkdir doppelgangR.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=doppelgangR.buildbin-libdir doppelgangR_1.23.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL doppelgangR_1.23.0.zip && rm doppelgangR_1.23.0.tar.gz doppelgangR_1.23.0.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 71757  100 71757    0     0   464k      0 --:--:-- --:--:-- --:--:--  464k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'doppelgangR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'doppelgangR'
    finding HTML links ... done
    DoppelGang-class                        html  
    colFinder                               html  
    corFinder                               html  
    doppelgangR-package                     html  
    doppelgangR                             html  
    dst                                     html  
    mst.mle                                 html  
    outlierFinder                           html  
    phenoDist                               html  
    phenoFinder                             html  
    plot-methods                            html  
    smokingGunFinder                        html  
    vectorHammingDist                       html  
    vectorWeightedDist                      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
* MD5 sums
packaged installation of 'doppelgangR' as doppelgangR_1.23.0.zip
* DONE (doppelgangR)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'doppelgangR' successfully unpacked and MD5 sums checked

Tests output

doppelgangR.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(doppelgangR)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
> 
> test_check("doppelgangR")
Warning message:
In FUN(...) :
  m and n have different column names in phenoData.  Skipping phenotype checking for this pair.  Set phenoFinger.args=NULL to disable phenotype checking altogether.
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  17.23    0.65  238.06 

Example timings

doppelgangR.Rcheck/doppelgangR-Ex.timings

nameusersystemelapsed
corFinder3.850.404.30
doppelgangR 2.89 0.3023.33
dst000
mst.mle0.060.000.06
outlierFinder1.220.191.41
phenoDist1.890.262.16
phenoFinder2.250.252.50
plot-methods 6.46 0.5738.78
smokingGunFinder1.910.222.14
vectorHammingDist000
vectorWeightedDist000