Package: GeneticsBase

Version: 1.14.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings GeneticsBase_1.14.0.tar.gz

StartedAt: 2010-10-04 17:43:21 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:44:36 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 75.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneticsBase.Rcheck

Warnings: 2

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 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 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: 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: LDband-class.Rd:43-44: Dropping empty section \seealso
prepare_Rd: LD-class.Rd:50-51: Dropping empty section \seealso
prepare_Rd: makeMarkerInfo.Rd:16-17: Dropping empty section \details
prepare_Rd: makeMarkerInfo.Rd:27-28: Dropping empty section \examples
prepare_Rd: makeTransTableList.Rd:14-15: Dropping empty section \details
prepare_Rd: makeTransTable.Rd:16-17: Dropping empty section \details
prepare_Rd: makeTransTable.Rd:24-25: Dropping empty section \examples
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
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  \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 '\dots'

Auto-generated content requiring editing in Rd object 'alleles':
  \title
  \description
  \details
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Auto-generated content requiring editing in Rd object 'callCodes':
  \title
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  \arguments, description of item 'marker'
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Auto-generated content requiring editing in Rd object 'description':
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Auto-generated content requiring editing in Rd object 'errorMetrics':
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Auto-generated content requiring editing in Rd object 'geneSet-class':
  \note

Auto-generated content requiring editing in Rd object 'genotypeLevels':
  \title
  \description
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  \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':
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Auto-generated content requiring editing in Rd object 'markerInfo':
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Auto-generated content requiring editing in Rd object 'markerNames':
  \title
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Argument items with no description in Rd object 'markerSummary':
  covariate

Auto-generated content requiring editing in Rd object 'missingCodes':
  \title
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Auto-generated content requiring editing in Rd object 'nallele':
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Auto-generated content requiring editing in Rd object 'nmarker':
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Auto-generated content requiring editing in Rd object 'notes':
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Auto-generated content requiring editing in Rd object 'phase':
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Auto-generated content requiring editing in Rd object 'ploidy':
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Auto-generated content requiring editing in Rd object 'read.pfizer':
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Auto-generated content requiring editing in Rd object 'sampleInfo':
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Auto-generated content requiring editing in Rd object 'studyInfo':
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Auto-generated content requiring editing in Rd object 'transTables':
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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
  /loc/home/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/00check.log
for details

* install options are ' --no-html'

* installing *source* package 'GeneticsBase' ...
** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c LdMax.cpp -o LdMax.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c R_bitArrayVector.cpp -o R_bitArrayVector.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c bitArrayVector.cpp -o bitArrayVector.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c convert.cpp -o convert.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c getLDdist.cpp -o getLDdist.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readGenes.ped.cpp -o readGenes.ped.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c register.cpp -o register.o
g++ -shared -L/usr/local/lib64 -o GeneticsBase.so LdMax.o R_bitArrayVector.o bitArrayVector.o convert.o getLDdist.o readGenes.ped.o register.o -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/GeneticsBase.Rcheck/GeneticsBase/libs
** 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)

name	user	system	elapsed
ALZH	0.044	0.004	0.047
Armitage	0.000	0.000	0.001
CAMP	0.128	0.012	0.139
HWE	7.616	0.132	7.825
HWE.chisq	0.092	0.000	0.094
HWE.exact	0.088	0.004	0.091
LD-class	0	0	0
LD	0.364	0.008	0.375
LDband-class	0	0	0
PGtables	0	0	0
PerlgenExample	0.012	0.004	0.016
PfizerExample	0.052	0.000	0.052
alleleCount	0.000	0.000	0.001
alleleLevels	0	0	0
alleleSummary	0.288	0.004	0.294
alleles	0	0	0
as.geneSet	0.036	0.004	0.040
binsearch	0.004	0.004	0.006
callCodes	0	0	0
ci.balance	0.000	0.004	0.003
convert	0.000	0.000	0.002
decodeCallCodes	0.004	0.000	0.002
desMarkers	0	0	0
description	0	0	0
errorMetrics	0	0	0
founderGeneSet	0.084	0.000	0.083
geneSet-class	0	0	0
geneSet2Ped	0.096	0.000	0.095
genotypeCoding	0.272	0.000	0.274
genotypeLevels	0	0	0
genotypeSummary	1.312	0.004	1.315
genotypes	0	0	0
gregorius	0.000	0.000	0.002
haplo.em.w	0	0	0
haplo.scan.w	0	0	0
haplo.score.slide.w	0	0	0
haplo.score.w	0.000	0.000	0.001
hapmapchr	0.340	0.004	0.342
homozygote	0.124	0.008	0.133
html	3.980	0.008	3.989
left	0	0	0
makeTransTableList	0	0	0
markerInfo	0.004	0.000	0.000
markerNames	0	0	0
markerSummary	2.285	0.012	2.333
missingCodes	0	0	0
nallele	0	0	0
nmarker	0.000	0.000	0.001
notes	0	0	0
phase	0	0	0
ploidy	0	0	0
print.LD	0.184	0.000	0.183
qtlex	0.296	0.004	0.299
read.pfizer	0	0	0
read.phe	0.368	0.000	0.369
readGenes	0	0	0
readGenes.pfizer	0.056	0.000	0.056
sampleInfo	0	0	0
studyInfo	0	0	0
transTables	0.000	0.000	0.001
xbat	0.376	0.000	0.378