Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:14 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 comapr on riesling1


To the developers/maintainers of the comapr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/comapr.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 373/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
comapr 0.99.43  (landing page)
Ruqian Lyu
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/comapr
git_branch: master
git_last_commit: 915d97c
git_last_commit_date: 2022-03-09 17:31:55 -0400 (Wed, 09 Mar 2022)
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  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: comapr
Version: 0.99.43
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:comapr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings comapr_0.99.43.tar.gz
StartedAt: 2022-03-17 18:47:10 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:54:00 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 410.6 seconds
RetCode: 0
Status:   OK  
CheckDir: comapr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:comapr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings comapr_0.99.43.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/comapr.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 'comapr/DESCRIPTION' ... OK
* this is package 'comapr' version '0.99.43'
* 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 'comapr' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
bootstrapDist 1.56      0   17.96
* 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

comapr.Rcheck/00install.out

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


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'comapr' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'comapr'
    finding HTML links ... done
    bootstrapDist                           html  
    calGeneticDist                          html  
    coCount                                 html  
    comapr                                  html  
    combineHapState                         html  
    correctGT                               html  
    countBinState                           html  
    countCOs                                html  
    countGT                                 html  
    dot-change_missing                      html  
    dot-filterCOsExtra                      html  
    dot-label_gt                            html  
    fill_fail                               html  
    filterGT                                html  
    findDupSamples                          html  
    getAFTracks                             html  
    getCellAFTrack                          html  
    getCellCORange                          html  
    getCellDPTrack                          html  
    getDistortedMarkers                     html  
    getMeanDPTrack                          html  
    getSNPDensityTrack                      html  
    parents_geno                            html  
    perCellChrQC                            html  
    perSegChrQC                             html  
    permuteDist                             html  
    plotCount                               html  
    plotGTFreq                              html  
    plotGeneticDist                         html  
    plotWholeGenome                         html  
    readColMM                               html  
    readHapState                            html  
    snp_geno                                html  
    snp_geno_gr                             html  
    twoSamples                              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 (comapr)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'coMET' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'metaseqR2' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'scruff' is missing or broken
 done

Tests output

comapr.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(comapr)
> 
> test_check("comapr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 91 ]
> 
> proc.time()
   user  system elapsed 
  43.85    1.64  130.84 

Example timings

comapr.Rcheck/comapr-Ex.timings

nameusersystemelapsed
bootstrapDist 1.56 0.0017.96
calGeneticDist0.100.000.09
combineHapState0.580.160.73
correctGT0.010.020.04
countBinState0.270.030.71
countCOs0.560.150.72
countGT0.080.000.08
filterGT0.040.020.06
findDupSamples0.000.010.02
getAFTracks0.750.040.78
getCellAFTrack0.820.000.81
getCellCORange0.340.000.35
getCellDPTrack0.390.000.39
getDistortedMarkers0.240.000.23
getMeanDPTrack0.030.000.03
getSNPDensityTrack0.030.000.03
perCellChrQC0.030.000.04
perSegChrQC0.030.010.04
permuteDist0.020.000.02
plotCount0.530.020.55
plotGTFreq0.180.010.20
plotGeneticDist0.210.000.20
plotWholeGenome0.220.000.22
readColMM000
readHapState0.070.000.08