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CHECK report for GeneticsPed on merida1

This page was generated on 2019-04-16 11:54:38 -0400 (Tue, 16 Apr 2019).

Package 613/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneticsPed 1.44.0
David Henderson
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneticsPed
Branch: RELEASE_3_8
Last Commit: 2af303a
Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneticsPed
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneticsPed.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneticsPed_1.44.0.tar.gz
StartedAt: 2019-04-16 00:10:49 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:11:23 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 33.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneticsPed.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneticsPed_1.44.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneticsPed.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneticsPed/DESCRIPTION’ ... OK
* this is package ‘GeneticsPed’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... 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
* 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneticsPed.Rcheck/00check.log’
for details.



Installation output

GeneticsPed.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneticsPed
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GeneticsPed’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ainverse.cc -o ainverse.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c eibd.cc -o eibd.o
gfortran   -fPIC  -g -O2  -c ggmatmult.f -o ggmatmult.o
gfortran   -fPIC  -g -O2  -c gpi.f -o gpi.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inbreed.cc -o inbreed.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inverseAdditive.cc -o inverseAdditive.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c meuwissen.cc -o meuwissen.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pedSort.cc -o pedSort.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pedtemplate.cc -o pedtemplate.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c register.cc -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sargolzaei.c -o sargolzaei.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sortped.cc -o sortped.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GeneticsPed.so ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/GeneticsPed/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneticsPed)

Tests output

GeneticsPed.Rcheck/tests/doRUnit.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 <hpages@fhcrc.org> 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] "/Users/biocbuild/bbs-3.8-bioc/meat/GeneticsPed.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.5/Resources/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 16 00:11:15 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 
  0.866   0.146   0.998 

Example timings

GeneticsPed.Rcheck/GeneticsPed-Ex.timings

nameusersystemelapsed
TDT0.3620.0680.479
check0.0500.0030.054
datasets0.0160.0030.019
extend0.0620.0070.069
family0.0270.0020.029
founder0.0030.0000.003
geneContribution0.0680.0030.071
generatePedigree0.0930.0460.139
generation0.0460.0010.047
gpi0.0120.0020.015
gpiUtil0.3870.0520.448
inbreeding0.1040.0010.105
model.matrix0.0150.0010.016
nIndividual0.0030.0010.004
pedigree0.0070.0010.009
prune0.0290.0010.030
relationshipAdditive0.1020.0040.107
removeIndividual0.0090.0010.010
sort.pedigree0.0220.0030.025
summary.pedigree0.0040.0010.005