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Package 151/389HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsBase 1.14.0
The R Genetics Project
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GeneticsBase
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS [ OK ]
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GeneticsBase
Version: 1.14.0
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GeneticsBase.buildbin-libdir GeneticsBase_1.14.0.tar.gz
StartedAt: 2010-10-04 19:26:57 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 19:27:57 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 60.5 seconds
RetCode: 0
Status:  OK  
PackageFile: GeneticsBase_1.14.0.zip
PackageFileSize: 3.852 MiB

Command output

* installing *source* package 'GeneticsBase' ...
** libs
  making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c LdMax.cpp -o LdMax.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: no return statement in function returning non-void
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp:157: warning: no return statement in function returning non-void
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -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:550: warning: suggest parentheses around '-' inside '<<'
bitArrayVector.cpp:551: warning: suggest parentheses around '-' inside '<<'
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
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c convert.cpp -o convert.o
convert.cpp:1:2: warning: #import is a deprecated GCC extension
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c getLDdist.cpp -o getLDdist.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c readGenes.ped.cpp -o readGenes.ped.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -c register.cpp -o register.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o GeneticsBase.dll tmp.def LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.buildbin-libdir/GeneticsBase/libs/x64
  ... done
** 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 

** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneticsBase' as GeneticsBase_1.14.0.zip

* DONE (GeneticsBase)