[GenABEL-dev] Problems installing VariABEL
L.C. Karssen
l.karssen at erasmusmc.nl
Tue Jun 21 16:53:34 CEST 2011
Dear Ozzie,
I noticed you brought this up on the GenABEL forum as well [1]. Let's
have further discussion there, so that more people can benefit from it.
Regards,
Lennart Karssen.
[1] http://forum.genabel.org/viewtopic.php?f=6&t=478&p=744#p744
On Tue, 2011-06-21 at 15:01 +0100, MATIKA Oswald wrote:
> 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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--
-----------------------------------------------
L.C. Karssen
Erasmus MC
Department of Epidemiology
Room Ee2224
Postbus 2040
3000 CA Rotterdam
The Netherlands
phone: +31-10-7044217
fax: +31-10-7044657
email: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
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