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Package 153/389HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.10.0
David Henderson
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GeneticsPed
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneticsPed
Version: 1.10.0
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneticsPed_1.10.0.tar.gz
StartedAt: 2010-10-04 16:59:18 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:00:13 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 54.3 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsPed' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

GeneticsPed.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'GeneticsPed' ...
** libs
  making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c ainverse.cc -o ainverse.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c eibd.cc -o eibd.o
x86_64-w64-mingw32-gfortran     -O2  -c ggmatmult.f -o ggmatmult.o
x86_64-w64-mingw32-gfortran     -O2  -c gpi.f -o gpi.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c inbreed.cc -o inbreed.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c meuwissen.cc -o meuwissen.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c pedSort.cc -o pedSort.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c register.cc -o register.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c sargolzaei.c -o sargolzaei.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c sortped.cc -o sortped.o
x86_64-w64-mingw32-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 -lgfortran -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/x64
  ... done
** R
** data
** inst
** preparing package for lazy loading
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: combinat

Attaching package: 'combinat'

The following object(s) are masked from 'package:utils':

    combn

Loading required package: gtools
Loading required package: MASS
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 object(s) are masked from 'package:base':

    %in%, as.factor, order

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneticsPed)

GeneticsPed.Rcheck/GeneticsPed-Ex.timings:

nameusersystemelapsed
TDT0.030.000.06
check0.060.000.06
datasets0.020.010.04
extend0.140.000.14
family0.050.000.04
founder0.010.000.02
geneContribution0.140.000.14
generatePedigree0.080.000.08
generation0.090.000.09
gpi000
gpiUtil0.020.000.02
inbreeding0.090.020.11
model.matrix0.020.000.01
nIndividual000
pedigree000
prune0.060.000.06
relationshipAdditive0.110.020.12
removeIndividual0.030.000.04
sort.pedigree0.030.000.03
summary.pedigree0.020.000.01