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This page was generated on 2025-09-22 12:05 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 419/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
comapr 1.13.0  (landing page)
Ruqian Lyu
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/comapr
git_branch: devel
git_last_commit: 30e00f7
git_last_commit_date: 2025-04-15 12:44:28 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for comapr on kjohnson3

To the developers/maintainers of the comapr package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-09-21 18:50:12 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 18:52:53 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 161.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: comapr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/comapr.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘comapr/DESCRIPTION’ ... OK
* this is package ‘comapr’ version ‘1.13.0’
* 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 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 code 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 ... NOTE
checkRd: (-1) perCellChrQC.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx,
       |                                                          ^
checkRd: (-1) perCellChrQC.Rd:23: Lost braces; missing escapes or markup?
    23 | *{chrom}_viSegInfo.txt, end with slash}
       |  ^
checkRd: (-1) perSegChrQC.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx,
       |                                                          ^
checkRd: (-1) perSegChrQC.Rd:22: Lost braces; missing escapes or markup?
    22 | *{chrom}_viSegInfo.txt, end with slash}
       |  ^
checkRd: (-1) readHapState.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{path, }{the path to the files, with name patterns *{chrom}_vi.mtx,
       |                                                          ^
checkRd: (-1) readHapState.Rd:29: Lost braces; missing escapes or markup?
    29 | *{chrom}_viSegInfo.txt, end with slash}
       |  ^
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plotmissingGT.R:12:3'): Plot missing GT works ────────────────
  class(p1)[1] == "gg" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-plotmissingGT.R:15:3'): Plot missing GT works ────────────────
  class(p4)[1] == "gg" is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 3 | SKIP 0 | PASS 89 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/comapr.Rcheck/00check.log’
for details.


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/4.5-arm64/Resources/library’
* installing *source* package ‘comapr’ ...
** this is package ‘comapr’ version ‘1.13.0’
** 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.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 2 | WARN 3 | SKIP 0 | PASS 89 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotmissingGT.R:12:3'): Plot missing GT works ────────────────
class(p1)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-plotmissingGT.R:15:3'): Plot missing GT works ────────────────
class(p4)[1] == "gg" is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 2 | WARN 3 | SKIP 0 | PASS 89 ]
Error: Test failures
Execution halted

Example timings

comapr.Rcheck/comapr-Ex.timings

nameusersystemelapsed
bootstrapDist2.0610.0622.123
calGeneticDist0.0390.0330.073
combineHapState0.7020.1240.840
correctGT0.0020.0020.004
countBinState0.1110.0130.540
countCOs0.1870.0150.210
countGT0.0610.0070.069
filterGT0.0250.0030.028
findDupSamples0.0020.0010.003
getAFTracks0.3930.0060.407
getCellAFTrack0.2830.0020.296
getCellCORange0.1160.0010.126
getCellDPTrack0.1250.0010.137
getDistortedMarkers0.1240.0020.130
getMeanDPTrack0.0150.0010.016
getSNPDensityTrack0.0150.0000.021
perCellChrQC0.0330.0010.038
perSegChrQC0.0210.0020.022
permuteDist0.0080.0010.008
plotCount0.2390.0020.242
plotGTFreq0.1970.0030.200
plotGeneticDist0.1480.0020.157
plotWholeGenome0.1540.0020.156
readColMM0.0020.0000.003
readHapState0.0410.0010.051