Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 403/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
comapr 1.9.0  (landing page)
Ruqian Lyu
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/comapr
git_branch: devel
git_last_commit: 68eb288
git_last_commit_date: 2024-04-30 11:39:48 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for comapr on palomino6

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: 1.9.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:comapr.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings comapr_1.9.0.tar.gz
StartedAt: 2024-07-15 22:53:27 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:01:20 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 473.8 seconds
RetCode: 0
Status:   OK  
CheckDir: comapr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:comapr.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings comapr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/comapr.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'comapr/DESCRIPTION' ... OK
* this is package 'comapr' version '1.9.0'
* 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 '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 3.65   0.03   20.65
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/comapr.Rcheck/00check.log'
for details.


Installation output

comapr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL comapr
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-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
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  38.89    2.34  136.34 

Example timings

comapr.Rcheck/comapr-Ex.timings

nameusersystemelapsed
bootstrapDist 3.65 0.0320.65
calGeneticDist0.090.020.11
combineHapState1.750.001.77
correctGT0.000.010.01
countBinState0.270.020.49
countCOs0.560.050.61
countGT0.100.000.09
filterGT0.080.000.08
findDupSamples0.010.000.02
getAFTracks0.940.030.97
getCellAFTrack0.750.030.78
getCellCORange0.340.000.34
getCellDPTrack0.440.000.44
getDistortedMarkers0.240.000.23
getMeanDPTrack0.040.000.05
getSNPDensityTrack0.030.000.03
perCellChrQC0.050.000.04
perSegChrQC0.050.000.05
permuteDist0.020.000.01
plotCount0.560.040.60
plotGTFreq0.360.030.39
plotGeneticDist0.230.000.23
plotWholeGenome0.250.000.25
readColMM0.020.000.02
readHapState0.110.000.11