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GeneticsPed.Rcheck/tests_i386/doRUnit.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.
> ### doRUnit.R
> ###------------------------------------------------------------------------
> ### What: Run unit tests with RUnit
> ### $Id$
> ### Time-stamp: <2007-04-19 00:32:42 ggorjan>
> ###------------------------------------------------------------------------
>
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "GeneticsPed"
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ 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)
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ 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=""))
+
+ ## Report to HTML file
+ ## NOTE from H. Pages from the Gentleman Lab (Oct 16,
+ ## 2008): I've added the test below because printHTMLProtocol() seems
+ ## to be broken in RUnit 0.4.19 on the OS X platform.
+ if (substring(R.Version()$os, 1, 6) != "darwin")
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$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] "GeneticsPed"
$getwd
[1] "C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/GeneticsPed/unitTests"
Loading required package: MASS
Attaching package: 'GeneticsPed'
The following object is masked from 'package:stats':
family
Executing test function test.extend ... done successfully.
Executing test function test.A ... done successfully.
Executing test function test.F ... done successfully.
Executing test function test.Z ... done successfully.
Executing test function test.gpLong2Wide ... Error in gpLong2Wide(x = 1) : 'x' must be a data.frame
Error in gpLong2Wide(x = tmp, id = 2, genotype = "gen", prob = "pro") :
'id', 'genotype', and 'prob' must be character
Error in gpLong2Wide(x = tmp, id = "id", genotype = "gen", prob = "pro") :
'id', 'genotype', and 'prob' must be column names of 'x'
Error in gpLong2Wide(x = tmp, id = "ind", genotype = "gen", prob = "pro") :
'x' must be of a genotype class
Loading required package: genetics
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
done successfully.
Executing test function test.gpi ... Error in gpi(gp = -1, hwp = 0.5) :
probabilities should lie on interval 0, 1
Error in gpi(gp = 0.5, hwp = 5) :
probabilities should lie on interval 0, 1
Error in gpi(gp = "0.5", hwp = 0.2) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = 0.5, hwp = list(0.2)) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = matrix("0.5"), hwp = 0.2) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = gp, hwp = gp[, 1, drop = FALSE]) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5), hwp = gp[, 1, drop = FALSE]) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5), hwp = c(0.1)) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5, 0.2, 0), hwp = c(0.1, 0.6, 0.1, 0.1)) :
nonconformant dimensions of 'gp':
no. dimensions (k)= 4
no. alleles (n) = 2.70156211871642
k = n*(n + 1))/2 - 1?
done successfully.
Executing test function test.hwp ... Error in hwp(x = "A/A") : 'x' must be of a genotype class
done successfully.
Executing test function test.Pedigree ... Error in Pedigree(x = Mrode3.1, subject = "calf", ascendant = c("sire", :
values of 'ascendantSex' must accord with values of 'sex' column
done successfully.
Executing test function test.prune ... done successfully.
Executing test function test.TODO ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Wed Oct 16 03:57:51 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneticsPed unit testing - 10 test functions, 0 errors, 0 failures
>
> ###------------------------------------------------------------------------
> ### doRUnit.R ends here
>
> proc.time()
user system elapsed
0.59 0.20 1.67
|
GeneticsPed.Rcheck/tests_x64/doRUnit.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.
> ### doRUnit.R
> ###------------------------------------------------------------------------
> ### What: Run unit tests with RUnit
> ### $Id$
> ### Time-stamp: <2007-04-19 00:32:42 ggorjan>
> ###------------------------------------------------------------------------
>
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "GeneticsPed"
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ 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)
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ 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=""))
+
+ ## Report to HTML file
+ ## NOTE from H. Pages from the Gentleman Lab (Oct 16,
+ ## 2008): I've added the test below because printHTMLProtocol() seems
+ ## to be broken in RUnit 0.4.19 on the OS X platform.
+ if (substring(R.Version()$os, 1, 6) != "darwin")
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$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] "GeneticsPed"
$getwd
[1] "C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/GeneticsPed/unitTests"
Loading required package: MASS
Attaching package: 'GeneticsPed'
The following object is masked from 'package:stats':
family
Executing test function test.extend ... done successfully.
Executing test function test.A ... done successfully.
Executing test function test.F ... done successfully.
Executing test function test.Z ... done successfully.
Executing test function test.gpLong2Wide ... Error in gpLong2Wide(x = 1) : 'x' must be a data.frame
Error in gpLong2Wide(x = tmp, id = 2, genotype = "gen", prob = "pro") :
'id', 'genotype', and 'prob' must be character
Error in gpLong2Wide(x = tmp, id = "id", genotype = "gen", prob = "pro") :
'id', 'genotype', and 'prob' must be column names of 'x'
Error in gpLong2Wide(x = tmp, id = "ind", genotype = "gen", prob = "pro") :
'x' must be of a genotype class
Loading required package: genetics
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
done successfully.
Executing test function test.gpi ... Error in gpi(gp = -1, hwp = 0.5) :
probabilities should lie on interval 0, 1
Error in gpi(gp = 0.5, hwp = 5) :
probabilities should lie on interval 0, 1
Error in gpi(gp = "0.5", hwp = 0.2) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = 0.5, hwp = list(0.2)) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = matrix("0.5"), hwp = 0.2) :
'gp' and 'hwp' must be numeric vector or matrix
Error in gpi(gp = gp, hwp = gp[, 1, drop = FALSE]) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5), hwp = gp[, 1, drop = FALSE]) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5), hwp = c(0.1)) :
'gp' and 'hwp' must be of the same dimension
Error in gpi(gp = c(0.1, 0.5, 0.2, 0), hwp = c(0.1, 0.6, 0.1, 0.1)) :
nonconformant dimensions of 'gp':
no. dimensions (k)= 4
no. alleles (n) = 2.70156211871642
k = n*(n + 1))/2 - 1?
done successfully.
Executing test function test.hwp ... Error in hwp(x = "A/A") : 'x' must be of a genotype class
done successfully.
Executing test function test.Pedigree ... Error in Pedigree(x = Mrode3.1, subject = "calf", ascendant = c("sire", :
values of 'ascendantSex' must accord with values of 'sex' column
done successfully.
Executing test function test.prune ... done successfully.
Executing test function test.TODO ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Wed Oct 16 03:57:53 2019
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
GeneticsPed unit testing - 10 test functions, 0 errors, 0 failures
>
> ###------------------------------------------------------------------------
> ### doRUnit.R ends here
>
> proc.time()
user system elapsed
0.57 0.15 1.26
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