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Package 83/233HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsBase 1.2.0
Gregory Warnes
Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/GeneticsBase
Last Changed Rev: 27709 / Revision: 30807
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: GeneticsBase
Version: 1.2.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check GeneticsBase_1.2.0.tar.gz
StartedAt: 2008-04-02 19:28:50 -0700 (Wed, 02 Apr 2008)
EndedAt: 2008-04-02 19:32:24 -0700 (Wed, 02 Apr 2008)
EllapsedTime: 213.8 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsBase.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.2.0'
* 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 ... OK
* 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 ...
make[1]: Entering directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck/tests'
  Running 'ExampleScript001.R'
  Running 'test.R'
make[1]: Leaving directory `/cygdrive/d/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsBase-manual.tex ... OK
* checking GeneticsBase-manual.tex ... OK

GeneticsBase.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/GeneticsBase.Rcheck


---------- Making package GeneticsBase ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making LdMax.d from LdMax.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++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c LdMax.cpp -o LdMax.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c convert.cpp -o convert.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c getLDdist.cpp -o getLDdist.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c readGenes.ped.cpp -o readGenes.ped.o
g++-sjlj   -Id:/biocbld/bbs-2.1-bioc/R/include     -O2 -Wall  -c register.cpp -o register.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i GeneticsBase_res.rc -o GeneticsBase_res.o
g++-sjlj   -shared -s  -o GeneticsBase.dll GeneticsBase.def LdMax.o convert.o getLDdist.o readGenes.ped.o register.o GeneticsBase_res.o  -Ld:/biocbld/bbs-2.1-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
  Armitage                          text    html    latex   example chm
  CAMP                              text    html    latex   example chm
  HWE                               text    html    latex   example chm
  HWE.chisq                         text    html    latex   example chm
  HWE.exact                         text    html    latex   example chm
  LD-class                          text    html    latex   example chm
  LD                                text    html    latex   example chm
  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
  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
  decodeCallCodes                   text    html    latex   example chm
  desMarkers                        text    html    latex   example chm
  description                       text    html    latex   example chm
  diseq                             text    html    latex   example chm
  errorMetrics                      text    html    latex   example chm
  extractAlleles                    text    html    latex   example chm
  fastGrid                          text    html    latex   example chm
  founderGeneSet                    text    html    latex   example chm
  geneSet-class                     text    html    latex   example chm
  geneSet2Ped                       text    html    latex   example chm
  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
  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
  makeMarkerInfo                    text    html    latex   example chm
  makeTransTable                    text    html    latex   example chm
  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
  readGenes.ped                     text    html    latex   example chm
  readGenes.perlegen                text    html    latex   example 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
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "n;c:\Program Files\UltraEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL".
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\GeneticsBase.Rcheck\00_pkg_src\GeneticsBase\chm\GeneticsBase.chm

HHC4016: Warning: Cannot open "n;c:\Program Files\UltraEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL".


The following files were not compiled:
  adding MD5 sums

* DONE (GeneticsBase)