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This page was generated on 2024-03-28 11:32:18 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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

Package 407/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
comapr 1.6.1  (landing page)
Ruqian Lyu
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/comapr
git_branch: RELEASE_3_18
git_last_commit: fe01419
git_last_commit_date: 2023-10-27 00:06:38 -0400 (Fri, 27 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for comapr on kjohnson1


To the developers/maintainers of the comapr package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: comapr
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:comapr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings comapr_1.6.1.tar.gz
StartedAt: 2024-03-27 09:24:55 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 09:32:37 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 462.0 seconds
RetCode: 0
Status:   OK  
CheckDir: comapr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:comapr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings comapr_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/comapr.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘comapr/DESCRIPTION’ ... OK
* this is package ‘comapr’ version ‘1.6.1’
* 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 for sufficient/correct file permissions ... 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 5.466  0.172   5.547
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL comapr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘comapr’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output

comapr.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 3 | SKIP 0 | PASS 91 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 91 ]
> 
> proc.time()
   user  system elapsed 
 49.248   4.488  48.888 

Example timings

comapr.Rcheck/comapr-Ex.timings

nameusersystemelapsed
bootstrapDist5.4660.1725.547
calGeneticDist0.1470.0810.230
combineHapState2.1430.3052.454
correctGT0.0090.0040.013
countBinState0.3500.0260.845
countCOs0.6390.0350.674
countGT0.1220.0030.125
filterGT0.0750.0020.077
findDupSamples0.0090.0020.011
getAFTracks1.3310.0311.363
getCellAFTrack0.9200.0080.928
getCellCORange0.3740.0020.377
getCellDPTrack0.4310.0030.434
getDistortedMarkers0.2540.0060.259
getMeanDPTrack0.0500.0010.050
getSNPDensityTrack0.0460.0010.047
perCellChrQC0.0480.0020.050
perSegChrQC0.0660.0060.072
permuteDist0.0240.0020.027
plotCount0.7100.0100.721
plotGTFreq0.3930.0080.401
plotGeneticDist0.4320.0060.438
plotWholeGenome0.2870.0050.293
readColMM0.0080.0000.009
readHapState0.0950.0010.097