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CHECK report for hierGWAS on tokay2

This page was generated on 2019-10-16 12:33:25 -0400 (Wed, 16 Oct 2019).

Package 756/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hierGWAS 1.14.0
Laura Buzdugan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/hierGWAS
Branch: RELEASE_3_9
Last Commit: 53eefbb
Last Changed Date: 2019-05-02 11:53:55 -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: hierGWAS
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:hierGWAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hierGWAS_1.14.0.tar.gz
StartedAt: 2019-10-16 04:24:11 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:25:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 86.2 seconds
RetCode: 0
Status:  OK  
CheckDir: hierGWAS.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:hierGWAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings hierGWAS_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/hierGWAS.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 'hierGWAS/DESCRIPTION' ... OK
* this is package 'hierGWAS' version '1.14.0'
* 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 'hierGWAS' 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 ... NOTE
MEL: no visible global function definition for 'glm'
MEL: no visible binding for global variable 'binomial'
MEL: no visible global function definition for 'glm.control'
MEL: no visible global function definition for 'coef'
adj.pval: no visible global function definition for 'quantile'
cluster.snp: no visible global function definition for 'cor'
cluster.snp: no visible global function definition for 'as.dist'
cluster.snp: no visible global function definition for 'as.dendrogram'
return.r2: no visible global function definition for 'lm'
test.hierarchy: no visible global function definition for
  'order.dendrogram'
test.snp: no visible global function definition for 'anova'
test.snp: no visible global function definition for 'lm'
Undefined global functions or variables:
  anova as.dendrogram as.dist binomial coef cor glm glm.control lm
  order.dendrogram quantile
Consider adding
  importFrom("stats", "anova", "as.dendrogram", "as.dist", "binomial",
             "coef", "cor", "glm", "glm.control", "lm",
             "order.dendrogram", "quantile")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/hierGWAS.Rcheck/00check.log'
for details.



Installation output

hierGWAS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/hierGWAS_1.14.0.tar.gz && rm -rf hierGWAS.buildbin-libdir && mkdir hierGWAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=hierGWAS.buildbin-libdir hierGWAS_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL hierGWAS_1.14.0.zip && rm hierGWAS_1.14.0.tar.gz hierGWAS_1.14.0.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  200k  100  200k    0     0  3984k      0 --:--:-- --:--:-- --:--:-- 4552k

install for i386

* installing *source* package 'hierGWAS' ...
** 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 'hierGWAS'
    finding HTML links ... done
    cluster.snp                             html  
    compute.r2                              html  
    hierGWAS                                html  
    multisplit                              html  
    finding level-2 HTML links ... done

    simGWAS                                 html  
    test.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 'hierGWAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hierGWAS' as hierGWAS_1.14.0.zip
* DONE (hierGWAS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'hierGWAS' successfully unpacked and MD5 sums checked

Tests output

hierGWAS.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("hierGWAS")


RUNIT TEST PROTOCOL -- Wed Oct 16 04:25:24 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
hierGWAS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.57    0.15    2.93 

hierGWAS.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("hierGWAS")


RUNIT TEST PROTOCOL -- Wed Oct 16 04:25:27 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
hierGWAS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.68    0.28    2.95 

Example timings

hierGWAS.Rcheck/examples_i386/hierGWAS-Ex.timings

nameusersystemelapsed
cluster.snp0.030.000.03
compute.r20.260.020.28
multisplit0.250.030.28
simGWAS000
test.hierarchy2.340.012.36

hierGWAS.Rcheck/examples_x64/hierGWAS-Ex.timings

nameusersystemelapsed
cluster.snp0.010.010.04
compute.r20.250.030.28
multisplit0.270.000.27
simGWAS000
test.hierarchy3.160.003.16