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CHECK report for hierinf on tokay2

This page was generated on 2019-10-16 12:42:02 -0400 (Wed, 16 Oct 2019).

Package 757/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hierinf 1.2.0
Claude Renaux
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/hierinf
Branch: RELEASE_3_9
Last Commit: e7bf526
Last Changed Date: 2019-05-02 11:54:12 -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: hierinf
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hierinf.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hierinf_1.2.0.tar.gz
StartedAt: 2019-10-16 04:24:14 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:31:02 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 407.1 seconds
RetCode: 0
Status:  OK  
CheckDir: hierinf.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:hierinf.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hierinf_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hierinf.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 'hierinf/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'hierinf' version '1.2.0'
* 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 'hierinf' 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
simGWAS             72.97   0.21   73.17
test_hierarchy      12.47   0.00   12.47
test_only_hierarchy 11.34   0.01   11.39
compute_r2           8.45   0.15    8.61
print.hierT          5.41   0.06    5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
simGWAS             73.20   0.19   73.84
test_hierarchy      13.50   0.02   13.53
test_only_hierarchy 13.06   0.03   13.10
print.hierT          7.69   0.00    7.69
compute_r2           7.39   0.29    7.68
* 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

hierinf.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/hierinf_1.2.0.tar.gz && rm -rf hierinf.buildbin-libdir && mkdir hierinf.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hierinf.buildbin-libdir hierinf_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL hierinf_1.2.0.zip && rm hierinf_1.2.0.tar.gz hierinf_1.2.0.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  215k  100  215k    0     0  3385k      0 --:--:-- --:--:-- --:--:-- 3840k

install for i386

* installing *source* package 'hierinf' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'hierinf'
    finding HTML links ... done
    cluster_position                        html  
    cluster_var                             html  
    compute_r2                              html  
    finding level-2 HTML links ... done

    hierinf                                 html  
    multisplit                              html  
    print.hierT                             html  
    simGWAS                                 html  
    test_hierarchy                          html  
    test_only_hierarchy                     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 'hierinf' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hierinf' as hierinf_1.2.0.zip
* DONE (hierinf)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'hierinf' successfully unpacked and MD5 sums checked

Tests output

hierinf.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.

> # All tests are in the folder testthat
> require("testthat")
Loading required package: testthat
> test_check("hierinf")
Loading required package: hierinf
== testthat results  ===========================================================
[ OK: 141 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  63.46    0.39   63.85 

hierinf.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.

> # All tests are in the folder testthat
> require("testthat")
Loading required package: testthat
> test_check("hierinf")
Loading required package: hierinf
== testthat results  ===========================================================
[ OK: 141 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  60.29    0.15   60.43 

Example timings

hierinf.Rcheck/examples_i386/hierinf-Ex.timings

nameusersystemelapsed
cluster_position0.060.000.06
cluster_var1.300.021.31
compute_r28.450.158.61
multisplit1.120.081.21
print.hierT5.410.065.47
simGWAS72.97 0.2173.17
test_hierarchy12.47 0.0012.47
test_only_hierarchy11.34 0.0111.39

hierinf.Rcheck/examples_x64/hierinf-Ex.timings

nameusersystemelapsed
cluster_position0.090.000.09
cluster_var1.220.021.24
compute_r27.390.297.68
multisplit1.050.031.08
print.hierT7.690.007.69
simGWAS73.20 0.1973.84
test_hierarchy13.50 0.0213.53
test_only_hierarchy13.06 0.0313.10