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 working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.3-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneticsBase' 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 ... NOTE
plot,LD: no visible binding for global variable ‘y’
* 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 GeneticsBase-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.3-bioc/meat/GeneticsBase.Rcheck/tests'
Running 'ExampleScript001.R'
Running 'test.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.3-bioc/meat/GeneticsBase.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... OK
* creating GeneticsBase-manual.tex ... OK
* checking GeneticsBase-manual.tex using pdflatex ... OK
* Installing *source* package 'GeneticsBase' ...
** libs
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -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:549: warning: suggest parentheses around + or - inside shift
bitArrayVector.cpp:550: warning: suggest parentheses around + or - inside shift
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++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c convert.cpp -o convert.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c getLDdist.cpp -o getLDdist.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c LdMax.cpp -o LdMax.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -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++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I/home/biocbuild/bbs-2.3-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c register.cpp -o register.o
g++ -shared -L/usr/local/lib64 -o GeneticsBase.so bitArrayVector.o convert.o getLDdist.o LdMax.o R_bitArrayVector.o readGenes.ped.o register.o -L/home/biocbuild/bbs-2.3-bioc/R/lib -lR
** 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'
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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)