Package: scoreInvHap

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scoreInvHap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings scoreInvHap_1.4.0.tar.gz

StartedAt: 2019-04-13 05:21:23 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:27:35 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 372.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: scoreInvHap.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scoreInvHap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings scoreInvHap_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/scoreInvHap.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scoreInvHap/DESCRIPTION' ... OK
* this is package 'scoreInvHap' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/scoreInvHap.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/scoreInvHap_1.4.0.tar.gz && rm -rf scoreInvHap.buildbin-libdir && mkdir scoreInvHap.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scoreInvHap.buildbin-libdir scoreInvHap_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL scoreInvHap_1.4.0.zip && rm scoreInvHap_1.4.0.tar.gz scoreInvHap_1.4.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  449k  100  449k    0     0  10.4M      0 --:--:-- --:--:-- --:--:-- 11.5M

install for i386

* installing *source* package 'scoreInvHap' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scoreInvHap'
    finding HTML links ... done
    Refs                                    html  
    SNPsR2                                  html  
    adaptRefs                               html  
    classifSNPs                             html  
    computeScore                            html  
    correctAlleleTable                      html  
    getAlleleTable                          html  
    getGenotypesTable                       html  
    getInvStatus                            html  
    hetRefs                                 html  
    prepareMap                              html  
    scoreInvHap                             html  
    scoreInvHapRes-class                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scoreInvHap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scoreInvHap' as scoreInvHap_1.4.0.zip
* DONE (scoreInvHap)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'scoreInvHap' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   9.84    0.68   10.53 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.32    0.54   13.87