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Package 107/294HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsBase 1.8.0
The R Genetics Project
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/GeneticsBase
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 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 (10.5.6) / i386  OK  OK  OK 
Package: GeneticsBase
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes GeneticsBase_1.8.0.tar.gz
StartedAt: 2009-04-18 16:57:00 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 16:59:01 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 121.5 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsBase.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.8.0'
* 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 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 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
* creating GeneticsBase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
  Running 'ExampleScript001.R'
  Running 'test.R'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsBase-manual.tex ... OK
* checking GeneticsBase-manual.tex using pdflatex ... OK

GeneticsBase.Rcheck/00install.out:

* Installing *source* package 'GeneticsBase' ...
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c LdMax.cpp -o LdMax.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c R_bitArrayVector.cpp -o R_bitArrayVector.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c bitArrayVector.cpp -o bitArrayVector.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c convert.cpp -o convert.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c getLDdist.cpp -o getLDdist.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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
Loading required package: combinat

Attaching package: 'combinat'


	The following object(s) are masked from package:utils :

	 combn 

Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
** help
 >>> Building/Updating help pages for package 'GeneticsBase'
     Formats: text html latex example 
  ALZH                              text    html    latex   example
Note: removing empty section \details in file 'Armitage.Rd'
Note: removing empty section \seealso in file 'Armitage.Rd'
  Armitage                          text    html    latex   example
  CAMP                              text    html    latex   example
  HWE                               text    html    latex   example
  HWE.chisq                         text    html    latex   example
  HWE.exact                         text    html    latex   example
Note: removing empty section \seealso in file 'LD-class.Rd'
  LD-class                          text    html    latex   example
  LD                                text    html    latex   example
Note: removing empty section \seealso in file 'LDband-class.Rd'
  LDband-class                      text    html    latex   example
  LDdist-class                      text    html    latex
  PGtables                          text    html    latex   example
  PerlgenExample                    text    html    latex   example
  PfizerExample                     text    html    latex   example
  alleleCount                       text    html    latex   example
  alleleLevels                      text    html    latex   example
  alleleSummary                     text    html    latex   example
  alleles                           text    html    latex   example
Note: removing empty section \details in file 'as.geneSet.Rd'
  as.geneSet                        text    html    latex   example
  binsearch                         text    html    latex   example
  callCodes                         text    html    latex   example
  ci.balance                        text    html    latex   example
  convert                           text    html    latex   example
Note: removing empty section \details in file 'decodeCallCodes.Rd'
  decodeCallCodes                   text    html    latex   example
  desMarkers                        text    html    latex   example
  description                       text    html    latex   example
Note: removing empty section \examples in file 'diseq.Rd'
  diseq                             text    html    latex
  errorMetrics                      text    html    latex   example
Note: removing empty section \examples in file 'extractAlleles.Rd'
  extractAlleles                    text    html    latex
Note: removing empty section \details in file 'fastGrid.Rd'
Note: removing empty section \examples in file 'fastGrid.Rd'
  fastGrid                          text    html    latex
  founderGeneSet                    text    html    latex   example
Note: removing empty section \seealso in file 'geneSet-class.Rd'
  geneSet-class                     text    html    latex   example
  geneSet2Ped                       text    html    latex   example
Note: removing empty section \details in file 'genotypeCoding.Rd'
Note: removing empty section \note in file 'genotypeCoding.Rd'
Note: removing empty section \references in file 'genotypeCoding.Rd'
Note: removing empty section \seealso in file 'genotypeCoding.Rd'
  genotypeCoding                    text    html    latex   example
  genotypeLevels                    text    html    latex   example
  genotypeSummary                   text    html    latex   example
  genotypes                         text    html    latex   example
  gregorius                         text    html    latex   example
  haplo.em.w                        text    html    latex   example
  haplo.scan.w                      text    html    latex   example
  haplo.score.slide.w               text    html    latex   example
Note: removing empty section \author in file 'haplo.score.w.Rd'
  haplo.score.w                     text    html    latex   example
  hapmapchr                         text    html    latex   example
  homozygote                        text    html    latex   example
  html                              text    html    latex   example
  left                              text    html    latex   example
Note: removing empty section \details in file 'makeMarkerInfo.Rd'
Note: removing empty section \examples in file 'makeMarkerInfo.Rd'
  makeMarkerInfo                    text    html    latex
Note: removing empty section \details in file 'makeTransTable.Rd'
Note: removing empty section \examples in file 'makeTransTable.Rd'
  makeTransTable                    text    html    latex
Note: removing empty section \details in file 'makeTransTableList.Rd'
  makeTransTableList                text    html    latex   example
  markerInfo                        text    html    latex   example
  markerNames                       text    html    latex   example
  markerSummary                     text    html    latex   example
  missingCodes                      text    html    latex   example
  nallele                           text    html    latex   example
  nmarker                           text    html    latex   example
  notes                             text    html    latex   example
  ped2geneSet                       text    html    latex
  phase                             text    html    latex   example
  ploidy                            text    html    latex   example
  print.LD                          text    html    latex   example
  qtlex                             text    html    latex   example
  read.pfizer                       text    html    latex   example
  read.phe                          text    html    latex   example
  readGenes                         text    html    latex   example
Note: removing empty section \examples in file 'readGenes.ped.Rd'
  readGenes.ped                     text    html    latex
Note: removing empty section \examples in file 'readGenes.perlegen.Rd'
  readGenes.perlegen                text    html    latex
  readGenes.pfizer                  text    html    latex   example
  sampleInfo                        text    html    latex   example
  studyInfo                         text    html    latex   example
  transTables                       text    html    latex   example
  xbat                              text    html    latex   example
** building package indices ...
Loading required package: methods
Loading required package: combinat

Attaching package: 'combinat'


	The following object(s) are masked from package:utils :

	 combn 

Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
* DONE (GeneticsBase)