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BioC 3.4: CHECK report for DOQTL on moscato1

This page was generated on 2016-09-21 03:45:58 -0700 (Wed, 21 Sep 2016).

Package 333/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOQTL 1.9.5
Daniel Gatti
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DOQTL
Last Changed Rev: 120772 / Revision: 121152
Last Changed Date: 2016-09-06 12:24:24 -0700 (Tue, 06 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DOQTL
Version: 1.9.5
Command: rm -rf DOQTL.buildbin-libdir DOQTL.Rcheck && mkdir DOQTL.buildbin-libdir DOQTL.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.9.5.tar.gz >DOQTL.Rcheck\00install.out 2>&1 && cp DOQTL.Rcheck\00install.out DOQTL-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DOQTL.buildbin-libdir --install="check:DOQTL-install.out" --force-multiarch --no-vignettes --timings DOQTL_1.9.5.tar.gz
StartedAt: 2016-09-20 07:21:32 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:31:14 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 581.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DOQTL.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DOQTL.buildbin-libdir DOQTL.Rcheck && mkdir DOQTL.buildbin-libdir DOQTL.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.9.5.tar.gz >DOQTL.Rcheck\00install.out 2>&1 && cp DOQTL.Rcheck\00install.out DOQTL-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DOQTL.buildbin-libdir --install="check:DOQTL-install.out" --force-multiarch --no-vignettes --timings DOQTL_1.9.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DOQTL.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DOQTL/DESCRIPTION' ... OK
* this is package 'DOQTL' version '1.9.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'DOQTL' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'genoprob.helper'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
impute.genotypes: warning in GRanges(seqnames = seqnames(gr), range =
  IRanges(start = start(gr) * 1e+06, end = end(gr) * 1e+06)): partial
  argument match of 'range' to 'ranges'
add.sig.thr: no visible global function definition for 'lines'
add.sig.thr: no visible global function definition for 'abline'
assoc.map: no visible binding for global variable 'sdps'
assoc.plot: no visible global function definition for 'par'
assoc.plot: no visible global function definition for 'layout'
assoc.plot: no visible global function definition for 'plot'
assoc.plot: no visible global function definition for 'mtext'
assoc.scan1: no visible global function definition for 'pchisq'
assoc.scan1.perms: no visible global function definition for 'pchisq'
batch.normalize: no visible global function definition for 'read.delim'
batch.normalize: no visible global function definition for
  'write.table'
bayesint: no visible global function definition for 'approx'
calc.genoprob: no visible binding for global variable 'code'
calc.genoprob.intensity: no visible global function definition for
  'aggregate'
calc.genoprob2: no visible global function definition for 'makeCluster'
calc.genoprob2: no visible binding for global variable 'i'
calc.genoprob2: no visible global function definition for 'stopCluster'
check.do.coat.color: no visible global function definition for
  'check.genotypes'
check.genotype: no visible binding for global variable 'marker'
check.genotype: no visible global function definition for 'name'
check.genotype: no visible binding for global variable 'gt.ok'
check.genotype: no visible binding for global variable 'coat.ok'
chr.skeletons: no visible global function definition for 'par'
chr.skeletons: no visible global function definition for 'plot'
chr.skeletons: no visible global function definition for 'lines'
chr.skeletons: no visible global function definition for 'abline'
chr.skeletons: no visible global function definition for 'mtext'
cluster.strains: no visible global function definition for 'hclust'
cluster.strains: no visible global function definition for 'as.dist'
coefplot: no visible global function definition for 'par'
coefplot: no visible global function definition for 'layout'
coefplot: no visible global function definition for 'plot'
coefplot: no visible global function definition for 'abline'
coefplot: no visible global function definition for 'points'
coefplot: no visible global function definition for 'axis'
coefplot: no visible global function definition for 'rect'
coefplot: no visible global function definition for 'rgb'
coefplot: no visible global function definition for 'mtext'
condense.sanger.snps: no visible global function definition for
  'makeCluster'
condense.sanger.snps: no visible binding for global variable 'chr'
condense.sanger.snps: no visible global function definition for
  'stopCluster'
condense.sanger.snps: no visible global function definition for
  'read.delim'
convert.genes.to.GRanges: no visible global function definition for
  'metadata<-'
convert.variants.to.GRanges: no visible global function definition for
  'metadata<-'
create.Rdata.files: no visible global function definition for
  'read.delim'
create.html.page: no visible global function definition for 'png'
create.html.page: no visible global function definition for 'dev.off'
do.pca: no visible global function definition for 'impute.knn'
do.pca: no visible global function definition for 'princomp'
dohap2sanger: no visible global function definition for 'runValue'
estimate.cluster.params: no visible global function definition for
  'aggregate'
estimate.cluster.params2: no visible global function definition for
  'aggregate'
extract.raw.data: no visible global function definition for
  'read.delim'
extract.raw.data: no visible global function definition for
  'write.table'
fast.qtlrel: no visible global function definition for 'pchisq'
filter.samples: no visible global function definition for 'read.delim'
filter.samples: no visible global function definition for 'write.table'
find.overlapping.genes: no visible global function definition for
  'subjectHits'
founder.F1.intensity.plot: no visible global function definition for
  'plot'
founder.F1.intensity.plot: no visible global function definition for
  'points'
gene.plot: no visible global function definition for 'plot'
gene.plot: no visible global function definition for 'par'
gene.plot: no visible global function definition for 'mtext'
gene.plot: no visible global function definition for 'strwidth'
gene.plot: no visible binding for global variable 'strwidth'
gene.plot: no visible global function definition for 'strheight'
gene.plot: no visible global function definition for 'rect'
gene.plot: no visible global function definition for 'text'
genomic.points: no visible global function definition for 'points'
genoprob.helper: no visible binding for global variable
  'theta.rho.means'
genoprob.helper: no visible binding for global variable
  'theta.rho.covars'
genotype.by.sample.barplot: no visible global function definition for
  'par'
genotype.by.sample.barplot: no visible global function definition for
  'colorRampPalette'
genotype.by.sample.barplot: no visible global function definition for
  'rgb'
genotype.by.sample.barplot: no visible global function definition for
  'text'
genotype.by.snp.barplot: no visible global function definition for
  'layout'
genotype.by.snp.barplot: no visible global function definition for
  'par'
genotype.by.snp.barplot: no visible global function definition for
  'barplot'
genotype.by.snp.barplot: no visible global function definition for
  'axis'
genotype.by.snp.barplot: no visible global function definition for
  'abline'
genotype.by.snp.barplot: no visible global function definition for
  'mtext'
genotype.by.snp.barplot: no visible global function definition for
  'text'
get.chr.lengths: no visible global function definition for 'seqlengths'
get.gene.locations: no visible global function definition for
  'strheight'
get.gene.locations: no visible global function definition for
  'strwidth'
get.snp.details: no visible global function definition for 'rowRanges'
get.snp.details: no visible global function definition for
  'rowRanges<-'
get.snp.patterns: no visible global function definition for
  'unstrsplit'
get.snp.patterns: no visible global function definition for 'rowRanges'
html.report: no visible global function definition for 'write.csv'
impute.genotypes: no visible global function definition for 'rowRanges'
intensity.mean.covar.plot: no visible global function definition for
  'par'
intensity.mean.covar.plot: no visible global function definition for
  'plot'
intensity.mean.covar.plot: no visible global function definition for
  'lines'
intensity.mean.covar.plot: no visible global function definition for
  'points'
permutations.qtl.LRS: no visible global function definition for
  'pchisq'
plot.doqtl: no visible global function definition for 'par'
plot.doqtl: no visible global function definition for 'plot'
plot.doqtl: no visible global function definition for 'rect'
plot.doqtl: no visible global function definition for 'rgb'
plot.doqtl: no visible global function definition for 'text'
plot.doqtl : <anonymous>: no visible global function definition for
  'points'
plot.genoprobs: no visible global function definition for 'par'
plot.genoprobs.max: no visible global function definition for 'rect'
plot.genoprobs.probs: no visible global function definition for 'rect'
plot.haplogroups: no visible global function definition for 'layout'
plot.haplogroups: no visible global function definition for 'plot'
plot.scanone.assoc: no visible global function definition for 'plot'
plot.scanone.assoc: no visible global function definition for 'axis'
plot.scanone.assoc: no visible global function definition for 'mtext'
prsmth.plot: no visible global function definition for 'par'
prsmth.plot: no visible global function definition for 'grey'
prsmth.plot: no visible global function definition for 'abline'
prsmth.plot: no visible global function definition for 'mtext'
pxg.plot: no visible global function definition for 'par'
pxg.plot: no visible global function definition for 'plot'
pxg.plot: no visible global function definition for 'abline'
pxg.plot: no visible global function definition for 'points'
pxg.plot: no visible global function definition for 'rgb'
pxg.plot: no visible global function definition for 'title'
pxg.plot: no visible global function definition for 'axis'
pxg.plot: no visible global function definition for 'lines'
qtl.LRS: no visible global function definition for 'pchisq'
qtl.heatmap: no visible global function definition for 'par'
qtl.heatmap: no visible global function definition for 'hclust'
qtl.heatmap: no visible global function definition for 'as.dist'
qtl.heatmap: no visible global function definition for 'as.dendrogram'
qtl.heatmap: no visible global function definition for 'layout'
qtl.heatmap: no visible global function definition for 'plot'
qtl.heatmap: no visible global function definition for
  'colorRampPalette'
qtl.heatmap: no visible global function definition for 'gray'
qtl.heatmap: no visible global function definition for 'rgb'
qtl.heatmap: no visible global function definition for 'abline'
qtl.heatmap: no visible global function definition for 'mtext'
qtl.heatmap: no visible global function definition for 'rect'
qtl.qtlrel: no visible global function definition for 'pchisq'
qtl.simulate: no visible global function definition for 'rnorm'
qtl.simulate: no visible global function definition for 'rexp'
qtl.simulate: no visible global function definition for 'runif'
query.pubmed: no visible binding for global variable
  'org.Mm.egSYMBOL2EG'
query.pubmed: no visible global function definition for 'read.delim'
query.pubmed: no visible binding for global variable 'org.Mm.egPMID'
query.pubmed: no visible binding for global variable 'org.Hs.egPMID'
rankZ: no visible global function definition for 'qnorm'
read.muga.data: no visible binding for global variable 'MM_geno'
s1.assoc: no visible global function definition for 'subjectHits'
s1.assoc: no visible global function definition for 'queryHits'
s1.assoc: no visible global function definition for 'pchisq'
s1.assoc: no visible global function definition for 'Rle'
scanone.assoc: no visible global function definition for 'makeCluster'
scanone.assoc: no visible binding for global variable 'obj'
scanone.assoc: no visible global function definition for 'stopCluster'
scanone.perm: no visible global function definition for 'write.table'
sdp.plot: no visible global function definition for 'plot'
sdp.plot: no visible global function definition for 'abline'
sdp.plot: no visible global function definition for 'box'
sdp.plot: no visible global function definition for 'mtext'
sdp.plot: no visible global function definition for 'axis'
sdp.plot: no visible global function definition for 'lines'
sex.predict: no visible global function definition for 'lm'
sex.predict: no visible global function definition for 'predict'
sex.predict: no visible global function definition for 'par'
sex.predict: no visible global function definition for 'legend'
snp.plot: no visible global function definition for 'par'
snp.plot: no visible global function definition for 'layout'
snp.plot: no visible global function definition for 'mtext'
snp.plot: no visible global function definition for 'abline'
snp.plot: no visible global function definition for 'axis'
snp.plot: no visible global function definition for 'rect'
snp.plot: no visible global function definition for 'rgb'
snp.plot: no visible global function definition for 'lines'
snp.plot: no visible global function definition for 'text'
snp.plot: no visible global function definition for 'approx'
snp.plot: no visible global function definition for 'colorRampPalette'
tabulate.geno: no visible global function definition for 'rnorm'
write.founder.genomes: no visible global function definition for
  'write.csv'
write.genoprob.plots: no visible global function definition for 'png'
write.genoprob.plots: no visible global function definition for
  'dev.off'
write.results: no visible global function definition for 'write.table'
Undefined global functions or variables:
  MM_geno Rle abline aggregate approx as.dendrogram as.dist axis
  barplot box check.genotypes chr coat.ok code colorRampPalette dev.off
  gray grey gt.ok hclust i impute.knn layout legend lines lm
  makeCluster marker metadata<- mtext name obj org.Hs.egPMID
  org.Mm.egPMID org.Mm.egSYMBOL2EG par pchisq plot png points predict
  princomp qnorm queryHits read.delim rect rexp rgb rnorm rowRanges
  rowRanges<- runValue runif sdps seqlengths stopCluster strheight
  strwidth subjectHits text theta.rho.covars theta.rho.means title
  unstrsplit write.csv write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "gray", "grey",
             "png", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
             "legend", "lines", "mtext", "par", "plot", "points", "rect",
             "strheight", "strwidth", "text", "title")
  importFrom("stats", "aggregate", "approx", "as.dendrogram", "as.dist",
             "hclust", "lm", "pchisq", "predict", "princomp", "qnorm",
             "rexp", "rnorm", "runif")
  importFrom("utils", "read.delim", "write.csv", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plot.doqtl.Rd':
  'get.sig.thr()'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'dof1.trans.probs' 'genoprobs2hapblocks'
  'get.diplotype2haplotype.matrix' 'get.genotype' 'get.haplogroup'
  'get.snp.patterns' 'haploprobs2hapblocks' 'hs.colors' 'hsrat.colors'
  'write.unc.hap.file'
Undocumented data sets:
  'hs.colors' 'hsrat.colors'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'add.missing.F1s':
add.missing.F1s
  Code: function(founders, snps, sampletype = c("DO", "CC", "DOF1",
                 "HS", "HSrat", "other"))
  Docs: function(founders, snps, sampletype = c("DO", "CC", "DOF1",
                 "HS", "other"))
  Mismatches in argument default values:
    Name: 'sampletype' Code: c("DO", "CC", "DOF1", "HS", "HSrat", "other") Docs: c("DO", "CC", "DOF1", "HS", "other")

Codoc mismatches from documentation object 'assoc.map':
assoc.map
  Code: function(pheno, pheno.col = 1, probs, K, addcovar, snps, chr,
                 start, end, model = c("additive", "dominance",
                 "full"), scan = c("one", "two"), output = c("lod",
                 "p-value", "bic"), snp.file =
                 "ftp://ftp.jax.org/SNPtools/variants/mgp.v5.merged.snps_all.dbSNP142.vcf.gz",
                 cross = c("DO", "CC", "HS"))
  Docs: function(pheno, pheno.col = 1, probs, K, addcovar, snps, chr,
                 start, end, model = c("additive", "dominance",
                 "full"), scan = c("one", "two"), output = c("lod",
                 "p-value", "bic"), snp.file =
                 "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz")
  Argument names in code not in docs:
    cross
  Mismatches in argument default values:
    Name: 'snp.file' Code: "ftp://ftp.jax.org/SNPtools/variants/mgp.v5.merged.snps_all.dbSNP142.vcf.gz" Docs: "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz"

Codoc mismatches from documentation object 'assoc.plot':
assoc.plot
  Code: function(results, mgi.file =
                 "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz",
                 highlight, highlight.col = "red", thr, show.sdps =
                 FALSE, ...)
  Docs: function(results, mgi.file =
                 "ftp://ftp.jax.org/SNPtools/genes/MGI.20130703.sorted.txt.gz",
                 highlight, highlight.col = "red", thr, show.sdps =
                 FALSE, ...)
  Mismatches in argument default values:
    Name: 'mgi.file' Code: "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz" Docs: "ftp://ftp.jax.org/SNPtools/genes/MGI.20130703.sorted.txt.gz"

Codoc mismatches from documentation object 'assoc.scan1':
assoc.scan1
  Code: function(pheno, pheno.col, probs, K, addcovar, sdps, markers,
                 model, output)
  Docs: function(pheno, pheno.col, probs, K, addcovar, sdps, snps,
                 model, output)
  Argument names in code not in docs:
    markers
  Argument names in docs not in code:
    snps
  Mismatches in argument names:
    Position: 7 Code: markers Docs: snps

Codoc mismatches from documentation object 'calc.genoprob':
calc.genoprob
  Code: function(data, chr = "all", output.dir = ".", plot = TRUE,
                 array = c("gigamuga", "megamuga", "muga", "other"),
                 sampletype = c("DO", "CC", "DOF1", "HS", "HSrat",
                 "other"), method = c("intensity", "allele"), clust =
                 c("mclust", "pamk"), founders, transprobs, snps)
  Docs: function(data, chr = "all", output.dir = ".", plot = TRUE,
                 array = c("gigamuga", "megamuga", "muga", "other"),
                 sampletype = c("DO", "CC", "DOF1", "other"), method =
                 c("intensity", "allele"), founders, transprobs, snps)
  Argument names in code not in docs:
    clust
  Mismatches in argument names:
    Position: 8 Code: clust Docs: founders
    Position: 9 Code: founders Docs: transprobs
    Position: 10 Code: transprobs Docs: snps
  Mismatches in argument default values:
    Name: 'sampletype' Code: c("DO", "CC", "DOF1", "HS", "HSrat", "other") Docs: c("DO", "CC", "DOF1", "other")

Codoc mismatches from documentation object 'calc.genoprob.intensity':
calc.genoprob.intensity
  Code: function(data, chr, founders, snps, output.dir = ".",
                 trans.prob.fxn, plot = FALSE, clust = c("mclust",
                 "pamk"))
  Docs: function(data, chr, founders, snps, output.dir = ".",
                 trans.prob.fxn, plot = FALSE)
  Argument names in code not in docs:
    clust

Codoc mismatches from documentation object 'convert.allele.calls':
convert.allele.calls
  Code: function(geno1, geno2)
  Docs: function(geno)
  Argument names in code not in docs:
    geno1 geno2
  Argument names in docs not in code:
    geno
  Mismatches in argument names:
    Position: 1 Code: geno1 Docs: geno

Codoc mismatches from documentation object 'do.trans.probs':
do.trans.probs
  Code: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"),
                 gen)
  Docs: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"),
                 do.gen)
  Argument names in code not in docs:
    gen
  Argument names in docs not in code:
    do.gen
  Mismatches in argument names:
    Position: 5 Code: gen Docs: do.gen

Codoc mismatches from documentation object 'do2sanger':
do2sanger
  Code: function(do.files, snps, output.file = "do2sanger.txt",
                 snp.file =
                 "ftp://ftp.jax.org/SNPtools/variants/mgp.v4.snps.dbSNP.vcf.gz",
                 return.val = c("numeric", "character"))
  Docs: function(do.files, snps, output.file = "do2sanger.txt",
                 snp.file =
                 "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz")
  Argument names in code not in docs:
    return.val
  Mismatches in argument default values:
    Name: 'snp.file' Code: "ftp://ftp.jax.org/SNPtools/variants/mgp.v4.snps.dbSNP.vcf.gz" Docs: "ftp://ftp.jax.org/SNPtools/variants/cc.snps.NCBI38.txt.gz"

Codoc mismatches from documentation object 'estimate.cluster.params':
estimate.cluster.params
  Code: function(founders, data, chr, clust = c("mclust", "pamk"))
  Docs: function(founders, data, chr)
  Argument names in code not in docs:
    clust

Codoc mismatches from documentation object 'extract.raw.data':
extract.raw.data
  Code: function(in.path = ".", prefix, out.path = ".", array =
                 c("gigamuga", "megamuga", "muga"))
  Docs: function(in.path = ".", prefix, out.path = ".", array =
                 c("megamuga", "muga"))
  Mismatches in argument default values:
    Name: 'array' Code: c("gigamuga", "megamuga", "muga") Docs: c("megamuga", "muga")

Codoc mismatches from documentation object 'generic.trans.probs':
generic.trans.probs
  Code: function(states, snps, chr = "1", sex = c("M", "F"))
  Docs: function(states, snps, chr = c(1:19, "X"), sex = c("M", "F"))
  Mismatches in argument default values:
    Name: 'chr' Code: "1" Docs: c(1:19, "X")

Codoc mismatches from documentation object 'plot.genoprobs':
plot.genoprobs
  Code: function(x, snps, colors = "DO", chrlen = "mm10", type =
                 c("max", "probs"), legend = TRUE, ...)
  Docs: function(x, snps, colors = "DO", chrlen = "mm10", ...)
  Argument names in code not in docs:
    type legend
  Mismatches in argument names:
    Position: 5 Code: type Docs: ...
write.genoprob.plots
  Code: function(path = ".", snps, type = c("max", "probs"))
  Docs: function(path = ".", snps)
  Argument names in code not in docs:
    type

Codoc mismatches from documentation object 'get.mgi.features':
get.mgi.features
  Code: function(file =
                 "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz",
                 chr = NULL, start = NULL, end = NULL, source =
                 c("all", "MGI", "VEGA", "ENSEMBL", "Blat",
                 "NCBI_Gene"), type = c("all", "gene",
                 "pseudogenic_transcript", "pseudogenic_exon",
                 "pseudogene", "match", "match-part", "transcript",
                 "exon", "mRNA", "five_prime_UTR", "start_codon",
                 "CDS", "stop_codon", "three_prime_UTR",
                 "pseudogenic_mRNA", "pseudogenic_start_codon",
                 "pseudogenic_CDS", "pseudogenic_stop_codon",
                 "pseudogenic_five_prime_UTR",
                 "pseudogenic_three_prime_UTR", "sequence_feature"))
  Docs: function(file =
                 "ftp://ftp.jax.org/SNPtools/genes/MGI.20140803.sorted.txt",
                 chr = NULL, start = NULL, end = NULL, source =
                 c("all", "MGI", "VEGA", "ENSEMBL", "Blat",
                 "NCBI_Gene"), type = c("all", "gene",
                 "pseudogenic_transcript", "pseudogenic_exon",
                 "pseudogene", "match", "match-part", "transcript",
                 "exon", "mRNA", "five_prime_UTR", "start_codon",
                 "CDS", "stop_codon", "three_prime_UTR",
                 "pseudogenic_mRNA", "pseudogenic_start_codon",
                 "pseudogenic_CDS", "pseudogenic_stop_codon",
                 "pseudogenic_five_prime_UTR",
                 "pseudogenic_three_prime_UTR", "sequence_feature"))
  Mismatches in argument default values:
    Name: 'file' Code: "ftp://ftp.jax.org/SNPtools/genes/MGI.sorted.txt.gz" Docs: "ftp://ftp.jax.org/SNPtools/genes/MGI.20140803.sorted.txt"

Codoc mismatches from documentation object 'get.trans.probs':
get.trans.probs
  Code: function(r, do.gen, alpha, chr = "1", sex = c("M", "F"))
  Docs: function(r, do.gen, alpha, chr = c(1:19, "X"), sex = c("M",
                 "F"))
  Mismatches in argument default values:
    Name: 'chr' Code: "1" Docs: c(1:19, "X")

Codoc mismatches from documentation object 'hmm':
hmm.intensity
  Code: function(data, founders, sex, snps, chr, trans.prob.fxn, clust
                 = c("mclust", "pamk"))
  Docs: function(data, founders, sex, snps, chr, trans.prob.fxn)
  Argument names in code not in docs:
    clust

Codoc mismatches from documentation object 'qtl.LRS':
permutations.qtl.LRS
  Code: function(pheno, probs, snps, addcovar, nperm = 1000, return.val
                 = c("lod", "p"))
  Docs: function(pheno, probs, snps, addcovar, nperm = 1000, return.val
                 = c("lrs", "p"))
  Mismatches in argument default values:
    Name: 'return.val' Code: c("lod", "p") Docs: c("lrs", "p")

Codoc mismatches from documentation object 'scanone.assoc':
scanone.assoc
  Code: function(pheno, pheno.col, probs, K, addcovar, intcovar,
                 markers, cross = c("DO", "CC", "HS"), sdp.file, ncl)
  Docs: function(pheno, pheno.col, probs, K, addcovar, markers, cross =
                 c("DO", "CC", "HS"), sdp.file, ncl)
  Argument names in code not in docs:
    intcovar
  Mismatches in argument names (first 3):
    Position: 6 Code: intcovar Docs: markers
    Position: 7 Code: markers Docs: cross
    Position: 8 Code: cross Docs: sdp.file

Codoc mismatches from documentation object 'scanone.perm':
scanone.perm
  Code: function(pheno, pheno.col = 1, probs, K = K, addcovar,
                 intcovar, snps, model = c("additive", "full"), path =
                 ".", nperm = 1000, return.val = c("lod", "p"))
  Docs: function(pheno, pheno.col = 1, probs, addcovar, intcovar, snps,
                 model = c("additive", "full"), path = ".", nperm =
                 1000)
  Argument names in code not in docs:
    K return.val
  Mismatches in argument names (first 3):
    Position: 4 Code: K Docs: addcovar
    Position: 5 Code: addcovar Docs: intcovar
    Position: 6 Code: intcovar Docs: snps

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plot.genoprobs':
  'genome'

Undocumented arguments in documentation object 'get.chr.lengths'
  'genome'

Undocumented arguments in documentation object 'interpolate.markers'
  'from' 'to'

Bad \usage lines found in documentation object 'condense.sanger.snps':
    condense.sanger.snps = function(markers, snp.file, strains, hdf.file, ncl = 1)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386/DOQTL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/DOQTL.Rcheck/00check.log'
for details.


DOQTL.Rcheck/00install.out:


install for i386

* installing *source* package 'DOQTL' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c emission_prob2.c -o emission_prob2.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transition.c -o transition.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c update.c -o update.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DOQTL' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c emission_prob2.c -o emission_prob2.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transition.c -o transition.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c update.c -o update.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DOQTL' as DOQTL_1.9.5.zip
* DONE (DOQTL)

DOQTL.Rcheck/examples_i386/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s000
add.sig.thr000
add.slash0.010.000.01
addLog000
addLogVector000
assoc.map000
assoc.plot000
bayesint000
calc.genoprob000
calc.genoprob.alleles000
calc.genoprob.intensity000
categorize.variants0.860.003.42
cc.trans.probs000
cluster.strains0.530.010.55
coef.doqtl0.420.130.54
coefplot000
colSumsLog000
condense.model.probs000
condense.sanger.snps000
convert.allele.calls000
convert.genes.to.GRanges000
convert.genotypes000
convert.variants.to.GRanges0.530.000.51
convert.variants.to.numeric0.500.010.52
create.Rdata.files000
create.genotype.states000
create.html.page000
do.colors0.010.000.01
do.states000
do.trans.probs000
do2sanger000
emission.probs.allele000
estimate.cluster.params000
example.genes0.000.020.02
example.pheno000
example.qtl000
example.snps0.000.010.02
extract.raw.data000
fast.qtlrel000
fill.in.snps000
filter.geno.probs000
filter.samples000
find.overlapping.genes000
gene.plot000
generic.trans.probs000
genome.plots000
genome.summary.plots000
get.chr.lengths000
get.do.states000
get.gene.name000
get.machine.precision000
get.max.geno000
get.mgi.features000
get.num.auto000
get.pattern.variants000
get.pgw000
get.sig.thr000
get.strains000
get.trans.probs000
get.variants000
html.report000
impute.genotypes000
intensity.plots000
interpolate.markers000
kinship000
muga.snps.to.keep0.050.000.05
normalize.batches000
plot.doqtl000
pxg.plot000
qtl.LRS000
qtl.heatmap000
qtl.qtlrel000
qtl.simulate000
rankZ000
read.vcf000
scanone000
scanone.assoc000
scanone.eqtl000
scanone.perm000
sdp.plot000
sex.predict000
snp.plot000
summarize.genotype.transitions000
variant.plot000
write.founder.genomes000

DOQTL.Rcheck/examples_x64/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s000
add.sig.thr000
add.slash000
addLog000
addLogVector000
assoc.map000
assoc.plot000
bayesint000
calc.genoprob000
calc.genoprob.alleles000
calc.genoprob.intensity000
categorize.variants1.610.053.81
cc.trans.probs000
cluster.strains0.780.020.80
coef.doqtl0.420.040.47
coefplot000
colSumsLog000
condense.model.probs000
condense.sanger.snps000
convert.allele.calls000
convert.genes.to.GRanges000
convert.genotypes000
convert.variants.to.GRanges0.640.000.64
convert.variants.to.numeric0.640.010.66
create.Rdata.files000
create.genotype.states000
create.html.page000
do.colors000
do.states000
do.trans.probs000
do2sanger000
emission.probs.allele000
estimate.cluster.params000
example.genes000
example.pheno000
example.qtl000
example.snps000
extract.raw.data0.020.000.01
fast.qtlrel000
fill.in.snps000
filter.geno.probs000
filter.samples000
find.overlapping.genes000
gene.plot000
generic.trans.probs000
genome.plots000
genome.summary.plots000
get.chr.lengths000
get.do.states000
get.gene.name000
get.machine.precision000
get.max.geno000
get.mgi.features000
get.num.auto000
get.pattern.variants000
get.pgw000
get.sig.thr000
get.strains000
get.trans.probs000
get.variants000
html.report000
impute.genotypes000
intensity.plots000
interpolate.markers000
kinship000
muga.snps.to.keep0.030.000.03
normalize.batches000
plot.doqtl000
pxg.plot000
qtl.LRS000
qtl.heatmap000
qtl.qtlrel000
qtl.simulate000
rankZ000
read.vcf000
scanone000
scanone.assoc000
scanone.eqtl000
scanone.perm000
sdp.plot000
sex.predict000
snp.plot000
summarize.genotype.transitions000
variant.plot000
write.founder.genomes000