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CHECK report for RVS on tokay2

This page was generated on 2019-10-16 12:39:02 -0400 (Wed, 16 Oct 2019).

Package 1443/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RVS 1.6.0
Thomas Sherman
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RVS
Branch: RELEASE_3_9
Last Commit: fde2fb2
Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RVS
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RVS_1.6.0.tar.gz
StartedAt: 2019-10-16 06:51:29 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:57:05 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 335.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RVS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RVS_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RVS.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RVS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RVS' 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 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 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 ... OK
* 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
Examples with CPU or elapsed time > 5s
        user system elapsed
RVgene 12.36   0.94   13.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
RVgene 11.85   0.31   12.58
* 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: OK


Installation output

RVS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RVS_1.6.0.tar.gz && rm -rf RVS.buildbin-libdir && mkdir RVS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RVS.buildbin-libdir RVS_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RVS_1.6.0.zip && rm RVS_1.6.0.tar.gz RVS_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  752k  100  752k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.6M

install for i386

* installing *source* package 'RVS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RVS'
    finding HTML links ... done
    ComputeKinshipPropCoef-methods          html  
    GeneDrop                                html  
    RVS                                     html  
    RVgene                                  html  
    RVsharing-methods                       html  
    SnpMatrixToCount                        html  
    ancestorDistance                        html  
    areMating                               html  
    checkArgs                               html  
    computePFU                              html  
    computePhiVec                           html  
    convertMatrix                           html  
    createNetwork                           html  
    denomProb                               html  
    enrichmentPValue                        html  
    ex.ped.mat                              html  
    exactSharingProb                        html  
    extract_carriers                        html  
    fam15157.vcf                            html  
    fam28003.vcf                            html  
    founderOccurence                        html  
    get.psubset                             html  
    inferNumAlleles                         html  
    inferTheta                              html  
    isDescendant                            html  
    marginalProb                            html  
    monteCarloSharingProb                   html  
    multipleFamilyPValue                    html  
    multipleVariantPValue                   html  
    numerProb                               html  
    oldArgs                                 html  
    oneFounderSharingProb                   html  
    oneFounderSharingProbSplitting          html  
    ped2trio                                html  
    processPedigree-methods                 html  
    relatedFoundersCorrection               html  
    runMonteCarlo                           html  
    samplePedigrees                         html  
    simulatePedigree                        html  
    snpMat                                  html  
    twoFounderSharingProb                   html  
** 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

install for x64

* installing *source* package 'RVS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RVS' as RVS_1.6.0.zip
* DONE (RVS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RVS' successfully unpacked and MD5 sums checked

Tests output

RVS.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(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
== testthat results  ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  76.18    0.54   81.43 

RVS.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(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
== testthat results  ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  95.34    0.40   95.78 

Example timings

RVS.Rcheck/examples_i386/RVS-Ex.timings

nameusersystemelapsed
ComputeKinshipPropCoef-methods0.010.020.03
GeneDrop000
RVgene12.36 0.9413.34
RVsharing-methods0.050.050.09
SnpMatrixToCount0.010.000.02
get.psubset1.560.101.67
multipleFamilyPValue0.920.421.38
ped2trio000
processPedigree-methods0.020.000.01

RVS.Rcheck/examples_x64/RVS-Ex.timings

nameusersystemelapsed
ComputeKinshipPropCoef-methods0.000.040.03
GeneDrop000
RVgene11.85 0.3112.58
RVsharing-methods0.050.000.05
SnpMatrixToCount000
get.psubset0.840.010.86
multipleFamilyPValue0.830.020.84
ped2trio000
processPedigree-methods0.000.020.02