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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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 1814/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RVS 1.29.0  (landing page)
Alexandre Bureau
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/RVS
git_branch: devel
git_last_commit: b6690b7
git_last_commit_date: 2024-10-29 10:21:14 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for RVS on lconway

To the developers/maintainers of the RVS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RVS.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: RVS
Version: 1.29.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RVS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RVS_1.29.0.tar.gz
StartedAt: 2024-12-23 22:53:11 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:57:03 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 232.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RVS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RVS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RVS_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RVS.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘RVS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RVS’ version ‘1.29.0’
* 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 ‘RVS’ 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'RVsharing-methods.Rd':
RVsharing
  Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, distinguishHomo = FALSE,
                 ...)
  Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, ...)
  Argument names in code not in docs:
    distinguishHomo
  Mismatches in argument names:
    Position: 11 Code: distinguishHomo Docs: ...
\S4method{RVsharing}{pedigree}
  Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, distinguishHomo = FALSE,
                 ...)
  Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, ...)
  Argument names in code not in docs:
    distinguishHomo
  Mismatches in argument names:
    Position: 11 Code: distinguishHomo Docs: ...
\S4method{RVsharing}{list}
  Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, distinguishHomo = FALSE,
                 ...)
  Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff =
                 NA, nSim = NA, founderDist = NULL, useAffected =
                 FALSE, kinshipOrder = 5, splitPed = FALSE,
                 useFounderCouples = TRUE, ...)
  Argument names in code not in docs:
    distinguishHomo
  Mismatches in argument names:
    Position: 11 Code: distinguishHomo Docs: ...

Codoc mismatches from Rd file 'oneFounderSharingProb.Rd':
oneFounderSharingProb
  Code: function(procPed, distinguishHomo = FALSE)
  Docs: function(procPed)
  Argument names in code not in docs:
    distinguishHomo

Codoc mismatches from Rd file 'twoFounderSharingProb.Rd':
twoFounderSharingProb
  Code: function(procPed, kinshipCoeff, kinshipOrder, distinguishHomo =
                 FALSE)
  Docs: function(procPed, kinshipCoeff, kinshipOrder)
  Argument names in code not in docs:
    distinguishHomo

* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'denomProb.Rd':
  ‘gRain’

Documented arguments not in \usage in Rd file 'numerProb.Rd':
  ‘gRain’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 LazyData ... 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
RVgene 14.305  0.516  14.938
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RVS.Rcheck/00check.log’
for details.


Installation output

RVS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RVS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RVS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (RVS)

Tests output

RVS.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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(RVS)
> 
> test_check('RVS')
Founder  2  subped size  20 
Founder  4  subped size  11 
Founder  5  subped size  16 
Founder  9  subped size  5 
Founder  13  subped size  5 
Founder  14  subped size  3 
Founder  16  subped size  5 
[1] 0.01873 0.49970 0.48150
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_multipleFamilyCalculations.R:19:1',
  'test_multipleFamilyCalculations.R:42:1'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
105.475   1.066 107.138 

Example timings

RVS.Rcheck/RVS-Ex.timings

nameusersystemelapsed
ComputeKinshipPropCoef-methods0.0100.0020.011
GeneDrop0.0010.0000.002
RVgene14.305 0.51614.938
RVsharing-methods0.0810.0100.091
SnpMatrixToCount0.0020.0020.004
get.psubset2.3680.1142.505
multipleFamilyPValue1.2170.0171.241
ped2trio0.0000.0010.001
processPedigree-methods0.0010.0010.002