GeneticsBase 1.8.0
The R Genetics Project
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/GeneticsBase | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | OK | OK | OK |
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* preparing 'GeneticsBase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'GeneticsBase' ...
** libs
** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c LdMax.cpp -o LdMax.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c R_bitArrayVector.cpp -o R_bitArrayVector.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c bitArrayVector.cpp -o bitArrayVector.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c convert.cpp -o convert.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c getLDdist.cpp -o getLDdist.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c register.cpp -o register.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c LdMax.cpp -o LdMax.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c R_bitArrayVector.cpp -o R_bitArrayVector.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c bitArrayVector.cpp -o bitArrayVector.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c convert.cpp -o convert.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c getLDdist.cpp -o getLDdist.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c readGenes.ped.cpp -o readGenes.ped.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c register.cpp -o register.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: combinat
Attaching package: 'combinat'
The following object(s) are masked from package:utils :
combn
Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
** help
>>> Building/Updating help pages for package 'GeneticsBase'
Formats: text html latex example
ALZH text html latex example
Note: removing empty section \details in file 'Armitage.Rd'
Note: removing empty section \seealso in file 'Armitage.Rd'
Armitage text html latex example
CAMP text html latex example
HWE text html latex example
HWE.chisq text html latex example
HWE.exact text html latex example
Note: removing empty section \seealso in file 'LD-class.Rd'
LD-class text html latex example
LD text html latex example
Note: removing empty section \seealso in file 'LDband-class.Rd'
LDband-class text html latex example
LDdist-class text html latex
PGtables text html latex example
PerlgenExample text html latex example
PfizerExample text html latex example
alleleCount text html latex example
alleleLevels text html latex example
alleleSummary text html latex example
alleles text html latex example
Note: removing empty section \details in file 'as.geneSet.Rd'
as.geneSet text html latex example
binsearch text html latex example
callCodes text html latex example
ci.balance text html latex example
convert text html latex example
Note: removing empty section \details in file 'decodeCallCodes.Rd'
decodeCallCodes text html latex example
desMarkers text html latex example
description text html latex example
Note: removing empty section \examples in file 'diseq.Rd'
diseq text html latex
errorMetrics text html latex example
Note: removing empty section \examples in file 'extractAlleles.Rd'
extractAlleles text html latex
Note: removing empty section \details in file 'fastGrid.Rd'
Note: removing empty section \examples in file 'fastGrid.Rd'
fastGrid text html latex
founderGeneSet text html latex example
Note: removing empty section \seealso in file 'geneSet-class.Rd'
geneSet-class text html latex example
geneSet2Ped text html latex example
Note: removing empty section \details in file 'genotypeCoding.Rd'
Note: removing empty section \note in file 'genotypeCoding.Rd'
Note: removing empty section \references in file 'genotypeCoding.Rd'
Note: removing empty section \seealso in file 'genotypeCoding.Rd'
genotypeCoding text html latex example
genotypeLevels text html latex example
genotypeSummary text html latex example
genotypes text html latex example
gregorius text html latex example
haplo.em.w text html latex example
haplo.scan.w text html latex example
haplo.score.slide.w text html latex example
Note: removing empty section \author in file 'haplo.score.w.Rd'
haplo.score.w text html latex example
hapmapchr text html latex example
homozygote text html latex example
html text html latex example
left text html latex example
Note: removing empty section \details in file 'makeMarkerInfo.Rd'
Note: removing empty section \examples in file 'makeMarkerInfo.Rd'
makeMarkerInfo text html latex
Note: removing empty section \details in file 'makeTransTable.Rd'
Note: removing empty section \examples in file 'makeTransTable.Rd'
makeTransTable text html latex
Note: removing empty section \details in file 'makeTransTableList.Rd'
makeTransTableList text html latex example
markerInfo text html latex example
markerNames text html latex example
markerSummary text html latex example
missingCodes text html latex example
nallele text html latex example
nmarker text html latex example
notes text html latex example
ped2geneSet text html latex
phase text html latex example
ploidy text html latex example
print.LD text html latex example
qtlex text html latex example
read.pfizer text html latex example
read.phe text html latex example
readGenes text html latex example
Note: removing empty section \examples in file 'readGenes.ped.Rd'
readGenes.ped text html latex
Note: removing empty section \examples in file 'readGenes.perlegen.Rd'
readGenes.perlegen text html latex
readGenes.pfizer text html latex example
sampleInfo text html latex example
studyInfo text html latex example
transTables text html latex example
xbat text html latex example
** building package indices ...
Loading required package: methods
Loading required package: combinat
Attaching package: 'combinat'
The following object(s) are masked from package:utils :
combn
Loading required package: xtable
Loading required package: mvtnorm
Loading required package: haplo.stats
* DONE (GeneticsBase)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'GeneticsBase_1.8.0.tar.gz'