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 |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* 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 `/loc/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck/tests'
Running 'doRUnit.R'
make[1]: *** [doRUnit.Rout] Error 1
make[1]: Leaving directory `/loc/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
/loc/home/biocbuild/bbs-2.2-bioc/meat/GeneticsPed.Rcheck
* 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
In file included from ../include/inbreed.h:21,
from ../include/ainverse.h:23,
from ainverse.cc:9:
../include/math_utilities.h: In function ‘double dabs(double)’:
../include/math_utilities.h:86: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double erfinv(double)’:
../include/math_utilities.h:104: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double incomplete_beta(double, double, double)’:
../include/math_utilities.h:170: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double betacf(double, double, double)’:
../include/math_utilities.h:243: warning: deprecated conversion from string constant to ‘char*’
ainverse.cc: In function ‘void AddCoeff(EIBDMat&, Pedigree&, VecMap&)’:
ainverse.cc:59: warning: deprecated conversion from string constant to ‘char*’
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
eibd.cc: In member function ‘void EIBDMember::Show()’:
eibd.cc:90: warning: deprecated conversion from string constant to ‘char*’
eibd.cc:93: warning: deprecated conversion from string constant to ‘char*’
eibd.cc:97: warning: deprecated conversion from string constant to ‘char*’
eibd.cc:99: warning: deprecated conversion from string constant to ‘char*’
eibd.cc: In member function ‘void EIBDMat::Show()’:
eibd.cc:289: warning: deprecated conversion from string constant to ‘char*’
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
In file included from ../include/inbreed.h:21,
from inbreed.cc:10:
../include/math_utilities.h: In function ‘double dabs(double)’:
../include/math_utilities.h:86: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double erfinv(double)’:
../include/math_utilities.h:104: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double incomplete_beta(double, double, double)’:
../include/math_utilities.h:170: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double betacf(double, double, double)’:
../include/math_utilities.h:243: warning: deprecated conversion from string constant to ‘char*’
inbreed.cc: In member function ‘void AmatRow::Show()’:
inbreed.cc:125: warning: deprecated conversion from string constant to ‘char*’
inbreed.cc:128: warning: deprecated conversion from string constant to ‘char*’
inbreed.cc:131: warning: deprecated conversion from string constant to ‘char*’
inbreed.cc: In member function ‘void Amat::Show()’:
inbreed.cc:193: warning: deprecated conversion from string constant to ‘char*’
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
In file included from ../include/inbreed.h:21,
from ../include/ainverse.h:23,
from inverseAdditive.cc:8:
../include/math_utilities.h: In function ‘double dabs(double)’:
../include/math_utilities.h:86: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double erfinv(double)’:
../include/math_utilities.h:104: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double incomplete_beta(double, double, double)’:
../include/math_utilities.h:170: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double betacf(double, double, double)’:
../include/math_utilities.h:243: warning: deprecated conversion from string constant to ‘char*’
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
In file included from ../include/inbreed.h:21,
from meuwissen.cc:5:
../include/math_utilities.h: In function ‘double dabs(double)’:
../include/math_utilities.h:86: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double erfinv(double)’:
../include/math_utilities.h:104: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double incomplete_beta(double, double, double)’:
../include/math_utilities.h:170: warning: deprecated conversion from string constant to ‘char*’
../include/math_utilities.h: In function ‘double betacf(double, double, double)’:
../include/math_utilities.h:243: warning: deprecated conversion from string constant to ‘char*’
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
pedtemplate.cc: In member function ‘void TPed::ShowPed()’:
pedtemplate.cc:428: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:431: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:437: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:441: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:445: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:449: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc:454: warning: deprecated conversion from string constant to ‘char*’
pedtemplate.cc: In member function ‘void Pedigree::ShowPed()’:
pedtemplate.cc:478: warning: deprecated conversion from string constant to ‘char*’
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
In file included from ../include/../include/inbreed.h:21,
from ../include/meuwissen.h:9,
from register.cc:8:
../include/../include/math_utilities.h: In function ‘double dabs(double)’:
../include/../include/math_utilities.h:86: warning: deprecated conversion from string constant to ‘char*’
../include/../include/math_utilities.h: In function ‘double erfinv(double)’:
../include/../include/math_utilities.h:104: warning: deprecated conversion from string constant to ‘char*’
../include/../include/math_utilities.h: In function ‘double incomplete_beta(double, double, double)’:
../include/../include/math_utilities.h:170: warning: deprecated conversion from string constant to ‘char*’
../include/../include/math_utilities.h: In function ‘double betacf(double, double, double)’:
../include/../include/math_utilities.h:243: warning: deprecated conversion from string constant to ‘char*’
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: ‘S’ may be used uninitialized in this function
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
sortped.cc: In function ‘void SortPed(Pedigree&, TPedVec&)’:
sortped.cc:24: warning: deprecated conversion from string constant to ‘char*’
sortped.cc:29: warning: deprecated conversion from string constant to ‘char*’
sortped.cc:39: warning: deprecated conversion from string constant to ‘char*’
sortped.cc:44: warning: deprecated conversion from string constant to ‘char*’
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)