GeneticsBase 1.13.0
The R Genetics Project
| Bioconductor Changelog | | Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsBase | | Last Changed Rev: 42686 / Revision: 43434 | | Last Changed Date: 2009-10-27 16:45:24 -0700 (Tue, 27 Oct 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | [ OK ] | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* 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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -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: 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/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c convert.cpp -o convert.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c register.cpp -o register.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c LdMax.cpp -o LdMax.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c R_bitArrayVector.cpp -o R_bitArrayVector.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c bitArrayVector.cpp -o bitArrayVector.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c convert.cpp -o convert.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c getLDdist.cpp -o getLDdist.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c register.cpp -o register.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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
Attaching package: 'combinat'
The following object(s) are masked from package:utils :
combn
** help
*** installing help indices
** building package indices ...
Reading 2 markers and 901 subjects from ` ALZH.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` ALZH.ped '.
Number of Markers: 2
Number of Subjects: 901
Number of Families: 308
Reading 8 markers and 2011 subjects from ` CAMP.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` CAMP.ped '.
Number of Markers: 8
Number of Subjects: 2011
Number of Families: 651
Reading 12 vars from `CAMPZ.phe' ... Done.
Number of Phenotype Variables: 12
Number of Observations : 2011
Loading file... done.
Number of markers : 29
Number of observations: 1008
Read 95 lines containing 3 Markers from 2 Genes on 33 Samples.
Reading 722 markers and 90 subjects from ` hapmapchr22.ped ' ...
generating 'geneSet' object...
100 200 300 400 500 600 700 Successfully read the pedigree file ` hapmapchr22.ped '.
Number of Markers: 722
Number of Subjects: 90
Number of Families: 20
Reading 53 markers and 3000 subjects from ` qtl.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` qtl.ped '.
Number of Markers: 53
Number of Subjects: 3000
Number of Families: 1000
Reading 1 vars from `qtl.phe' ... Done.
Number of Phenotype Variables: 1
Number of Observations : 1000
Reading 50 markers and 3000 subjects from ` xbat.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` xbat.ped '.
Number of Markers: 50
Number of Subjects: 3000
Number of Families: 1000
Reading 22 vars from `xbat.phe' ... Done.
Number of Phenotype Variables: 22
Number of Observations : 1000
* DONE (GeneticsBase)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GeneticsBase_1.13.0.tar.gz'