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Package 119/319HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: GeneticsBase
Version: 1.10.0
Command: /home/biocbuild/bbs-2.4-bioc/R/bin/R CMD check --no-vignettes GeneticsBase_1.10.0.tar.gz
StartedAt: 2009-10-20 16:23:38 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:24:41 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 62.5 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsBase.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 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 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

GeneticsBase.Rcheck/00install.out:

* Installing *source* package 'GeneticsBase' ...
** libs
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -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/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -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:549: warning: suggest parentheses around + or - inside shift
bitArrayVector.cpp:550: warning: suggest parentheses around + or - inside shift
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/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c convert.cpp -o convert.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c register.cpp -o register.o
g++ -shared -L/usr/local/lib64 -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** 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 
  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 ...
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 

* DONE (GeneticsBase)