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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 411/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
comapr 1.10.0  (landing page)
Ruqian Lyu
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/comapr
git_branch: RELEASE_3_20
git_last_commit: c9af54a
git_last_commit_date: 2024-10-29 11:07:37 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for comapr on merida1

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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-12-20 01:29:11 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:42:58 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 827.3 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/comapr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘comapr/DESCRIPTION’ ... OK
* this is package ‘comapr’ version ‘1.10.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bootstrapDist 5.273  0.247   5.551
* 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:
  > library(comapr)
  > 
  > test_check("comapr")
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 90 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-getCellAFTrack.R:38:3'): get cell CO range works ─────────────
  GenomicRanges::seqnames(co_ranges) == "chr1" is not TRUE
  
  `actual` is an S4 object of class <Rle>
  `expected` is a logical vector (TRUE)
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 90 ]
  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-3.20-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/4.4-x86_64/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.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 1 | WARN 3 | SKIP 0 | PASS 90 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-getCellAFTrack.R:38:3'): get cell CO range works ─────────────
GenomicRanges::seqnames(co_ranges) == "chr1" is not TRUE

`actual` is an S4 object of class <Rle>
`expected` is a logical vector (TRUE)

[ FAIL 1 | WARN 3 | SKIP 0 | PASS 90 ]
Error: Test failures
Execution halted

Example timings

comapr.Rcheck/comapr-Ex.timings

nameusersystemelapsed
bootstrapDist5.2730.2475.551
calGeneticDist0.3030.0730.390
combineHapState2.7850.3473.265
correctGT0.0170.0080.025
countBinState0.7490.1131.118
countCOs1.3260.1711.526
countGT0.3000.0410.344
filterGT0.2370.0310.282
findDupSamples0.0160.0060.022
getAFTracks2.4930.1252.728
getCellAFTrack2.1920.0162.293
getCellCORange1.0150.0091.068
getCellDPTrack1.0340.0061.078
getDistortedMarkers0.8300.0090.877
getMeanDPTrack0.1210.0020.127
getSNPDensityTrack0.1080.0010.113
perCellChrQC0.0880.0020.094
perSegChrQC0.1130.0080.126
permuteDist0.0560.0040.062
plotCount1.6170.0131.710
plotGTFreq1.0840.0101.137
plotGeneticDist0.6520.0080.692
plotWholeGenome0.7730.0100.813
readColMM0.0130.0020.014
readHapState0.2420.0040.254