GeneticsBase 1.15.1
The R Genetics Project
| Snapshot Date: 2011-04-03 11:16:35 -0700 (Sun, 03 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsBase | | Last Changed Rev: 51561 / Revision: 54396 | | Last Changed Date: 2010-12-15 15:12:44 -0800 (Wed, 15 Dec 2010) |
| lamb1 | Linux (openSUSE 11.3) / 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
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function ‘SEXPREC* finalizeBitArrayVector(SEXPREC*)’:
R_bitArrayVector.cpp:36:3: warning: no return statement in function returning non-void
R_bitArrayVector.cpp: In function ‘int test()’:
R_bitArrayVector.cpp:145:28: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp:157:1: warning: no return statement in function returning non-void
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bAV.cpp -o bAV.o
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int, unsigned int)’:
bAV.cpp:43:17: warning: comparison between signed and unsigned integer expressions
bAV.cpp:50:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)’:
bAV.cpp:89:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:93:18: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)’:
bAV.cpp:110:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:114:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:119:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)’:
bAV.cpp:136:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:140:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:145:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)’:
bAV.cpp:165:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:169:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:174:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)’:
bAV.cpp:191:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:194:18: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)’:
bAV.cpp:210:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:214:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:219:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)’:
bAV.cpp:247:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:253:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:258:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)’:
bAV.cpp:285:15: warning: comparison between signed and unsigned integer expressions
bAV.cpp:292:31: warning: comparison between signed and unsigned integer expressions
bAV.cpp:297:20: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::vector<unsigned int>&, unsigned int, unsigned int, bool)’:
bAV.cpp:321:30: warning: comparison between signed and unsigned integer expressions
bAV.cpp:327:30: warning: comparison between signed and unsigned integer expressions
bAV.cpp: In member function ‘unsigned int bitArrayVector::getElement(unsigned int, bool)’:
bAV.cpp:347:43: warning: unused variable ‘mask’
bAV.cpp: In member function ‘void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)’:
bAV.cpp:463:18: warning: comparison between signed and unsigned integer expressions
bAV.cpp:550:34: warning: suggest parentheses around ‘-’ inside ‘<<’
bAV.cpp:551:34: warning: suggest parentheses around ‘-’ inside ‘<<’
bAV.cpp: In function ‘int main()’:
bAV.cpp:858:18: warning: comparison between signed and unsigned integer expressions
bAV.cpp:867:18: warning: comparison between signed and unsigned integer expressions
bAV.cpp:984:35: warning: comparison between signed and unsigned integer expressions
bAV.cpp:1012:41: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int, unsigned int)’:
bitArrayVector.cpp:43:17: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:50:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:89:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:93:18: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:110:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:114:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:119:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:136:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:140:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:145:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)’:
bitArrayVector.cpp:165:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:169:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:174:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)’:
bitArrayVector.cpp:191:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:194:18: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:210:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:214:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:219:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)’:
bitArrayVector.cpp:247:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:253:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:258:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)’:
bitArrayVector.cpp:285:15: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:292:31: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:297:20: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor ‘bitArrayVector::bitArrayVector(std::vector<unsigned int>&, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:321:30: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:327:30: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function ‘unsigned int bitArrayVector::getElement(unsigned int, bool)’:
bitArrayVector.cpp:347:43: warning: unused variable ‘mask’
bitArrayVector.cpp: In member function ‘void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)’:
bitArrayVector.cpp:463:18: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:550:34: warning: suggest parentheses around ‘-’ inside ‘<<’
bitArrayVector.cpp:551:34: warning: suggest parentheses around ‘-’ inside ‘<<’
bitArrayVector.cpp: In function ‘int main()’:
bitArrayVector.cpp:858:18: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:867:18: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:984:35: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1012:41: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c convert.cpp -o convert.o
convert.cpp:1:2: warning: #import is a deprecated GCC extension
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c register.cpp -o register.o
g++ -shared -L/usr/local/lib64 -o GeneticsBase.so LdMax.o R_bitArrayVector.o bAV.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
bitArrayVector.o: In function `main':
/tmp/Rtmp4sNqO0/Rbuild51dcce63/GeneticsBase/src/bitArrayVector.cpp:772: multiple definition of `main'
bAV.o:/tmp/Rtmp4sNqO0/Rbuild51dcce63/GeneticsBase/src/bAV.cpp:814: first defined here
collect2: ld returned 1 exit status
make: *** [GeneticsBase.so] Error 1
ERROR: compilation failed for package ‘GeneticsBase’
* removing ‘/tmp/Rtmp4sNqO0/Rinst5ee1264c/GeneticsBase’
-----------------------------------
ERROR: package installation failed