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Package 121/319HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.6.0
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/GeneticsPed
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: GeneticsPed
Version: 1.6.0
Command: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes GeneticsPed_1.6.0.tar.gz
StartedAt: 2009-10-20 17:08:23 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:09:12 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 49.7 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsPed' 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 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 'doRUnit.R'
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

GeneticsPed.Rcheck/00install.out:

* Installing *source* package 'GeneticsPed' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c ainverse.cc -o ainverse.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c eibd.cc -o eibd.o
gfortran     -O3  -c ggmatmult.f -o ggmatmult.o
gfortran     -O3  -c gpi.f -o gpi.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c inbreed.cc -o inbreed.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c meuwissen.cc -o meuwissen.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c pedSort.cc -o pedSort.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c register.cc -o register.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O3 -Wall  -std=gnu99 -c sargolzaei.c -o sargolzaei.o
sargolzaei.c: In function 'sargolzaei':
sargolzaei.c:96: warning: comparison between pointer and integer
sargolzaei.c:19: warning: 'S' may be used uninitialized in this function
sargolzaei.c:19: warning: 'MIP' may be used uninitialized in this function
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include"        -O2 -Wall  -c sortped.cc -o sortped.o
g++ -shared -s -o GeneticsPed.dll tmp.def ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -lgfortran -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** R
** data
** inst
** preparing package for lazy loading

Attaching package: 'gdata'


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

	 object.size 

Loading required package: combinat

Attaching package: 'combinat'


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

	 combn 

Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm

NOTE: THIS PACKAGE IS NOW OBSOLETE.

  The R-Genetics project has developed an set of enhanced genetics
  packages to replace 'genetics'. Please visit the project homepage
  at http://rgenetics.org for informtion.


Attaching package: 'genetics'


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

	 %in%,
	 as.factor,
	 order 

** help
*** installing help indices
 >>> Building/Updating help pages for package 'GeneticsPed'
     Formats: text html latex example chm 
  TDT                               text    html    latex   example chm
  check                             text    html    latex   example chm
  datasets                          text    html    latex   example chm
  extend                            text    html    latex   example chm
  family                            text    html    latex   example chm
  founder                           text    html    latex   example chm
  geneContribution                  text    html    latex   example chm
  generatePedigree                  text    html    latex   example chm
  generation                        text    html    latex   example chm
  gpi                               text    html    latex   example chm
  gpiUtil                           text    html    latex   example chm
  inbreeding                        text    html    latex   example chm
  model.matrix                      text    html    latex   example chm
  nIndividual                       text    html    latex   example chm
  pedigree                          text    html    latex   example chm
  prune                             text    html    latex   example chm
  relationshipAdditive              text    html    latex   example chm
  removeIndividual                  text    html    latex   example chm
  sort.pedigree                     text    html    latex   example chm
  summary.pedigree                  text    html    latex   example chm
  undocumented                      text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\GENETI~3.RCH\00_PKG~1\GENETI~1\chm\GeneticsPed.chm


Compile time: 0 minutes, 0 seconds
22	Topics
109	Local links
13	Internet links
1	Graphic


Created e:\biocbld\BBS-2~1.4-B\meat\GENETI~3.RCH\00_PKG~1\GENETI~1\chm\GeneticsPed.chm, 55,812 bytes
Compression decreased file by 47,298 bytes.
** building package indices ...
** MD5 sums
* DONE (GeneticsPed)