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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: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings GeneticsBase_1.14.0.tar.gz
StartedAt: 2010-10-04 17:09:38 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:11:39 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 121.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GeneticsBase.Rcheck
Warnings: 2

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.14.0'
* 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 for sufficient/correct file permissions ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
haplo.em.w: no visible global function definition for
  ‘haplo.em.control’
haplo.em.w: no visible global function definition for ‘haplo.em’
haplo.scan.w: no visible global function definition for
  ‘haplo.em.control’
haplo.scan.w: no visible global function definition for
  ‘score.sim.control’
haplo.scan.w: no visible global function definition for ‘haplo.scan’
haplo.score.slide.w: no visible global function definition for
  ‘score.sim.control’
haplo.score.slide.w: no visible global function definition for
  ‘haplo.em.control’
haplo.score.slide.w: no visible global function definition for
  ‘haplo.score.slide’
haplo.score.w: no visible global function definition for
  ‘score.sim.control’
haplo.score.w: no visible global function definition for
  ‘haplo.em.control’
haplo.score.w: no visible global function definition for ‘haplo.score’
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’, ‘haplo.stats’
* 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: D D' LOD P-value R^2 X^2 call n r
  Docs: D LOD P-value R^2 X^2 \special{D'}: call n r

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

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

* checking Rd \usage sections ... OK
* checking Rd contents ... WARNING
Auto-generated content requiring editing in Rd object 'LD-class':
  \note

Auto-generated content requiring editing in Rd object 'LDband-class':
  \note

Auto-generated content requiring editing in Rd object 'PGtables':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'x'
  \arguments, description of item 'filename'
  \arguments, description of item 'format'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'alleleCount':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'alleleLevels':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'alleles':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'callCodes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'marker'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'description':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'errorMetrics':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'geneSet-class':
  \note

Auto-generated content requiring editing in Rd object 'genotypeLevels':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'genotypes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'haplo.em.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.scan.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.score.slide.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.score.w':
  \note

Auto-generated content requiring editing in Rd object 'left':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'x'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'markerInfo':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'markerNames':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Argument items with no description in Rd object 'markerSummary':
  covariate

Auto-generated content requiring editing in Rd object 'missingCodes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'nallele':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'nmarker':
  \title
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  \details
  \author
  \note
  \arguments, description of item 'object'

Auto-generated content requiring editing in Rd object 'notes':
  \title
  \description
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  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'phase':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'ploidy':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'read.pfizer':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'file'
  \arguments, description of item 'verbose'

Auto-generated content requiring editing in Rd object 'sampleInfo':
  \title
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  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'studyInfo':
  \title
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  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'transTables':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

* 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 were 2 warnings, see
  /Users/biocbuild/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
*** 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 -fasm-blocks -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 -fasm-blocks -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 -fasm-blocks -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 -fasm-blocks -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 -fasm-blocks -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 -fasm-blocks -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 -fasm-blocks -c register.cpp -o register.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/GeneticsBase/libs/i386
*** 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 -Wall -fasm-blocks -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 -Wall -fasm-blocks -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 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 -Wall -fasm-blocks -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 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 -Wall -fasm-blocks -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 -Wall -fasm-blocks -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 -Wall -fasm-blocks -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 -Wall -fasm-blocks -c register.cpp -o register.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/GeneticsBase/libs/ppc
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c LdMax.cpp -o LdMax.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -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 x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -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 x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c convert.cpp -o convert.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c getLDdist.cpp -o getLDdist.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c register.cpp -o register.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -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
installing to /Users/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/GeneticsBase/libs/x86_64
** 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

* DONE (GeneticsBase)

GeneticsBase.Rcheck/GeneticsBase-Ex.timings:

nameusersystemelapsed
ALZH0.0670.0060.073
Armitage0.0020.0010.002
CAMP0.1760.0320.209
HWE11.232 1.30613.147
HWE.chisq0.1410.0310.172
HWE.exact0.1330.0240.156
LD-class000
LD0.6510.1340.791
LDband-class0.0000.0000.001
PGtables0.0010.0000.001
PerlgenExample0.0230.0030.027
PfizerExample0.0810.0030.084
alleleCount0.0000.0000.001
alleleLevels0.0000.0000.001
alleleSummary0.4410.0440.490
alleles000
as.geneSet0.0690.0020.078
binsearch0.0100.0010.010
callCodes000
ci.balance0.0040.0010.007
convert0.0030.0020.004
decodeCallCodes0.0040.0010.004
desMarkers0.0010.0000.001
description0.0000.0000.001
errorMetrics000
founderGeneSet0.1240.0250.149
geneSet-class0.0010.0000.001
geneSet2Ped0.1490.0430.226
genotypeCoding0.4320.0610.507
genotypeLevels0.0000.0000.001
genotypeSummary1.8800.0622.013
genotypes0.0000.0000.001
gregorius0.0040.0010.004
haplo.em.w0.0000.0000.001
haplo.scan.w0.0000.0010.000
haplo.score.slide.w0.0000.0000.001
haplo.score.w0.0000.0000.001
hapmapchr0.5450.0240.569
homozygote0.1990.0310.240
html5.7910.1986.222
left0.0000.0000.001
makeTransTableList0.0000.0000.001
markerInfo0.0010.0000.001
markerNames0.0000.0010.001
markerSummary3.0990.1103.319
missingCodes000
nallele0.0010.0000.000
nmarker0.0000.0010.000
notes0.0010.0000.000
phase000
ploidy000
print.LD0.2820.0580.404
qtlex0.4600.0930.570
read.pfizer000
read.phe0.5200.1720.709
readGenes0.0020.0000.003
readGenes.pfizer0.0700.0010.071
sampleInfo0.0000.0000.001
studyInfo0.0010.0010.001
transTables0.0000.0000.001
xbat0.5270.1750.713