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Package 189/479HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.15.0
David Henderson
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneticsPed
Version: 1.15.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GeneticsPed_1.15.0.tar.gz
StartedAt: 2011-07-07 01:56:24 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:57:17 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 53.6 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.15.0'
* 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 installed package size ... 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 ... NOTE
Package(s) unavailable to check Rd xrefs: 'kinship'
* 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 ... NOTE
'library' or 'require' call not declared from: 'gtools'
* 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 examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'RUnit'
* 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

GeneticsPed.Rcheck/00install.out:

* installing *source* package 'GeneticsPed' ...
** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c ainverse.cc -o ainverse.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c eibd.cc -o eibd.o
gfortran      -O3  -c ggmatmult.f -o ggmatmult.o
gfortran      -O3  -c gpi.f -o gpi.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c inbreed.cc -o inbreed.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c meuwissen.cc -o meuwissen.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c pedSort.cc -o pedSort.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c register.cc -o register.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c sargolzaei.c -o sargolzaei.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c sortped.cc -o sortped.o
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 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs/i386
** R
** data
** inst
** preparing package for lazy loading
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(s) are masked from 'package:stats':

    nobs

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 ...
*** tangling vignette sources ...
   '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
TDT0.020.020.15
check0.050.000.05
datasets0.010.000.02
extend0.110.000.11
family0.030.000.03
founder000
geneContribution0.060.010.08
generatePedigree0.060.000.06
generation0.070.000.07
gpi000
gpiUtil0.010.000.01
inbreeding0.060.000.06
model.matrix0.020.000.02
nIndividual000
pedigree0.020.000.01
prune0.040.000.05
relationshipAdditive0.060.000.14
removeIndividual0.020.000.02
sort.pedigree0.030.000.03
summary.pedigree0.020.000.01