[GenABEL-dev] Problems installing VariABEL

[MATIKA Oswald]

Dear All,
Please find below the error message received when we  tried to install VariAble:

[root at ris-vlx01 pkg]# /usr/local/shared_bin/R/R-2.13.0/ES5-64/bin/R CMD INSTALL VariABEL
* installing to library '/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/library'
* installing *source* package 'VariABEL' ...
** libs
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c AbstractMatrix.cpp -o AbstractMatrix.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c AbstractMatrix_R.cpp -o AbstractMatrix_R.o
CastUtils.h: In function 'void performCast(void*, DT&, int, bool&) [with DT = double]':
AbstractMatrix.h:27:   instantiated from 'void AbstractMatrix::writeVariableAs(long unsigned int, DT*) [with DT = double]'
AbstractMatrix_R.cpp:388:   instantiated from here
CastUtils.h:92: warning: converting to 'short unsigned int' from 'double'
CastUtils.h:95: warning: converting to 'short int' from 'double'
CastUtils.h:98: warning: converting to 'unsigned int' from 'double'
CastUtils.h:101: warning: converting to 'int' from 'double'
CastUtils.h:110: warning: converting to 'char' from 'double'
CastUtils.h:113: warning: converting to 'unsigned char' from 'double'
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c CastUtils.cpp -o CastUtils.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c FileVector.cpp -o FileVector.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c FilteredMatrix.cpp -o FilteredMatrix.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c FilteredMatrix_R.cpp -o FilteredMatrix_R.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c Logger.cpp -o Logger.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c RealHandlerWrapper.cpp -o RealHandlerWrapper.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c ReusableFileHandle.cpp -o ReusableFileHandle.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c Transposer.cpp -o Transposer.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c convert_util.cpp -o convert_util.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c dautil.cpp -o dautil.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c frutil.cpp -o frutil.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c gtps_container.cpp -o gtps_container.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c inverse_variance_metaanalysis.cpp -o inverse_variance_metaanalysis.o
g++ -I/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/include  -I/usr/local/include   -DCOMPILE_WITH_R -fpic  -g -O2 -c iterator.cpp -o iterator.o
iterator.cpp: In function 'SEXPREC* iterator(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, ...)':
iterator.cpp:222: error: 'va_start' was not declared in this scope
iterator.cpp:224: error: expected primary-expression before ')' token
iterator.cpp:224: error: 'va_arg' was not declared in this scope
iterator.cpp:226: error: 'va_end' was not declared in this scope
CastUtils.h: In function 'void performCast(void*, DT&, int, bool&) [with DT = double]':
AbstractMatrix.h:27:   instantiated from 'void AbstractMatrix::writeVariableAs(long unsigned int, DT*) [with DT = double]'
iterator.cpp:362:   instantiated from here
CastUtils.h:92: warning: converting to 'short unsigned int' from 'double'
CastUtils.h:95: warning: converting to 'short int' from 'double'
CastUtils.h:98: warning: converting to 'unsigned int' from 'double'
CastUtils.h:101: warning: converting to 'int' from 'double'
CastUtils.h:110: warning: converting to 'char' from 'double'
CastUtils.h:113: warning: converting to 'unsigned char' from 'double'
make: *** [iterator.o] Error 1
ERROR: compilation failed for package 'VariABEL'
* removing '/usr/local/shared_bin/R/R-2.13.0/ES5-64/lib64/R/library/VariABEL'


We do have gsl-1.13 installed and its lib directory is in LD_LIBRARY_PATH


Any help will be appreciated.

Thanks,

Ozzie





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