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 |
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/GeneticsBase.buildbin-libdir
Using auto-selected zip options ' GeneticsBase-HELP=ziponly'
---------- Making package GeneticsBase ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making LdMax.d from LdMax.cpp
making R_bitArrayVector.d from R_bitArrayVector.cpp
making bitArrayVector.d from bitArrayVector.cpp
making convert.d from convert.cpp
making getLDdist.d from getLDdist.cpp
making readGenes.ped.d from readGenes.ped.cpp
making register.d from register.cpp
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp:157: warning: control reaches end of non-void function
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: control reaches end of non-void function
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:42: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:49: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:88: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:92: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:109: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:113: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:118: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:135: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:139: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:144: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:164: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:168: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:173: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:190: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:193: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:209: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:213: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:218: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:246: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:252: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:257: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:284: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:291: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:296: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::vector<unsigned int, std::allocator<unsigned int> >&, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:320: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:326: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:346: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:462: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:857: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:866: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:983: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1011: warning: comparison between signed and unsigned integer expressions
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c convert.cpp -o convert.o
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -IE:/biocbld/bbs-2.3-bioc/R/include -O2 -Wall -c register.cpp -o register.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I E:/biocbld/bbs-2.3-bioc/R/include -i GeneticsBase_res.rc -o GeneticsBase_res.o
g++ -shared -s -o GeneticsBase.dll GeneticsBase.def LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o GeneticsBase_res.o -LE:/biocbld/bbs-2.3-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package GeneticsBase 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
installing man source files
installing 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
not zipping data
installing help
>>> Building/Updating help pages for package 'GeneticsBase'
Formats: text html latex example chm
ALZH text html latex example chm
Note: removing empty section \details in file 'Armitage.Rd'
Note: removing empty section \seealso in file 'Armitage.Rd'
Note: removing empty section \details in file 'Armitage.Rd'
Note: removing empty section \seealso in file 'Armitage.Rd'
Armitage text html latex example chm
CAMP text html latex example chm
HWE text html latex example chm
HWE.chisq text html latex example chm
HWE.exact text html latex example chm
Note: removing empty section \seealso in file 'LD-class.Rd'
Note: removing empty section \seealso in file 'LD-class.Rd'
LD-class text html latex example chm
LD text html latex example chm
Note: removing empty section \seealso in file 'LDband-class.Rd'
Note: removing empty section \seealso in file 'LDband-class.Rd'
LDband-class text html latex example chm
LDdist-class text html latex chm
PGtables text html latex example chm
PerlgenExample text html latex example chm
PfizerExample text html latex example chm
alleleCount text html latex example chm
alleleLevels text html latex example chm
alleleSummary text html latex example chm
alleles text html latex example chm
Note: removing empty section \details in file 'as.geneSet.Rd'
Note: removing empty section \details in file 'as.geneSet.Rd'
as.geneSet text html latex example chm
binsearch text html latex example chm
callCodes text html latex example chm
ci.balance text html latex example chm
convert text html latex example chm
Note: removing empty section \details in file 'decodeCallCodes.Rd'
Note: removing empty section \details in file 'decodeCallCodes.Rd'
decodeCallCodes text html latex example chm
desMarkers text html latex example chm
description text html latex example chm
Note: removing empty section \examples in file 'diseq.Rd'
Note: removing empty section \examples in file 'diseq.Rd'
diseq text html latex chm
errorMetrics text html latex example chm
Note: removing empty section \examples in file 'extractAlleles.Rd'
Note: removing empty section \examples in file 'extractAlleles.Rd'
extractAlleles text html latex chm
Note: removing empty section \details in file 'fastGrid.Rd'
Note: removing empty section \examples in file 'fastGrid.Rd'
Note: removing empty section \details in file 'fastGrid.Rd'
Note: removing empty section \examples in file 'fastGrid.Rd'
fastGrid text html latex chm
founderGeneSet text html latex example chm
Note: removing empty section \seealso in file 'geneSet-class.Rd'
Note: removing empty section \seealso in file 'geneSet-class.Rd'
geneSet-class text html latex example chm
geneSet2Ped text html latex example chm
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'
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 chm
genotypeLevels text html latex example chm
genotypeSummary text html latex example chm
genotypes text html latex example chm
gregorius text html latex example chm
haplo.em.w text html latex example chm
haplo.scan.w text html latex example chm
haplo.score.slide.w text html latex example chm
Note: removing empty section \author in file 'haplo.score.w.Rd'
Note: removing empty section \author in file 'haplo.score.w.Rd'
haplo.score.w text html latex example chm
hapmapchr text html latex example chm
homozygote text html latex example chm
html text html latex example chm
left text html latex example chm
Note: removing empty section \details in file 'makeMarkerInfo.Rd'
Note: removing empty section \examples in file 'makeMarkerInfo.Rd'
Note: removing empty section \details in file 'makeMarkerInfo.Rd'
Note: removing empty section \examples in file 'makeMarkerInfo.Rd'
makeMarkerInfo text html latex chm
Note: removing empty section \details in file 'makeTransTable.Rd'
Note: removing empty section \examples in file 'makeTransTable.Rd'
Note: removing empty section \details in file 'makeTransTable.Rd'
Note: removing empty section \examples in file 'makeTransTable.Rd'
makeTransTable text html latex chm
Note: removing empty section \details in file 'makeTransTableList.Rd'
Note: removing empty section \details in file 'makeTransTableList.Rd'
makeTransTableList text html latex example chm
markerInfo text html latex example chm
markerNames text html latex example chm
markerSummary text html latex example chm
missingCodes text html latex example chm
nallele text html latex example chm
nmarker text html latex example chm
notes text html latex example chm
ped2geneSet text html latex chm
phase text html latex example chm
ploidy text html latex example chm
print.LD text html latex example chm
qtlex text html latex example chm
read.pfizer text html latex example chm
read.phe text html latex example chm
readGenes text html latex example chm
Note: removing empty section \examples in file 'readGenes.ped.Rd'
Note: removing empty section \examples in file 'readGenes.ped.Rd'
readGenes.ped text html latex chm
Note: removing empty section \examples in file 'readGenes.perlegen.Rd'
Note: removing empty section \examples in file 'readGenes.perlegen.Rd'
readGenes.perlegen text html latex chm
readGenes.pfizer text html latex example chm
sampleInfo text html latex example chm
studyInfo text html latex example chm
transTables text html latex example chm
xbat text html latex example chm
zipping help files
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.4992\GeneticsBase\chm\GeneticsBase.chm
Compile time: 0 minutes, 2 seconds
71 Topics
269 Local links
8 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\R.INSTALL.4992\GeneticsBase\chm\GeneticsBase.chm, 106,971 bytes
Compression decreased file by 194,208 bytes.
adding MD5 sums
packaged installation of package 'GeneticsBase' as GeneticsBase_1.8.0.zip
* DONE (GeneticsBase)