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CHECK report for GENESIS on tokay2

This page was generated on 2019-10-16 12:32:44 -0400 (Wed, 16 Oct 2019).

Package 640/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.14.4
Stephanie M. Gogarten
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GENESIS
Branch: RELEASE_3_9
Last Commit: 29ee101
Last Changed Date: 2019-10-10 19:23:23 -0400 (Thu, 10 Oct 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: GENESIS
Version: 2.14.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GENESIS_2.14.4.tar.gz
StartedAt: 2019-10-16 03:56:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:05:45 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 549.4 seconds
RetCode: 0
Status:  OK  
CheckDir: GENESIS.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:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GENESIS_2.14.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GENESIS.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 'GENESIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENESIS' version '2.14.4'
* 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 'GENESIS' 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 ... NOTE
Unexported object imported by a ':::' call: 'survey:::saddle'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pcrelate: no visible binding for global variable 'k'
calcISAFBeta: no visible binding for global variable 'k'
pcrelateSampBlock: no visible binding for global variable 'k'
Undefined global functions or variables:
  k
* 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
fitNullModel 20.42   0.77   21.19
varCompCI    14.26   0.47   14.70
pcrelate     13.25   0.81   14.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
varCompCI    16.76   0.70   17.50
fitNullModel 15.50   0.70   16.21
pcrelate     10.98   0.47   11.46
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GENESIS.Rcheck/00check.log'
for details.



Installation output

GENESIS.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/GENESIS_2.14.4.tar.gz && rm -rf GENESIS.buildbin-libdir && mkdir GENESIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GENESIS.buildbin-libdir GENESIS_2.14.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GENESIS_2.14.4.zip && rm GENESIS_2.14.4.tar.gz GENESIS_2.14.4.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 2080k  100 2080k    0     0  25.0M      0 --:--:-- --:--:-- --:--:-- 27.4M

install for i386

* installing *source* package 'GENESIS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GENESIS'
    finding HTML links ... done
    GENESIS-package                         html  
    HapMap_ASW_MXL_KINGmat                  html  
    admixMap                                html  
    finding level-2 HTML links ... done

    assocTestAggregate                      html  
    assocTestSingle                         html  
    defunct                                 html  
    fitNullModel                            html  
    kin2gds                                 html  
    kingToMatrix                            html  
    makeSparseMatrix                        html  
    pcair                                   html  
    pcairPartition                          html  
    pcrelate                                html  
    pcrelateToMatrix                        html  
    plot.pcair                              html  
    print.pcair                             html  
    sample_annotation_1KG                   html  
    varCompCI                               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 'GENESIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.14.4.zip
* DONE (GENESIS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GENESIS' successfully unpacked and MD5 sums checked

Tests output

GENESIS.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(GENESIS)
> 
> test_check("GENESIS")
== testthat results  ===========================================================
[ OK: 383 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  98.98    4.93  112.75 

GENESIS.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(GENESIS)
> 
> test_check("GENESIS")
== testthat results  ===========================================================
[ OK: 383 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  83.90    3.34   87.67 

Example timings

GENESIS.Rcheck/examples_i386/GENESIS-Ex.timings

nameusersystemelapsed
admixMap1.410.081.62
assocTestAggregate2.890.003.24
assocTestSingle3.670.123.95
fitNullModel20.42 0.7721.19
kin2gds3.360.033.64
kingToMatrix1.650.061.79
pcair0.490.000.49
pcairPartition0.030.000.03
pcrelate13.25 0.8114.06
plot.pcair0.480.070.55
print.pcair0.410.040.45
varCompCI14.26 0.4714.70

GENESIS.Rcheck/examples_x64/GENESIS-Ex.timings

nameusersystemelapsed
admixMap1.550.081.62
assocTestAggregate2.440.042.48
assocTestSingle2.950.103.04
fitNullModel15.50 0.7016.21
kin2gds1.400.081.48
kingToMatrix0.720.050.75
pcair0.490.010.50
pcairPartition0.030.000.03
pcrelate10.98 0.4711.46
plot.pcair0.450.000.46
print.pcair0.410.020.42
varCompCI16.76 0.7017.50