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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RVS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RVS_1.28.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RVS.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 '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 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 14.39   0.69   15.11
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/RVS.Rcheck/00check.log'
for details.