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Package 138/354HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: GeneticsBase
Version: 1.13.0
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes GeneticsBase_1.13.0.tar.gz
StartedAt: 2009-12-07 17:06:39 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 17:08:14 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 95.0 seconds
RetCode: 0
Status: WARNINGS
CheckDir: GeneticsBase.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.13.0'
* 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 ... NOTE
prepare_Rd: Armitage.Rd:30-31: Dropping empty section \details
prepare_Rd: Armitage.Rd:73: Dropping empty section \seealso
prepare_Rd: LD-class.Rd:50-51: Dropping empty section \seealso
prepare_Rd: LDband-class.Rd:43-44: Dropping empty section \seealso
prepare_Rd: as.geneSet.Rd:78-80: Dropping empty section \details
prepare_Rd: decodeCallCodes.Rd:29-30: Dropping empty section \details
prepare_Rd: diseq.Rd:113-114: Dropping empty section \examples
prepare_Rd: extractAlleles.Rd:25-27: Dropping empty section \examples
prepare_Rd: fastGrid.Rd:13-14: Dropping empty section \details
prepare_Rd: fastGrid.Rd:24-25: Dropping empty section \examples
prepare_Rd: geneSet-class.Rd:159-160: Dropping empty section \seealso
prepare_Rd: genotypeCoding.Rd:19-20: Dropping empty section \details
prepare_Rd: genotypeCoding.Rd:31: Dropping empty section \note
prepare_Rd: genotypeCoding.Rd:25: Dropping empty section \references
prepare_Rd: genotypeCoding.Rd:32: Dropping empty section \seealso
prepare_Rd: haplo.score.w.Rd:119: Dropping empty section \author
prepare_Rd: makeMarkerInfo.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMarkerInfo.Rd:27-28: Dropping empty section \examples
prepare_Rd: makeTransTable.Rd:16-17: Dropping empty section \details
prepare_Rd: makeTransTable.Rd:24-25: Dropping empty section \examples
prepare_Rd: makeTransTableList.Rd:14-15: Dropping empty section \details
prepare_Rd: readGenes.ped.Rd:35-36: Dropping empty section \examples
prepare_Rd: readGenes.perlegen.Rd:19-20: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: 'bootstrap'
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'LD-class':
Slots for class 'LD'
  Code: call D D' LOD n P-value r R^2 X^2
  Docs: \special{D'}: call D LOD n P-value r R^2 X^2

S4 class codoc mismatches from documentation object 'LDband-class':
Slots for class 'LDband'
  Code: call D D' LOD n P-value r R^2 X^2
  Docs: \special{D'}: call D LOD n P-value r R^2 X^2

S4 class codoc mismatches from documentation object 'LDdist-class':
Slots for class 'LDdist'
  Code: call D D' LOD n P-value r R^2 X^2
  Docs: \special{D'}: call D LOD n P-value r R^2 X^2

* 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

WARNING: There was 1 warning, see
  E:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/00check.log
for details

GeneticsBase.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'GeneticsBase' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include"        -O2 -Wall  -c LdMax.cpp -o LdMax.o
g++ -I"e:/biocbld/bbs-2.6-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-2.6-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: 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++ -I"e:/biocbld/bbs-2.6-bioc/R/include"        -O2 -Wall  -c convert.cpp -o convert.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include"        -O2 -Wall  -c getLDdist.cpp -o getLDdist.o
g++ -I"e:/biocbld/bbs-2.6-bioc/R/include"        -O2 -Wall  -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I"e:/biocbld/bbs-2.6-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-2.6-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 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)