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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RVS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RVS_1.28.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RVS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RVS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RVS’ version ‘1.28.0’
* 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 loading without being on the library search path ... 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 10.022  0.486   11.07
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RVS.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RVS
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 70.473   0.463  74.229