David Henderson
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneticsPed |
| Branch: master |
| Last Commit: 7f7dabf |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:55:41 -0400 (Tue, 09 Apr 2019).
| Package 635/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneticsPed 1.45.0 David Henderson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: GeneticsPed |
| Version: 1.45.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneticsPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneticsPed_1.45.0.tar.gz |
| StartedAt: 2019-04-09 02:59:11 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:00:08 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 56.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneticsPed.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneticsPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneticsPed_1.45.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.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 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.45.0'
* 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 'GeneticsPed' 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
summary.Pedigree
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generatePedigree: no visible global function definition for 'runif'
model.matrix.Pedigree: no visible global function definition for
'model.matrix'
writeMendel: no visible global function definition for '?'
writeMendel: no visible global function definition for 'write.csv'
Undefined global functions or variables:
? model.matrix runif write.csv
Consider adding
importFrom("stats", "model.matrix", "runif")
importFrom("utils", "?", "write.csv")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... 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 '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-3.9-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details.
GeneticsPed.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/GeneticsPed_1.45.0.tar.gz && rm -rf GeneticsPed.buildbin-libdir && mkdir GeneticsPed.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneticsPed.buildbin-libdir GeneticsPed_1.45.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneticsPed_1.45.0.zip && rm GeneticsPed_1.45.0.tar.gz GeneticsPed_1.45.0.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 68714 100 68714 0 0 1197k 0 --:--:-- --:--:-- --:--:-- 1369k
install for i386
* installing *source* package 'GeneticsPed' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ainverse.cc -o ainverse.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c eibd.cc -o eibd.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c ggmatmult.f -o ggmatmult.o
C:/Rtools/mingw_32/bin/gfortran -O3 -mtune=generic -c gpi.f -o gpi.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inbreed.cc -o inbreed.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inverseAdditive.cc -o inverseAdditive.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meuwissen.cc -o meuwissen.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pedSort.cc -o pedSort.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pedtemplate.cc -o pedtemplate.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c register.cc -o register.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sargolzaei.c -o sargolzaei.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sortped.cc -o sortped.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GeneticsPed.dll tmp.def ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.buildbin-libdir/00LOCK-GeneticsPed/00new/GeneticsPed/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneticsPed'
finding HTML links ... done
TDT html
check html
datasets html
extend html
family html
founder html
geneContribution html
generatePedigree html
generation html
gpi html
gpiUtil html
inbreeding html
model.matrix html
nIndividual html
pedigree html
prune html
relationshipAdditive html
removeIndividual html
sort.pedigree html
summary.pedigree html
undocumented 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 'GeneticsPed' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c ainverse.cc -o ainverse.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c eibd.cc -o eibd.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c ggmatmult.f -o ggmatmult.o
C:/Rtools/mingw_64/bin/gfortran -O2 -mtune=generic -c gpi.f -o gpi.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inbreed.cc -o inbreed.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c inverseAdditive.cc -o inverseAdditive.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c meuwissen.cc -o meuwissen.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pedSort.cc -o pedSort.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c pedtemplate.cc -o pedtemplate.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c register.cc -o register.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sargolzaei.c -o sargolzaei.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c sortped.cc -o sortped.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GeneticsPed.dll tmp.def ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneticsPed.buildbin-libdir/GeneticsPed/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneticsPed' as GeneticsPed_1.45.0.zip
* DONE (GeneticsPed)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneticsPed' successfully unpacked and MD5 sums checked
|
GeneticsPed.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.
> ### 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 <[email protected]> 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 -- Tue Apr 09 03:00:01 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
0.62 0.21 1.92
|
GeneticsPed.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.
> ### 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 <[email protected]> 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 -- Tue Apr 09 03:00:02 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
0.65 0.17 1.46
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GeneticsPed.Rcheck/examples_i386/GeneticsPed-Ex.timings
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GeneticsPed.Rcheck/examples_x64/GeneticsPed-Ex.timings
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