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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DOQTL_1.9.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DOQTL.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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: 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 ... 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
‘/home/biocbuild/bbs-3.4-bioc/meat/DOQTL.Rcheck/00check.log’
for details.
