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GeneticsBase

1.0.0

Gregory Warnes
Last Changed Date: 2007-04-24 11:21:48 -0700
Last Changed Rev: 24214
lamb1 Linux (SUSE 10.1) x86_64  ERROR skipped
wellington Linux (SUSE 9.2) i686 [ ERROR ]skipped
lemming Windows Server 2003 (32-bit) x64  ERROR skippedskipped
Package: GeneticsBase
Version: 1.0.0
Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD build GeneticsBase
RetCode: 1
Time: 49.8 seconds
Status: ERROR
PackageFile: None

Command output

* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* preparing 'GeneticsBase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'GeneticsBase' ...
** libs
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c convert.cpp -o convert.o
convert.cpp:1:2: warning: #import is obsolete, use an #ifndef wrapper in the header file
convert.cpp: In function `SEXPREC* convert2(SEXPREC*, SEXPREC*, SEXPREC*)':
convert.cpp:6: warning: unused variable `int maxlen'
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
readGenes.ped.cpp: In function `int countLines(FILE*, int, int)':
readGenes.ped.cpp:86: warning: `int tmpnc2' might be used uninitialized in this 
   function
g++ -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c register.cpp -o register.o
g++ -shared -L/usr/local/lib -o GeneticsBase.so convert.o getLDdist.o LdMax.o readGenes.ped.o register.o   -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** data
** inst
** save image
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
** help
 >>> Building/Updating help pages for package 'GeneticsBase'
     Formats: text html latex example 
  ALZH                              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
  LD-class                          text    html    latex   example
  LD                                text    html    latex   example
  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
  binsearch                         text    html    latex   example
  callCodes                         text    html    latex   example
  ci.balance                        text    html    latex   example
  convert                           text    html    latex   example
  decodeCallCodes                   text    html    latex   example
  desMarkers                        text    html    latex   example
  description                       text    html    latex   example
  diseq                             text    html    latex   example
  errorMetrics                      text    html    latex   example
  extractAlleles                    text    html    latex   example
  fastGrid                          text    html    latex   example
  founderGeneSet                    text    html    latex   example
  geneSet-class                     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
  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
  makeMarkerInfo                    text    html    latex   example
  makeTransTable                    text    html    latex   example
  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
  power.casectl                     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
  readGenes.ped                     text    html    latex   example
  readGenes.perlegen                text    html    latex   example
  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
* DONE (GeneticsBase)
* creating vignettes ... ERROR
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

Error: processing vignette 'SummaryTables.Rnw' failed with diagnostics:
 chunk 23 
Error in write.GeneticsBaseSummary(x = x, filename = filename, ..., format = "latex") : 
	could not find function "print.xtable"
In addition: There were 15 warnings (use warnings() to see them)
Execution halted