GeneticsBase 1.10.0
The R Genetics Project
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/GeneticsBase | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.10.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsBase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot,LD: no visible binding for global variable 'y'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
Running 'ExampleScript001.R'
Running 'test.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'GeneticsBase' ...
** libs
making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -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++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: 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:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c convert.cpp -o convert.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -O2 -Wall -c register.cpp -o register.o
g++ -shared -s -o GeneticsBase.dll tmp.def LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... 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/Updating help pages for package 'GeneticsBase'
Formats: text html latex example chm
ALZH text html latex example chm
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Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\GENETI~1.RCH\00_PKG~1\GENETI~1\chm\GeneticsBase.chm
Compile time: 0 minutes, 1 second
71 Topics
292 Local links
8 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\GENETI~1.RCH\00_PKG~1\GENETI~1\chm\GeneticsBase.chm, 107,265 bytes
Compression decreased file by 196,653 bytes.
** 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
** MD5 sums
* DONE (GeneticsBase)