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Package 151/389HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: GeneticsBase
Version: 1.14.0
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneticsBase_1.14.0.tar.gz
StartedAt: 2010-10-04 16:58:42 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:00:19 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 96.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneticsBase.Rcheck
Warnings: 2

Command output

* 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
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'alleles':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'callCodes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'marker'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'description':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'errorMetrics':
  \title
  \description
  \details
  \author
  \note
  \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
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'genotypes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'haplo.em.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.scan.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.score.slide.w':
  \note

Auto-generated content requiring editing in Rd object 'haplo.score.w':
  \note

Auto-generated content requiring editing in Rd object 'left':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'x'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'markerInfo':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'markerNames':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Argument items with no description in Rd object 'markerSummary':
  covariate

Auto-generated content requiring editing in Rd object 'missingCodes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'nallele':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'nmarker':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'

Auto-generated content requiring editing in Rd object 'notes':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'phase':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'ploidy':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'read.pfizer':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'file'
  \arguments, description of item 'verbose'

Auto-generated content requiring editing in Rd object 'sampleInfo':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

Auto-generated content requiring editing in Rd object 'studyInfo':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'

Auto-generated content requiring editing in Rd object 'transTables':
  \title
  \description
  \details
  \author
  \note
  \arguments, description of item 'object'
  \arguments, description of item 'value'
  \arguments, description of item '\dots'

* 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

GeneticsBase.Rcheck/00install.out:

* 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)

GeneticsBase.Rcheck/GeneticsBase-Ex.timings:

nameusersystemelapsed
ALZH0.080.000.08
Armitage000
CAMP0.210.020.22
HWE8.640.298.94
HWE.chisq0.120.030.15
HWE.exact0.140.020.16
LD-class000
LD0.520.020.53
LDband-class000
PGtables000
PerlgenExample0.010.000.01
PfizerExample0.050.000.05
alleleCount000
alleleLevels000
alleleSummary0.360.000.36
alleles000
as.geneSet0.050.000.05
binsearch000
callCodes000
ci.balance000
convert000
decodeCallCodes000
desMarkers000
description000
errorMetrics000
founderGeneSet0.120.020.15
geneSet-class000
geneSet2Ped0.160.000.15
genotypeCoding0.390.010.41
genotypeLevels000
genotypeSummary1.530.001.53
genotypes000
gregorius000
haplo.em.w000
haplo.scan.w000
haplo.score.slide.w000
haplo.score.w000
hapmapchr0.470.000.47
homozygote0.190.000.19
html4.640.054.70
left000
makeTransTableList000
markerInfo000
markerNames000
markerSummary2.390.002.40
missingCodes000
nallele000
nmarker000
notes000
phase000
ploidy000
print.LD0.260.000.27
qtlex0.520.000.52
read.pfizer000
read.phe0.590.020.61
readGenes000
readGenes.pfizer0.070.000.06
sampleInfo000
studyInfo000
transTables000
xbat0.540.030.58