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Package 107/294HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsBase 1.8.0
The R Genetics Project
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/GeneticsBase
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: GeneticsBase
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes GeneticsBase_1.8.0.tar.gz
StartedAt: 2009-04-18 17:28:24 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:30:06 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 102.0 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsBase.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsBase' 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 ... NOTE
plot,LD: no visible binding for global variable 'y'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating GeneticsBase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
  Running 'ExampleScript001.R'
  Running 'test.R'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsBase-manual.tex ... OK
* checking GeneticsBase-manual.tex using pdflatex ... OK

GeneticsBase.Rcheck/00install.out:

* Installing *source* package 'GeneticsBase' ...
** libs
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:157: warning: control reaches end of non-void function
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:157: warning: control reaches end of non-void function
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:157: warning: control reaches end of non-void function
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o   -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:157: warning: control reaches end of non-void function
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: combinat

Attaching package: 'combinat'


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

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Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
** help
 >>> Building/Updating help pages for package 'GeneticsBase'
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** building package indices ...
Loading required package: methods
Loading required package: combinat

Attaching package: 'combinat'


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

	 combn 

Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
* DONE (GeneticsBase)