Package: scoreInvHap

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scoreInvHap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scoreInvHap_1.6.0.tar.gz

StartedAt: 2019-10-16 06:39:01 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:46:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 471.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scoreInvHap.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:scoreInvHap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings scoreInvHap_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/scoreInvHap.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scoreInvHap/DESCRIPTION’ ... OK
* this is package ‘scoreInvHap’ version ‘1.6.0’
* 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 ‘scoreInvHap’ 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 R 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 documentation object 'classifSNPs':
classifSNPs
  Code: function(genos, R2, refs, BPPARAM =
                 BiocParallel::SerialParam())
  Docs: function(genos, R2, refs, BPPARAM = BiocParallel::bpparam())
  Mismatches in argument default values:
    Name: 'BPPARAM' Code: BiocParallel::SerialParam() Docs: BiocParallel::bpparam()
classifSNPsImpute
  Code: function(genos, R2, refs, BPPARAM =
                 BiocParallel::SerialParam())
  Docs: function(genos, R2, refs, BPPARAM = BiocParallel::bpparam())
  Mismatches in argument default values:
    Name: 'BPPARAM' Code: BiocParallel::SerialParam() Docs: BiocParallel::bpparam()

Codoc mismatches from documentation object 'scoreInvHap':
scoreInvHap
  Code: function(SNPlist, SNPsR2, hetRefs, Refs, R2 = 0, imputed =
                 FALSE, BPPARAM = BiocParallel::SerialParam(), verbose
                 = FALSE)
  Docs: function(SNPlist, SNPsR2, hetRefs, Refs, R2 = 0, imputed =
                 FALSE, BPPARAM = BiocParallel::bpparam(), verbose =
                 FALSE)
  Mismatches in argument default values:
    Name: 'BPPARAM' Code: BiocParallel::SerialParam() Docs: BiocParallel::bpparam()

* 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 or elapsed time > 5s
             user system elapsed
scoreInvHap 4.578  0.655   5.238
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/scoreInvHap.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scoreInvHap
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘scoreInvHap’ ...
** 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 (scoreInvHap)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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(scoreInvHap)
> 
> test_check("scoreInvHap")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 18.518   1.454  20.047 

name	user	system	elapsed
classifSNPs	0.189	0.045	0.234
scoreInvHap	4.578	0.655	5.238
scoreInvHapRes-class	2.910	0.393	3.305