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 ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneticsPed.buildbin-libdir GeneticsPed_1.22.0.tar.gz'
>>>>>>>
* installing *source* package 'GeneticsPed' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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 -g -O2 -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.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "GeneticsPed.buildbin-libdir/GeneticsPed/libs//GeneticsPed.so"