GeneticsPed 1.1.0
Gregor Gorjanc
| Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneticsPed | | Last Changed Rev: 29346 / Revision: 30951 | | Last Changed Date: 2007-12-28 12:30:41 -0800 (Fri, 28 Dec 2007) |
| 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 |
| pelham | Mac OS X Leopard (10.5.1) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/GeneticsPed.Rcheck'
* using R version 2.7.0 Under development (unstable) (2008-03-10 r44730)
* using session charset: ISO8859-1
* 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 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
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
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++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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*'
g++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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++ -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
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++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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*'
g++ -Ie:/biocbld/bbs-2.2-bioc/R/include -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*'
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, 55,366 bytes
Compression decreased file by 47,005 bytes.
adding MD5 sums
* DONE (GeneticsPed)