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Package 265/671HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.22.0
David Henderson
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GeneticsPed
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GeneticsPed
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneticsPed_1.22.0.tar.gz
StartedAt: 2013-05-01 05:54:47 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:55:38 -0700 (Wed, 01 May 2013)
EllapsedTime: 50.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.22.0'
* 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 ... [9s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [2s/2s]
 [3s/3s] 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck/00check.log'
for details.

GeneticsPed.Rcheck/00install.out:

* installing *source* package 'GeneticsPed' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ainverse.cc -o ainverse.o
In file included from ainverse.cc:9:
./../include/ainverse.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
In file included from ainverse.cc:9:
In file included from ./../include/ainverse.h:21:
./../include/eibd.h:72:39: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int GetLength() { return eibd.size(); }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
In file included from ainverse.cc:9:
In file included from ./../include/ainverse.h:22:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
In file included from ainverse.cc:9:
In file included from ./../include/ainverse.h:23:
In file included from ./../include/inbreed.h:21:
./../include/math_utilities.h:160:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ser += coef[ i ] / ++y;
           ˜˜˜˜  ^
ainverse.cc:25:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  EIBD.SetPedNumber( TNumAn );
  ˜˜˜˜               ^˜˜˜˜˜
ainverse.cc:39:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    EIBD.IncrValue( Dii , GetIndex( 0 , row , row , TNumAn ) , row , row );
                          ˜˜˜˜˜˜˜˜      ^˜˜
ainverse.cc:39:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    EIBD.IncrValue( Dii , GetIndex( 0 , row , row , TNumAn ) , row , row );
                          ˜˜˜˜˜˜˜˜            ^˜˜
ainverse.cc:39:53: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    EIBD.IncrValue( Dii , GetIndex( 0 , row , row , TNumAn ) , row , row );
                          ˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
ainverse.cc:39:64: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    EIBD.IncrValue( Dii , GetIndex( 0 , row , row , TNumAn ) , row , row );
    ˜˜˜˜                                                       ^˜˜
ainverse.cc:39:70: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    EIBD.IncrValue( Dii , GetIndex( 0 , row , row , TNumAn ) , row , row );
    ˜˜˜˜                                                             ^˜˜
ainverse.cc:44:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        col = Ped.GetParentIndex( parent , row );
            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ainverse.cc:46:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        Pcol = Ped.GetParentIndex( mate , row );
             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ainverse.cc:49:54: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        EIBD.IncrValue( coeff1 , GetIndex( 0 , col , row , TNumAn ) , col , row );
                                 ˜˜˜˜˜˜˜˜            ^˜˜
ainverse.cc:49:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        EIBD.IncrValue( coeff1 , GetIndex( 0 , col , row , TNumAn ) , col , row );
                                 ˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
ainverse.cc:49:77: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        EIBD.IncrValue( coeff1 , GetIndex( 0 , col , row , TNumAn ) , col , row );
        ˜˜˜˜                                                                ^˜˜
ainverse.cc:50:60: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        EIBD.IncrValue( coeff2 , GetIndex( 0 , col , col , TNumAn ) , col , col );
                                 ˜˜˜˜˜˜˜˜                  ^˜˜˜˜˜
ainverse.cc:53:63: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
          EIBD.IncrValue( coeff2 , GetIndex( 0 , Pcol , col , TNumAn ) , Pcol , col );
                                   ˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜
ainverse.cc:66:36: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  int index = 0, cindex = 0, max = GetIndex( 0 , EIBD.GetPedNumber() , EIBD.GetPedNumber() , EIBD.GetPedNumber() );
                             ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ainverse.cc:69:14: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    cindex = EIBD.GetNextCol( index );
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ainverse.cc:69:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    cindex = EIBD.GetNextCol( index );
             ˜˜˜˜             ^˜˜˜˜
ainverse.cc:70:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    index = EIBD.GetNext( index );
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ainverse.cc:70:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = EIBD.GetNext( index );
            ˜˜˜˜          ^˜˜˜˜
ainverse.cc:113:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , row1 );
            ˜˜˜˜˜˜˜˜      ^˜˜˜
ainverse.cc:113:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , row1 );
            ˜˜˜˜˜˜˜˜             ^˜˜˜
ainverse.cc:117:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , col1 );
            ˜˜˜˜˜˜˜˜      ^˜˜˜
ainverse.cc:117:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , col1 );
            ˜˜˜˜˜˜˜˜             ^˜˜˜
ainverse.cc:141:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , row1 , k );
            ˜˜˜˜˜˜˜˜      ^˜˜˜
ainverse.cc:141:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , row1 , k );
            ˜˜˜˜˜˜˜˜             ^˜˜˜
ainverse.cc:141:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , row1 , k );
            ˜˜˜˜˜˜˜˜                    ^
ainverse.cc:145:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , col1 , k );
            ˜˜˜˜˜˜˜˜      ^˜˜˜
ainverse.cc:145:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , col1 , k );
            ˜˜˜˜˜˜˜˜             ^˜˜˜
ainverse.cc:145:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    index = GetIndex( 1 , row1 , col1 , k );
            ˜˜˜˜˜˜˜˜                    ^
33 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c eibd.cc -o eibd.o
In file included from eibd.cc:15:
./../include/eibd.h:19:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
./../include/eibd.h:72:39: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int GetLength() { return eibd.size(); }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
eibd.cc:300:15: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    int col = e->second.GetCol(), row = e->second.GetRow();
        ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
eibd.cc:300:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    int col = e->second.GetCol(), row = e->second.GetRow();
                                  ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
eibd.cc:303:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[col * pednumber + row] = e->second.GetValue();
        ^˜˜ ˜
eibd.cc:303:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[col * pednumber + row] = e->second.GetValue();
                        ˜ ^˜˜
eibd.cc:307:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[col * pednumber + row] = e->second.GetValue();
        ^˜˜ ˜
eibd.cc:307:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[col * pednumber + row] = e->second.GetValue();
                        ˜ ^˜˜
eibd.cc:308:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[row * pednumber + col] = e->second.GetValue();
        ^˜˜ ˜
eibd.cc:308:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      f[row * pednumber + col] = e->second.GetValue();
                        ˜ ^˜˜
10 warnings generated.
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c ggmatmult.f -o ggmatmult.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -pedantic  -c gpi.f -o gpi.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inbreed.cc -o inbreed.o
In file included from inbreed.cc:10:
./../include/inbreed.h:14:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
In file included from inbreed.cc:10:
In file included from ./../include/inbreed.h:20:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
In file included from inbreed.cc:10:
In file included from ./../include/inbreed.h:21:
./../include/math_utilities.h:160:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ser += coef[ i ] / ++y;
           ˜˜˜˜  ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c inverseAdditive.cc -o inverseAdditive.o
In file included from inverseAdditive.cc:8:
In file included from ./../include/ainverse.h:21:
./../include/eibd.h:72:39: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int GetLength() { return eibd.size(); }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
In file included from inverseAdditive.cc:8:
In file included from ./../include/ainverse.h:22:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
In file included from inverseAdditive.cc:8:
In file included from ./../include/ainverse.h:23:
In file included from ./../include/inbreed.h:21:
./../include/math_utilities.h:160:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ser += coef[ i ] / ++y;
           ˜˜˜˜  ^
inverseAdditive.cc:55:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    idx[i] = Ped.GetSortIndex( i );
             ˜˜˜               ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c meuwissen.cc -o meuwissen.o
In file included from meuwissen.cc:5:
In file included from ./../include/inbreed.h:20:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
In file included from meuwissen.cc:5:
In file included from ./../include/inbreed.h:21:
./../include/math_utilities.h:160:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ser += coef[ i ] / ++y;
           ˜˜˜˜  ^
meuwissen.cc:60:32: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    idx[i] = ped.GetSortIndex( i );
             ˜˜˜               ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c pedSort.cc -o pedSort.o
In file included from pedSort.cc:8:
In file included from ./../include/pedSort.h:21:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
pedSort.cc:61:50: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    ind[i] = const_cast< char* >( Ped.GetMember( i ).c_str() );
                                  ˜˜˜            ^
pedSort.cc:62:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    if ( Ped.GetParent( 0 , i ) )
         ˜˜˜                ^
pedSort.cc:64:75: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      father[i] = const_cast< char* >( Ped.GetMember( Ped.GetParentIndex( i , SIRE ) ).c_str() );
                                                      ˜˜˜                 ^
pedSort.cc:70:29: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
    if ( Ped.GetParent( 0 , i ) )
         ˜˜˜                ^
pedSort.cc:72:75: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      mother[i] = const_cast< char* >( Ped.GetMember( Ped.GetParentIndex( i , DAM ) ).c_str() );
                                                      ˜˜˜                 ^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c pedtemplate.cc -o pedtemplate.o
In file included from pedtemplate.cc:15:
./../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
pedtemplate.cc:470:10: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  return pedigree.size();
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pedtemplate.cc:488:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ( pedigree[i].GetIndex( SIRE ) >= 0 )
         ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:499:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ( pedigree[i].GetIndex( DAM ) >= 0 )
         ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:512:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  return pedigree[i].GetSortIndex();
         ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:519:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return pedigree[i].GetIndex( SIRE );
           ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:523:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return pedigree[i].GetIndex( DAM );
           ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:529:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  return pedigree[i].GetIndex( par );
         ˜˜˜˜˜˜˜˜ ^
pedtemplate.cc:537:12: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
    return p - pedigree.begin();
    ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c register.cc -o register.o
In file included from register.cc:8:
./../include/meuwissen.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
In file included from register.cc:8:
In file included from ./../include/meuwissen.h:9:
In file included from ./../include/../include/inbreed.h:20:
./../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
In file included from register.cc:8:
In file included from ./../include/meuwissen.h:9:
In file included from ./../include/../include/inbreed.h:21:
./../include/math_utilities.h:160:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ser += coef[ i ] / ++y;
           ˜˜˜˜  ^
In file included from register.cc:9:
In file included from ./../include/ainverse.h:21:
./../include/eibd.h:72:39: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32]
    unsigned int GetLength() { return eibd.size(); }
                               ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sargolzaei.c -o sargolzaei.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c sortped.cc -o sortped.o
In file included from sortped.cc:1:
./../include/sortped.h:7:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
In file included from sortped.cc:1:
In file included from ./../include/sortped.h:9:
./../include/../include/pedtemplate.h:18:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
./../include/../include/pedtemplate.h:74:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int IsBase( int i ) { return pedigree[i].IsBase(); }
                                 ˜˜˜˜˜˜˜˜ ^
./../include/../include/pedtemplate.h:84:50: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    string GetMember( int i ) { return pedigree[ i ].ReturnAnimal(); }
                                       ˜˜˜˜˜˜˜˜  ^
sortped.cc:140:22: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
        q->SetIndex( a - all.begin() , SIRE );
        ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sortped.cc:144:24: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
          q->SetIndex( a - all.begin() , DAM );
          ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sortped.cc:181:24: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
          q->SetIndex( a - all.begin() , SIRE );
          ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sortped.cc:207:24: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
          q->SetIndex( a - all.begin() , DAM );
          ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sortped.cc:240:20: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
      o->SetIndex( a - all.begin() , SIRE );
      ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
sortped.cc:245:20: warning: implicit conversion loses integer precision: 'typename __normal_iterator<TPed *, vector<TPed, allocator<TPed> > >::difference_type' (aka 'long') to 'int' [-Wshorten-64-to-32]
      o->SetIndex( a - all.begin() , DAM );
      ˜            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
10 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneticsPed.Rcheck/GeneticsPed/libs
** 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
** 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
TDT0.0820.0050.088
check0.1580.0050.165
datasets0.0400.0030.043
extend0.1780.0130.191
family0.0690.0030.073
founder0.0170.0000.018
geneContribution0.1010.0040.109
generatePedigree0.0730.0510.125
generation0.0850.0020.086
gpi0.0610.0030.067
gpiUtil0.0210.0020.023
inbreeding0.1370.0040.144
model.matrix0.0280.0020.030
nIndividual0.0160.0010.017
pedigree0.0200.0020.024
prune0.1130.0030.118
relationshipAdditive0.1640.0040.174
removeIndividual0.0310.0020.034
sort.pedigree0.0510.0060.059
summary.pedigree0.0130.0010.015