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Package 95/260HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.2.0
Gregor Gorjanc
Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/GeneticsPed
Last Changed Rev: 31430 / Revision: 34573
Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008)
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 
pitt Mac OS X Tiger (10.4.11) / i386  OK  ERROR  OK 
Package: GeneticsPed
Version: 1.2.0
Command: E:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check GeneticsPed_1.2.0.tar.gz
StartedAt: 2008-10-16 05:53:51 -0700 (Thu, 16 Oct 2008)
EndedAt: 2008-10-16 05:54:51 -0700 (Thu, 16 Oct 2008)
EllapsedTime: 60.5 seconds
RetCode: 0
Status: OK
CheckDir: GeneticsPed.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' 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 '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 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 GeneticsPed-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/e/biocbld/bbs-2.2-bioc/meat/GeneticsPed.Rcheck/tests'
  Running 'doRUnit.R'
make[1]: Leaving directory `/cygdrive/e/biocbld/bbs-2.2-bioc/meat/GeneticsPed.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsPed-manual.tex ... OK
* checking GeneticsPed-manual.tex using pdflatex ... OK

GeneticsPed.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.2-bioc/meat/GeneticsPed.Rcheck


---------- Making package GeneticsPed ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making sargolzaei.d from sargolzaei.c
making ainverse.d from ainverse.cc
making eibd.d from eibd.cc
making inbreed.d from inbreed.cc
making inverseAdditive.d from inverseAdditive.cc
making meuwissen.d from meuwissen.cc
making pedSort.d from pedSort.cc
making pedtemplate.d from pedtemplate.cc
making register.d from register.cc
making sortped.d from sortped.cc
gcc  -std=gnu99  -Ie:/biocbld/bbs-2.2-bioc/R/include     -O3 -Wall  -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
gfortran   -O3  -c ggmatmult.f -o ggmatmult.o
gfortran   -O3  -c gpi.f -o gpi.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c ainverse.cc -o ainverse.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c eibd.cc -o eibd.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c inbreed.cc -o inbreed.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c inverseAdditive.cc -o inverseAdditive.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c meuwissen.cc -o meuwissen.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c pedSort.cc -o pedSort.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c pedtemplate.cc -o pedtemplate.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c register.cc -o register.o
g++   -Ie:/biocbld/bbs-2.2-bioc/R/include     -O2 -Wall  -c sortped.cc -o sortped.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include  -i GeneticsPed_res.rc -o GeneticsPed_res.o
g++   -shared -s  -o GeneticsPed.dll GeneticsPed.def sargolzaei.o ggmatmult.o gpi.o ainverse.o eibd.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sortped.o GeneticsPed_res.o  -Le:/biocbld/bbs-2.2-bioc/R/bin   -lgfortran -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  preparing package GeneticsPed for lazy loading
Loading required package: gdata
Loading required package: genetics
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

Attaching package: 'genetics'


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

	 %in%,
	 as.factor,
	 order 

  installing man source files
  installing indices
  not zipping data
  installing help
 >>> 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-2.2-bioc\meat\GeneticsPed.Rcheck\00_pkg_src\GeneticsPed\chm\GeneticsPed.chm


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


Created e:\biocbld\bbs-2.2-bioc\meat\GeneticsPed.Rcheck\00_pkg_src\GeneticsPed\chm\GeneticsPed.chm, 55,368 bytes
Compression decreased file by 47,003 bytes.
  adding MD5 sums

* DONE (GeneticsPed)