GeneticsBase 1.14.0
The R Genetics Project
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/GeneticsBase | | Last Changed Rev: 46401 / Revision: 49923 | | Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneticsBase/DESCRIPTION' ... OK
* this is package 'GeneticsBase' version '1.14.0'
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
haplo.em.w: no visible global function definition for
'haplo.em.control'
haplo.em.w: no visible global function definition for 'haplo.em'
haplo.scan.w: no visible global function definition for
'haplo.em.control'
haplo.scan.w: no visible global function definition for
'score.sim.control'
haplo.scan.w: no visible global function definition for 'haplo.scan'
haplo.score.slide.w: no visible global function definition for
'score.sim.control'
haplo.score.slide.w: no visible global function definition for
'haplo.em.control'
haplo.score.slide.w: no visible global function definition for
'haplo.score.slide'
haplo.score.w: no visible global function definition for
'score.sim.control'
haplo.score.w: no visible global function definition for
'haplo.em.control'
haplo.score.w: no visible global function definition for 'haplo.score'
plot,LD: no visible binding for global variable 'y'
* checking Rd files ... NOTE
prepare_Rd: Armitage.Rd:30-31: Dropping empty section \details
prepare_Rd: Armitage.Rd:73: Dropping empty section \seealso
prepare_Rd: LD-class.Rd:50-51: Dropping empty section \seealso
prepare_Rd: LDband-class.Rd:43-44: Dropping empty section \seealso
prepare_Rd: as.geneSet.Rd:78-80: Dropping empty section \details
prepare_Rd: decodeCallCodes.Rd:29-30: Dropping empty section \details
prepare_Rd: diseq.Rd:113-114: Dropping empty section \examples
prepare_Rd: extractAlleles.Rd:25-27: Dropping empty section \examples
prepare_Rd: fastGrid.Rd:13-14: Dropping empty section \details
prepare_Rd: fastGrid.Rd:24-25: Dropping empty section \examples
prepare_Rd: geneSet-class.Rd:159-160: Dropping empty section \seealso
prepare_Rd: genotypeCoding.Rd:19-20: Dropping empty section \details
prepare_Rd: genotypeCoding.Rd:31: Dropping empty section \note
prepare_Rd: genotypeCoding.Rd:25: Dropping empty section \references
prepare_Rd: genotypeCoding.Rd:32: Dropping empty section \seealso
prepare_Rd: haplo.score.w.Rd:119: Dropping empty section \author
prepare_Rd: makeMarkerInfo.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMarkerInfo.Rd:27-28: Dropping empty section \examples
prepare_Rd: makeTransTable.Rd:16-17: Dropping empty section \details
prepare_Rd: makeTransTable.Rd:24-25: Dropping empty section \examples
prepare_Rd: makeTransTableList.Rd:14-15: Dropping empty section \details
prepare_Rd: readGenes.ped.Rd:35-36: Dropping empty section \examples
prepare_Rd: readGenes.perlegen.Rd:19-20: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: 'bootstrap', 'haplo.stats'
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'LD-class':
Slots for class 'LD'
Code: call D D' LOD n P-value r R^2 X^2
Docs: \special{D'}: call D LOD n P-value r R^2 X^2
S4 class codoc mismatches from documentation object 'LDband-class':
Slots for class 'LDband'
Code: call D D' LOD n P-value r R^2 X^2
Docs: \special{D'}: call D LOD n P-value r R^2 X^2
S4 class codoc mismatches from documentation object 'LDdist-class':
Slots for class 'LDdist'
Code: call D D' LOD n P-value r R^2 X^2
Docs: \special{D'}: call D LOD n P-value r R^2 X^2
* checking Rd \usage sections ... OK
* checking Rd contents ... WARNING
Auto-generated content requiring editing in Rd object 'LD-class':
\note
Auto-generated content requiring editing in Rd object 'LDband-class':
\note
Auto-generated content requiring editing in Rd object 'PGtables':
\title
\description
\details
\author
\note
\arguments, description of item 'x'
\arguments, description of item 'filename'
\arguments, description of item 'format'
\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'alleleCount':
\title
\description
\details
\author
\note
\arguments, description of item 'object'
\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'alleleLevels':
\title
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\arguments, description of item 'object'
\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'alleles':
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\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'callCodes':
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\arguments, description of item 'marker'
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Auto-generated content requiring editing in Rd object 'errorMetrics':
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\arguments, description of item 'object'
\arguments, description of item 'value'
Auto-generated content requiring editing in Rd object 'geneSet-class':
\note
Auto-generated content requiring editing in Rd object 'genotypeLevels':
\title
\description
\details
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\arguments, description of item 'object'
\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'genotypes':
\title
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\arguments, description of item '\dots'
Auto-generated content requiring editing in Rd object 'haplo.em.w':
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Argument items with no description in Rd object 'markerSummary':
covariate
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* 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
* checking examples ... OK
* checking tests ...
Running 'ExampleScript001.R'
Running 'test.R'
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings, see
D:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/00check.log
for details
* install options are ' --no-html'
* installing *source* package 'GeneticsBase' ...
** libs
making DLL ...
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c LdMax.cpp -o LdMax.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c R_bitArrayVector.cpp -o R_bitArrayVector.o
R_bitArrayVector.cpp: In function 'SEXPREC* finalizeBitArrayVector(SEXPREC*)':
R_bitArrayVector.cpp:36: warning: no return statement in function returning non-void
R_bitArrayVector.cpp: In function 'int test()':
R_bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
R_bitArrayVector.cpp:157: warning: no return statement in function returning non-void
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c bitArrayVector.cpp -o bitArrayVector.o
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int, unsigned int)':
bitArrayVector.cpp:43: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:50: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(bool*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:89: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:93: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(short int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:110: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:114: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:119: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(int*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:136: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:140: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:145: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(unsigned int*, unsigned int, unsigned int, bool, bool)':
bitArrayVector.cpp:165: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:169: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:174: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(double*, unsigned int, unsigned int)':
bitArrayVector.cpp:191: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:194: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char*, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:210: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:214: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:219: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(char**, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:247: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:253: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:258: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In constructor 'bitArrayVector::bitArrayVector(std::string*, unsigned int, unsigned int, bool, int)':
bitArrayVector.cpp:285: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:292: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:297: 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:321: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:327: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp: In member function 'unsigned int bitArrayVector::getElement(unsigned int, bool)':
bitArrayVector.cpp:347: warning: unused variable 'mask'
bitArrayVector.cpp: In member function 'void bitArrayVector::setElement(unsigned int, unsigned int, unsigned int, bool)':
bitArrayVector.cpp:463: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:550: warning: suggest parentheses around '-' inside '<<'
bitArrayVector.cpp:551: warning: suggest parentheses around '-' inside '<<'
bitArrayVector.cpp: In function 'int main()':
bitArrayVector.cpp:858: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:867: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:984: warning: comparison between signed and unsigned integer expressions
bitArrayVector.cpp:1012: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c convert.cpp -o convert.o
convert.cpp:1:2: warning: #import is a deprecated GCC extension
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c getLDdist.cpp -o getLDdist.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c readGenes.ped.cpp -o readGenes.ped.o
x86_64-w64-mingw32-g++ -I"D:/biocbld/bbs-2.6-bioc/R/include" -O2 -Wall -c register.cpp -o register.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o GeneticsBase.dll tmp.def LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/GeneticsBase/libs/x64
... done
** R
** data
** inst
** preparing package for lazy loading
Attaching package: 'combinat'
The following object(s) are masked from 'package:utils':
combn
** help
*** installing help indices
** building package indices ...
Reading 2 markers and 901 subjects from ` ALZH.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` ALZH.ped '.
Number of Markers: 2
Number of Subjects: 901
Number of Families: 308
Reading 8 markers and 2011 subjects from ` CAMP.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` CAMP.ped '.
Number of Markers: 8
Number of Subjects: 2011
Number of Families: 651
Reading 12 vars from `CAMPZ.phe' ... Done.
Number of Phenotype Variables: 12
Number of Observations : 2011
Loading file... done.
Number of markers : 29
Number of observations: 1008
Read 95 lines containing 3 Markers from 2 Genes on 33 Samples.
Reading 722 markers and 90 subjects from ` hapmapchr22.ped ' ...
generating 'geneSet' object...
100 200 300 400 500 600 700 Successfully read the pedigree file ` hapmapchr22.ped '.
Number of Markers: 722
Number of Subjects: 90
Number of Families: 20
Reading 53 markers and 3000 subjects from ` qtl.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` qtl.ped '.
Number of Markers: 53
Number of Subjects: 3000
Number of Families: 1000
Reading 1 vars from `qtl.phe' ... Done.
Number of Phenotype Variables: 1
Number of Observations : 1000
Reading 50 markers and 3000 subjects from ` xbat.ped ' ...
generating 'geneSet' object...
Successfully read the pedigree file ` xbat.ped '.
Number of Markers: 50
Number of Subjects: 3000
Number of Families: 1000
Reading 22 vars from `xbat.phe' ... Done.
Number of Phenotype Variables: 22
Number of Observations : 1000
** testing if installed package can be loaded
* DONE (GeneticsBase)