Package: SNPchip

Version: 2.28.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPchip.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SNPchip_2.28.0.tar.gz

StartedAt: 2019-04-13 05:38:18 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 05:43:12 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 294.2 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPchip.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SNPchip_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SNPchip.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 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '2.28.0'
* 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 'SNPchip' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
centromereData: no visible global function definition for 'read.delim'
dataFrameFromRange: no visible binding for global variable 'data'
getCytoband: no visible global function definition for 'read.table'
Undefined global functions or variables:
  data read.delim read.table
Consider adding
  importFrom("utils", "data", "read.delim", "read.table")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
xyplot 4.95   0.31    5.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
xyplot 5.18   0.11     5.3
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.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-3.8-bioc/meat/SNPchip.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/SNPchip_2.28.0.tar.gz && rm -rf SNPchip.buildbin-libdir && mkdir SNPchip.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPchip.buildbin-libdir SNPchip_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SNPchip_2.28.0.zip && rm SNPchip_2.28.0.tar.gz SNPchip_2.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 37423  100 37423    0     0   904k      0 --:--:-- --:--:-- --:--:--  987k

install for i386

* installing *source* package 'SNPchip' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPchip'
    finding HTML links ... done
    arrangeFigs                             html  
    arrangeSideBySide                       html  
    centromere                              html  
    dataFrame-methods                       html  
    dataFrame                               html  
    defunct                                 html  
    getCytoband                             html  
    latticeFigs                             html  
    plotIdiogram                            html  
    xypanel                                 html  
    xypanelBaf                              html  
    xyplot                                  html  
    xyplotLrrBaf                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SNPchip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPchip' as SNPchip_2.28.0.zip
* DONE (SNPchip)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SNPchip' 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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "SNPchip"
+ 
+ 	if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ 		path <- file.path( getwd(), "..", "inst", "unitTests" )
+ 	} else {
+ 		path <- system.file( package=pkg, "unitTests" )
+ 	}
+ 
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 	##  fail on warnings (needed for SNPchip() test)
+ 	##options(warn=2)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ 	if( is.null( patt ) || nchar( patt ) == 0 ) {
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     dirs=path,
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	} else {
+ 		##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 					     dirs=path )
+ 	}
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "SNPchip"

$getwd
[1] "C:/Users/biocbuild/bbs-3.8-bioc/meat/SNPchip.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPchip/unitTests"

Welcome to SNPchip version 2.28.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Sat Apr 13 05:42:55 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SNPchip unit testing - 0 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
   6.14    0.53    6.70 

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.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "SNPchip"
+ 
+ 	if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ 		path <- file.path( getwd(), "..", "inst", "unitTests" )
+ 	} else {
+ 		path <- system.file( package=pkg, "unitTests" )
+ 	}
+ 
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 	##  fail on warnings (needed for SNPchip() test)
+ 	##options(warn=2)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ 	if( is.null( patt ) || nchar( patt ) == 0 ) {
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     dirs=path,
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	} else {
+ 		##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 					     dirs=path )
+ 	}
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "SNPchip"

$getwd
[1] "C:/Users/biocbuild/bbs-3.8-bioc/meat/SNPchip.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.8-bioc/R/library/SNPchip/unitTests"

Welcome to SNPchip version 2.28.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Sat Apr 13 05:43:03 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SNPchip unit testing - 0 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
   7.01    0.37    7.37