Package: GeneticsPed

Version: 1.0.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check GeneticsPed_1.0.0.tar.gz

RetCode: 0

Time: 142.9 seconds

Status: OK

CheckDir: GeneticsPed.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.0-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneticsPed' version '1.0.0'
* 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 for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GeneticsPed-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/biocbuild/bbs-2.0-bioc/meat/GeneticsPed.Rcheck/tests'
  Running 'doRUnit.R'
make[1]: Leaving directory `/loc/biocbuild/bbs-2.0-bioc/meat/GeneticsPed.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsPed-manual.tex ... OK
* checking GeneticsPed-manual.tex ... OK

* Installing *source* package 'GeneticsPed' ...
** libs
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c ainverse.cc -o ainverse.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c eibd.cc -o eibd.o
gfortran   -fPIC  -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran   -fPIC  -g -O2 -Wall -c gpi.f -o gpi.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inbreed.cc -o inbreed.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c inverseAdditive.cc -o inverseAdditive.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c meuwissen.cc -o meuwissen.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pedSort.cc -o pedSort.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c pedtemplate.cc -o pedtemplate.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c register.cc -o register.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function 'sargolzaei':
sargolzaei.c:62: warning: statement with no effect
sargolzaei.c:72: warning: 'N' is used uninitialized in this function
sargolzaei.c:19: warning: 'MIP' may be used uninitialized in this function
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c sortped.cc -o sortped.o
g++ -G -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 -lm -lgcc_s -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: gdata
Loading required package: MASS
** help
 >>> Building/Updating help pages for package 'GeneticsPed'
     Formats: text html latex example 
  Mrode                             text    html    latex   example
  TDT                               text    html    latex   example
  check                             text    html    latex   example
  codeUnit                          text    html    latex   example
  extend                            text    html    latex   example
  family                            text    html    latex   example
  founder                           text    html    latex   example
  geneContribution                  text    html    latex   example
  generatePedigree                  text    html    latex   example
  generation                        text    html    latex   example
  gpi                               text    html    latex   example
  inbreeding                        text    html    latex   example
  model.matrix                      text    html    latex   example
  nIndividual                       text    html    latex   example
  pedigree                          text    html    latex   example
  relationshipAdditive              text    html    latex   example
  removeIndividual                  text    html    latex   example
  sort.pedigree                     text    html    latex   example
  summary.pedigree                  text    html    latex   example
  undocumented                      text    html    latex
** building package indices ...
* DONE (GeneticsPed)