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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: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD INSTALL --build --library=GeneticsBase.buildbin-libdir GeneticsBase_1.8.0.tar.gz
StartedAt: 2009-04-18 20:34:50 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 20:36:03 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 72.5 seconds
RetCode: 0
Status: OK
PackageFile: GeneticsBase_1.8.0.zip
PackageFileSize: 3.842 MiB

Command output

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/GeneticsBase.buildbin-libdir

Using auto-selected zip options ' GeneticsBase-HELP=ziponly'

---------- Making package GeneticsBase ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making LdMax.d from LdMax.cpp
making R_bitArrayVector.d from R_bitArrayVector.cpp
making bitArrayVector.d from bitArrayVector.cpp
making convert.d from convert.cpp
making getLDdist.d from getLDdist.cpp
making readGenes.ped.d from readGenes.ped.cpp
making register.d from register.cpp
g++   -IE:/biocbld/bbs-2.3-bioc/R/include     -O2 -Wall  -c LdMax.cpp -o LdMax.o
g++   -IE:/biocbld/bbs-2.3-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++   -IE:/biocbld/bbs-2.3-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++   -IE:/biocbld/bbs-2.3-bioc/R/include     -O2 -Wall  -c convert.cpp -o convert.o
g++   -IE:/biocbld/bbs-2.3-bioc/R/include     -O2 -Wall  -c getLDdist.cpp -o getLDdist.o
g++   -IE:/biocbld/bbs-2.3-bioc/R/include     -O2 -Wall  -c readGenes.ped.cpp -o readGenes.ped.o
g++   -IE:/biocbld/bbs-2.3-bioc/R/include     -O2 -Wall  -c register.cpp -o register.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I E:/biocbld/bbs-2.3-bioc/R/include  -i GeneticsBase_res.rc -o GeneticsBase_res.o
g++   -shared -s  -o GeneticsBase.dll GeneticsBase.def LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o GeneticsBase_res.o  -LE:/biocbld/bbs-2.3-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package GeneticsBase 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
  installing man source files
  installing 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
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GeneticsBase'
     Formats: text html latex example chm 
  ALZH                              text    html    latex   example chm
Note: removing empty section \details in file 'Armitage.Rd'
Note: removing empty section \seealso in file 'Armitage.Rd'
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  Armitage                          text    html    latex   example chm
  CAMP                              text    html    latex   example chm
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  LD-class                          text    html    latex   example chm
  LD                                text    html    latex   example chm
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  LDband-class                      text    html    latex   example chm
  LDdist-class                      text    html    latex           chm
  PGtables                          text    html    latex   example chm
  PerlgenExample                    text    html    latex   example chm
  PfizerExample                     text    html    latex   example chm
  alleleCount                       text    html    latex   example chm
  alleleLevels                      text    html    latex   example chm
  alleleSummary                     text    html    latex   example chm
  alleles                           text    html    latex   example chm
Note: removing empty section \details in file 'as.geneSet.Rd'
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  as.geneSet                        text    html    latex   example chm
  binsearch                         text    html    latex   example chm
  callCodes                         text    html    latex   example chm
  ci.balance                        text    html    latex   example chm
  convert                           text    html    latex   example chm
Note: removing empty section \details in file 'decodeCallCodes.Rd'
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  decodeCallCodes                   text    html    latex   example chm
  desMarkers                        text    html    latex   example chm
  description                       text    html    latex   example chm
Note: removing empty section \examples in file 'diseq.Rd'
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  diseq                             text    html    latex           chm
  errorMetrics                      text    html    latex   example chm
Note: removing empty section \examples in file 'extractAlleles.Rd'
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  extractAlleles                    text    html    latex           chm
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  fastGrid                          text    html    latex           chm
  founderGeneSet                    text    html    latex   example chm
Note: removing empty section \seealso in file 'geneSet-class.Rd'
Note: removing empty section \seealso in file 'geneSet-class.Rd'
  geneSet-class                     text    html    latex   example chm
  geneSet2Ped                       text    html    latex   example chm
Note: removing empty section \details in file 'genotypeCoding.Rd'
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  genotypeCoding                    text    html    latex   example chm
  genotypeLevels                    text    html    latex   example chm
  genotypeSummary                   text    html    latex   example chm
  genotypes                         text    html    latex   example chm
  gregorius                         text    html    latex   example chm
  haplo.em.w                        text    html    latex   example chm
  haplo.scan.w                      text    html    latex   example chm
  haplo.score.slide.w               text    html    latex   example chm
Note: removing empty section \author in file 'haplo.score.w.Rd'
Note: removing empty section \author in file 'haplo.score.w.Rd'
  haplo.score.w                     text    html    latex   example chm
  hapmapchr                         text    html    latex   example chm
  homozygote                        text    html    latex   example chm
  html                              text    html    latex   example chm
  left                              text    html    latex   example chm
Note: removing empty section \details in file 'makeMarkerInfo.Rd'
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  makeMarkerInfo                    text    html    latex           chm
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  makeTransTable                    text    html    latex           chm
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  makeTransTableList                text    html    latex   example chm
  markerInfo                        text    html    latex   example chm
  markerNames                       text    html    latex   example chm
  markerSummary                     text    html    latex   example chm
  missingCodes                      text    html    latex   example chm
  nallele                           text    html    latex   example chm
  nmarker                           text    html    latex   example chm
  notes                             text    html    latex   example chm
  ped2geneSet                       text    html    latex           chm
  phase                             text    html    latex   example chm
  ploidy                            text    html    latex   example chm
  print.LD                          text    html    latex   example chm
  qtlex                             text    html    latex   example chm
  read.pfizer                       text    html    latex   example chm
  read.phe                          text    html    latex   example chm
  readGenes                         text    html    latex   example chm
Note: removing empty section \examples in file 'readGenes.ped.Rd'
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  readGenes.ped                     text    html    latex           chm
Note: removing empty section \examples in file 'readGenes.perlegen.Rd'
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  readGenes.perlegen                text    html    latex           chm
  readGenes.pfizer                  text    html    latex   example chm
  sampleInfo                        text    html    latex   example chm
  studyInfo                         text    html    latex   example chm
  transTables                       text    html    latex   example chm
  xbat                              text    html    latex   example chm
  zipping help files
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.4992\GeneticsBase\chm\GeneticsBase.chm





Compile time: 0 minutes, 2 seconds

71	Topics

269	Local links

8	Internet links

1	Graphic





Created e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.4992\GeneticsBase\chm\GeneticsBase.chm, 106,971 bytes

Compression decreased file by 194,208 bytes.

  adding MD5 sums

packaged installation of package 'GeneticsBase' as GeneticsBase_1.8.0.zip
* DONE (GeneticsBase)