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Package 242/609HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.20.0
David Henderson
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/GeneticsPed
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GeneticsPed
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneticsPed_1.20.0.tar.gz
StartedAt: 2013-03-24 23:41:30 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:42:16 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 46.4 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.20.0'
* 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 whether package 'GeneticsPed' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated 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
gpLong2Wide: warning in expectedGenotypes(allele = allele.names(x[,
  genotype])): partial argument match of 'allele' to 'alleles'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.Pedigree':
  'summary.Pedigree'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details.

GeneticsPed.Rcheck/00install.out:

* installing *source* package 'GeneticsPed' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c ainverse.cc -o ainverse.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c eibd.cc -o eibd.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c ggmatmult.f -o ggmatmult.o
gfortran -arch i386   -fPIC  -g -O2 -Wall -pedantic  -c gpi.f -o gpi.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c inbreed.cc -o inbreed.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c inverseAdditive.cc -o inverseAdditive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c meuwissen.cc -o meuwissen.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c pedSort.cc -o pedSort.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c pedtemplate.cc -o pedtemplate.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c register.cc -o register.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c sargolzaei.c -o sargolzaei.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c sortped.cc -o sortped.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/i386
** R
** data
** inst
** preparing package for lazy loading

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.

** help
*** installing help indices
** building package indices
** installing vignettes
   'geneticRelatedness.Rnw' 
   'pedigreeHandling.Rnw' 
   'quanGenAnimalModel.Rnw' 
** testing if installed package can be loaded

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.


* DONE (GeneticsPed)

GeneticsPed.Rcheck/GeneticsPed-Ex.timings:

nameusersystemelapsed
TDT0.0430.0070.050
check0.0440.0030.048
datasets0.0170.0020.019
extend0.1260.0340.161
family0.0320.0010.033
founder0.0040.0010.005
geneContribution0.0760.0020.078
generatePedigree0.0470.0400.088
generation0.0550.0020.057
gpi0.0040.0020.005
gpiUtil0.0130.0000.013
inbreeding0.0860.0030.088
model.matrix0.0150.0010.016
nIndividual0.0020.0000.003
pedigree0.0040.0010.006
prune0.0400.0040.044
relationshipAdditive0.0930.0020.096
removeIndividual0.0150.0010.015
sort.pedigree0.0220.0030.025
summary.pedigree0.0050.0000.005