GeneticsBase 1.15.0
The R Genetics Project
| Snapshot Date: 2010-10-14 23:20:14 -0700 (Thu, 14 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsBase | | Last Changed Rev: 48595 / Revision: 50215 | | Last Changed Date: 2010-07-30 10:44:04 -0700 (Fri, 30 Jul 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | ERROR | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | [ ERROR ] | skipped | skipped |
* checking for file ‘GeneticsBase/DESCRIPTION’ ... OK
* preparing ‘GeneticsBase’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
-----------------------------------
* installing *source* package ‘GeneticsBase’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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:157: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function ‘SEXPREC* finalizeBitArrayVector(SEXPREC*)’:
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c bAV.cpp -o bAV.o
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int, unsigned int)’:
bAV.cpp:43: warning: comparison between signed and unsigned integer expressions
bAV.cpp:50: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)’:
bAV.cpp:89: warning: comparison between signed and unsigned integer expressions
bAV.cpp:93: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)’:
bAV.cpp:110: warning: comparison between signed and unsigned integer expressions
bAV.cpp:114: warning: comparison between signed and unsigned integer expressions
bAV.cpp:119: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)’:
bAV.cpp:136: warning: comparison between signed and unsigned integer expressions
bAV.cpp:140: warning: comparison between signed and unsigned integer expressions
bAV.cpp:145: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)’:
bAV.cpp:165: warning: comparison between signed and unsigned integer expressions
bAV.cpp:169: warning: comparison between signed and unsigned integer expressions
bAV.cpp:174: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)’:
bAV.cpp:191: warning: comparison between signed and unsigned integer expressions
bAV.cpp:194: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)’:
bAV.cpp:210: warning: comparison between signed and unsigned integer expressions
bAV.cpp:214: warning: comparison between signed and unsigned integer expressions
bAV.cpp:219: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)’:
bAV.cpp:247: warning: comparison between signed and unsigned integer expressions
bAV.cpp:253: warning: comparison between signed and unsigned integer expressions
bAV.cpp:258: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)’:
bAV.cpp:285: warning: comparison between signed and unsigned integer expressions
bAV.cpp:292: warning: comparison between signed and unsigned integer expressions
bAV.cpp:297: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)’:
bAV.cpp:321: warning: comparison between signed and unsigned integer expressions
bAV.cpp:327: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In member function ‘unsigned int bitArrayVector::getElement(unsigned int, bool)’:
bAV.cpp:347: warning: unused variable ‘mask’
bAV.cpp: In member function ‘void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)’:
bAV.cpp:463: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In function ‘int main()’:
bAV.cpp:858: warning: comparison between signed and unsigned integer expressions
bAV.cpp:867: warning: comparison between signed and unsigned integer expressions
bAV.cpp:984: warning: comparison between signed and unsigned integer expressions
bAV.cpp:1012: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/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:43: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:50: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:89: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:93: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:110: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:114: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:119: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:136: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:140: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)’:
bitArrayVector.cpp:165: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:169: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:174: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)’:
bitArrayVector.cpp:191: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:194: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:210: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:214: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:219: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)’:
bitArrayVector.cpp:247: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:253: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:258: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)’:
bitArrayVector.cpp:285: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:292: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:297: 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:321: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:327: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function ‘unsigned int bitArrayVector::getElement(unsigned int, bool)’:
bitArrayVector.cpp:347: warning: unused variable ‘mask’
bitArrayVector.cpp: In member function ‘void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:463: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function ‘int main()’:
bitArrayVector.cpp:858: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:867: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:984: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1012: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++ -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 bAV.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: duplicate symbol _main in bitArrayVector.o and bAV.o
collect2: ld returned 1 exit status
make: *** [GeneticsBase.so] Error 1
ERROR: compilation failed for package ‘GeneticsBase’
* removing ‘/private/tmp/RtmpUYnqEv/Rinst33f527f4/GeneticsBase’
-----------------------------------
ERROR: Installation failed
Removing installation dir