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CHECK report for SNPchip on tokay2

This page was generated on 2019-04-09 11:54:58 -0400 (Tue, 09 Apr 2019).

Package 1519/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SNPchip 2.29.0
Robert Scharpf
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SNPchip
Branch: master
Last Commit: effab19
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: SNPchip
Version: 2.29.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPchip.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SNPchip_2.29.0.tar.gz
StartedAt: 2019-04-09 06:03:49 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:07:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 231.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: SNPchip.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SNPchip.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SNPchip_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPchip.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '2.29.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'VanillaICE'
* 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' ... ERROR
Running examples in 'SNPchip-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot
> ### Title: Plot copy number and physical position for a set of genomic
> ###   intervals.
> ### Aliases: xyplot2 xyplot2,formula,gSet-method
> ###   xyplot2,formula,SnpSet-method
> ### Keywords: dplot methods
> 
> ### ** Examples
> 
>   ## simulated data
>   library(oligoClasses)
Welcome to oligoClasses version 1.45.0
>   library(IRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

>   library(VanillaICE)
Error in library(VanillaICE) : there is no package called 'VanillaICE'
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'SNPchip-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot
> ### Title: Plot copy number and physical position for a set of genomic
> ###   intervals.
> ### Aliases: xyplot2 xyplot2,formula,gSet-method
> ###   xyplot2,formula,SnpSet-method
> ### Keywords: dplot methods
> 
> ### ** Examples
> 
>   ## simulated data
>   library(oligoClasses)
Welcome to oligoClasses version 1.45.0
>   library(IRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

>   library(VanillaICE)
Error in library(VanillaICE) : there is no package called 'VanillaICE'
Execution halted
* 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 ERRORs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SNPchip.Rcheck/00check.log'
for details.


Installation output

SNPchip.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SNPchip_2.29.0.tar.gz && rm -rf SNPchip.buildbin-libdir && mkdir SNPchip.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SNPchip.buildbin-libdir SNPchip_2.29.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SNPchip_2.29.0.zip && rm SNPchip_2.29.0.tar.gz SNPchip_2.29.0.zip
###
##############################################################################
##############################################################################


  % 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 37215  100 37215    0     0   562k      0 --:--:-- --:--:-- --:--:--  637k

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 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 'SNPchip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SNPchip' as SNPchip_2.29.0.zip
* DONE (SNPchip)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SNPchip' successfully unpacked and MD5 sums checked

Tests output

SNPchip.Rcheck/tests_i386/doRUnit.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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-3.9-bioc/meat/SNPchip.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPchip/unitTests"

Welcome to SNPchip version 2.29.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr 09 06:07:27 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 
   6.20    0.53    6.71 

SNPchip.Rcheck/tests_x64/doRUnit.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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-3.9-bioc/meat/SNPchip.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/SNPchip/unitTests"

Welcome to SNPchip version 2.29.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr 09 06:07:35 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 
   7.21    0.26    7.46 

Example timings

SNPchip.Rcheck/examples_i386/SNPchip-Ex.timings

nameusersystemelapsed
centromere0.080.000.11
getCytoband0.030.000.13
plotIdiogram0.670.050.76
xypanel000

SNPchip.Rcheck/examples_x64/SNPchip-Ex.timings

nameusersystemelapsed
centromere0.030.020.05
getCytoband0.040.000.03
plotIdiogram0.360.040.41
xypanel000