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BioC 3.5: CHECK report for DOQTL on veracruz2

This page was generated on 2017-08-16 13:32:07 -0400 (Wed, 16 Aug 2017).

Package 364/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOQTL 1.12.0
Daniel Gatti
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/DOQTL
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DOQTL
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DOQTL_1.12.0.tar.gz
StartedAt: 2017-08-16 02:09:58 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:16:42 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 403.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: DOQTL.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DOQTL_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DOQTL.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOQTL/DESCRIPTION’ ... OK
* this is package ‘DOQTL’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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
* 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.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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DOQTL.Rcheck/00check.log’
for details.


DOQTL.Rcheck/00install.out:

* installing *source* package ‘DOQTL’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DOrec.c -o DOrec.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DOstep.c -o DOstep.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c addlog.c -o addlog.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c emission_prob.c -o emission_prob.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c emission_prob2.c -o emission_prob2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter.smooth.allele.c -o filter.smooth.allele.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter.smooth.intensity.c -o filter.smooth.intensity.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c kinship.c -o kinship.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ri4hap.c -o ri4hap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c transition.c -o transition.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c update.alleles.c -o update.alleles.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c update.c -o update.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c viterbi.c -o viterbi.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DOQTL.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/DOQTL.Rcheck/DOQTL/libs
** 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
* DONE (DOQTL)

DOQTL.Rcheck/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s0.0010.0000.001
add.sig.thr0.0000.0000.001
add.slash0.0030.0010.004
addLog0.0010.0000.001
addLogVector0.0010.0000.001
assoc.map0.0010.0010.000
assoc.plot0.0010.0000.001
bayesint0.0010.0000.000
calc.genoprob0.0010.0010.001
calc.genoprob.alleles0.0000.0000.001
calc.genoprob.intensity0.0000.0000.001
categorize.variants0.9040.0322.236
cc.trans.probs0.0010.0000.000
cluster.strains0.6850.0150.738
coef.doqtl0.4690.2630.751
coefplot0.0010.0000.000
colSumsLog0.0020.0000.002
condense.model.probs0.0010.0000.001
condense.sanger.snps0.0010.0000.001
convert.allele.calls0.0000.0000.001
convert.genes.to.GRanges0.0000.0000.001
convert.genotypes0.0010.0000.000
convert.variants.to.GRanges0.3250.0150.343
convert.variants.to.numeric0.6640.0180.694
create.Rdata.files0.0010.0000.000
create.genotype.states0.0020.0000.003
create.html.page0.0010.0000.001
do.colors0.0020.0000.003
do.states0.0010.0000.001
do.trans.probs0.0000.0010.000
do2sanger000
emission.probs.allele000
estimate.cluster.params0.0010.0000.000
example.genes0.0010.0010.002
example.pheno0.0040.0010.004
example.qtl0.0010.0000.001
example.snps0.0020.0010.004
extract.raw.data0.0010.0000.001
fast.qtlrel0.0010.0000.000
fill.in.snps0.0010.0000.000
filter.geno.probs0.0000.0010.000
filter.samples0.0000.0000.001
find.overlapping.genes0.0000.0000.001
gene.plot0.0010.0000.001
generic.trans.probs0.0010.0000.001
genome.plots0.0000.0000.001
genome.summary.plots0.0000.0000.001
get.chr.lengths0.0030.0000.003
get.do.states0.0010.0010.002
get.gene.name0.0010.0000.001
get.machine.precision0.0010.0000.001
get.max.geno0.0000.0000.001
get.mgi.features000
get.num.auto000
get.pattern.variants000
get.pgw0.0000.0000.001
get.sig.thr0.0000.0000.001
get.strains0.0000.0000.001
get.trans.probs0.0000.0000.001
get.variants0.0010.0000.001
html.report0.0010.0000.000
impute.genotypes0.0010.0010.000
intensity.plots0.0000.0000.001
interpolate.markers0.0010.0000.000
kinship0.0000.0000.001
muga.snps.to.keep0.0880.0300.119
normalize.batches0.0000.0000.001
plot.doqtl0.0000.0000.001
pxg.plot0.0000.0000.001
qtl.LRS000
qtl.heatmap0.0000.0000.001
qtl.qtlrel0.0000.0010.001
qtl.simulate0.0010.0000.001
rankZ0.0020.0000.002
read.vcf0.0010.0010.000
scanone000
scanone.assoc000
scanone.eqtl0.0010.0000.000
scanone.perm0.0010.0000.000
sdp.plot0.0010.0000.001
sex.predict0.0000.0000.001
snp.plot0.0000.0000.001
summarize.genotype.transitions000
variant.plot000
write.founder.genomes000