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Package 90/251HostnameOS / ArchBUILDCHECKBUILD BIN
GeneticsPed 1.1.0
Gregor Gorjanc
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed
Last Changed Rev: 28616 / Revision: 29143
Last Changed Date: 2007-11-09 11:11:24 -0800 (Fri, 09 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK [ ERROR ]
wilson2 Linux (openSUSE 10.3) / x86_64  OK  ERROR 
wellington Linux (openSUSE 10.3) / i686  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  ERROR  OK 
Package: GeneticsPed
Version: 1.1.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check GeneticsPed_1.1.0.tar.gz
StartedAt: 2007-12-11 03:38:11 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:38:34 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 22.5 seconds
RetCode: 1
Status: ERROR
CheckDir: GeneticsPed.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-18 r43497)
* checking for file 'GeneticsPed/DESCRIPTION' ... OK
* this is package 'GeneticsPed' version '1.1.0'
* 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 for sufficient/correct file permissions ... 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 `/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck/tests'
  Running 'doRUnit.R'
make[1]: *** [doRUnit.Rout] Error 1
make[1]: Leaving directory `/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck/tests'
make: *** [all] Error 2
 ERROR
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
   
  1 Test Suite : 
  GeneticsPed unit testing - 14 test functions, 0 errors, 4 failures
  FAILURE in test.D: Error in checkIdentical(mendelianSamplingD(x2.1, matrix = FALSE, names = FALSE),  : 
    FALSE 
  FAILURE in test.M: Error in checkIdentical(gameteFlowM(x2.1, names = FALSE), test) : FALSE 
  FAILURE in test.T: Error in checkIdentical(geneFlowT(x2.1, names = FALSE), test) : FALSE 
  FAILURE in test.Tinv: Error in checkIdentical(geneFlowTinv(x2.1, names = FALSE), test) : FALSE 
  Error: 
  
  unit testing failed (#test failures: 4, #R errors: 0)
  
  Execution halted

GeneticsPed.Rcheck/00install.out:

* Installing *source* package 'GeneticsPed' ...
** libs
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ainverse.cc -o ainverse.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c eibd.cc -o eibd.o
gfortran   -fpic  -g -O2 -Wall -c ggmatmult.f -o ggmatmult.o
gfortran   -fpic  -g -O2 -Wall -c gpi.f -o gpi.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inbreed.cc -o inbreed.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inverseAdditive.cc -o inverseAdditive.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c meuwissen.cc -o meuwissen.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pedSort.cc -o pedSort.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c pedtemplate.cc -o pedtemplate.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c register.cc -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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: 'MIP' may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c sortped.cc -o sortped.o
g++ -shared -L/usr/local/lib64 -o GeneticsPed.so 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 -lm -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package 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

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
 >>> Building/Updating help pages for package 'GeneticsPed'
     Formats: text html latex example 
  TDT                               text    html    latex   example
  check                             text    html    latex   example
  datasets                          text    html    latex   example
  extend                            text    html    latex   example
  family                            text    html    latex   example
  founder                           text    html    latex   example
  geneContribution                  text    html    latex   example
  generatePedigree                  text    html    latex   example
  generation                        text    html    latex   example
  gpi                               text    html    latex   example
  gpiUtil                           text    html    latex   example
  inbreeding                        text    html    latex   example
  model.matrix                      text    html    latex   example
  nIndividual                       text    html    latex   example
  pedigree                          text    html    latex   example
  prune                             text    html    latex   example
  relationshipAdditive              text    html    latex   example
  removeIndividual                  text    html    latex   example
  sort.pedigree                     text    html    latex   example
  summary.pedigree                  text    html    latex   example
  undocumented                      text    html    latex
** building package indices ...
* DONE (GeneticsPed)