Multiple platform build/check report for BioC 3.10 - CHECK report for GeneticsPed on merida1

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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_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/GeneticsPed.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.48.0’
* 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 ... 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/GeneticsPed.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneticsPed
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GeneticsPed’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ainverse.cc -o ainverse.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c eibd.cc -o eibd.o
gfortran  -fPIC  -Wall -g -O2  -c ggmatmult.f -o ggmatmult.o
gfortran  -fPIC  -Wall -g -O2  -c gpi.f -o gpi.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c inbreed.cc -o inbreed.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c inverseAdditive.cc -o inverseAdditive.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c meuwissen.cc -o meuwissen.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pedSort.cc -o pedSort.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pedtemplate.cc -o pedtemplate.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c register.cc -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sargolzaei.c -o sargolzaei.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sortped.cc -o sortped.o
clang++ -std=gnu++11 -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/3.6/Resources/library/00LOCK-GeneticsPed/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneticsPed)

Tests output


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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-3.10-bioc/meat/GeneticsPed.Rcheck/tests"

$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/3.6/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 -- Wed Apr 15 02:35:15 2020 
*********************************************** 
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 
  0.895   0.164   1.042

name	user	system	elapsed
TDT	0.361	0.079	0.455
check	0.039	0.002	0.041
datasets	0.012	0.003	0.015
extend	0.044	0.005	0.049
family	0.025	0.002	0.027
founder	0.005	0.001	0.005
geneContribution	0.055	0.002	0.059
generatePedigree	0.087	0.041	0.128
generation	0.041	0.001	0.042
gpi	0.008	0.001	0.010
gpiUtil	0.351	0.051	0.408
inbreeding	0.095	0.002	0.099
model.matrix	0.010	0.002	0.011
nIndividual	0.002	0.000	0.002
pedigree	0.005	0.001	0.006
prune	0.029	0.001	0.032
relationshipAdditive	0.109	0.005	0.115
removeIndividual	0.011	0.001	0.012
sort.pedigree	0.025	0.003	0.029
summary.pedigree	0.003	0.000	0.003

CHECK report for GeneticsPed on merida1

Summary

Command output

Installation output

Tests output

Example timings