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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DOQTL_1.4.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DOQTL.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.4.4’
* 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 ... [31s/31s] 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
assoc.map: no visible binding for global variable ‘pos’
assoc.map: no visible binding for global variable ‘sdps’
calc.genoprob: no visible binding for global variable ‘code’
calc.genoprob.alleles: no visible binding for global variable
‘curr.chr’
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’
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’
convert.genes.to.GRanges: no visible global function definition for
‘metadata<-’
convert.variants.to.GRanges: no visible global function definition for
‘metadata<-’
dohap2sanger: no visible global function definition for ‘runValue’
emission.probs.intensity2: no visible binding for global variable
‘C_emission_prob2’
genoprob.helper: no visible binding for global variable
‘theta.rho.means’
genoprob.helper: no visible binding for global variable
‘theta.rho.covars’
get.chr.lengths: no visible global function definition for ‘seqlengths’
get.snp.patterns: no visible global function definition for
‘unstrsplit’
parameter.update.intensity2: no visible binding for global variable
‘C_update_intensity2’
query.pubmed: no visible binding for global variable
‘org.Mm.egSYMBOL2EG’
query.pubmed: no visible binding for global variable ‘org.Mm.egPMID’
query.pubmed: no visible binding for global variable ‘org.Hs.egPMID’
read.muga.data: no visible binding for global variable ‘MM_geno’
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’
Undefined global functions or variables:
C_emission_prob2 C_update_intensity2 MM_geno Rle check.genotypes chr
coat.ok code curr.chr gt.ok i makeCluster marker metadata<- name obj
org.Hs.egPMID org.Mm.egPMID org.Mm.egSYMBOL2EG pos runValue sdps
seqlengths stopCluster theta.rho.covars theta.rho.means unstrsplit
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘condense.sanger.snps’ ‘dof1.trans.probs’
‘get.diplotype2haplotype.matrix’ ‘get.snp.patterns’ ‘scanone.assoc’
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)
Argument names in code not in docs:
sampletype
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("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: 'array' Code: c("gigamuga", "megamuga", "muga", "other") Docs: c("megamuga", "muga", "other")
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 'condense.model.probs':
condense.model.probs
Code: function(path = ".", write = "founder.probs.Rdata", model =
c("additive", "dominance", "full"), cross = "DO")
Docs: function(path = ".", write, model = c("additive", "dominance",
"full"))
Argument names in code not in docs:
cross
Mismatches in argument default values:
Name: 'write' Code: "founder.probs.Rdata" Docs:
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 'create.Rdata.files':
create.Rdata.files
Code: function(prob.files, cross = "DO")
Docs: function(prob.files)
Argument names in code not in docs:
cross
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 = "mm10", chrlen = "mm10", ...)
Argument names in code not in docs:
type legend
Mismatches in argument names:
Position: 5 Code: type Docs: ...
Mismatches in argument default values:
Name: 'colors' Code: "DO" Docs: "mm10"
chr.skeletons
Code: function(chr, chrlen = "mm10", ...)
Docs: function(chr, genome = "mm10", ...)
Argument names in code not in docs:
chrlen
Argument names in docs not in code:
genome
Mismatches in argument names:
Position: 2 Code: chrlen Docs: genome
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.chr.lengths':
get.chr.lengths
Code: function(genome = "mm10")
Docs: function()
Argument names in code not in docs:
genome
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.20130703.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"))
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.20130703.sorted.txt.gz"
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 'read.vcf':
read.vcf
Code: function(vcf.file, gr, chr = 1, start = 4, end = 4.5, strains,
return.val = c("allele", "number"), return.qual =
TRUE, csq = FALSE)
Docs: function(vcf.file, chr = 1, start = 4, end = 4.5, strains,
return.val = c("allele", "number"), return.qual =
TRUE, csq = FALSE)
Argument names in code not in docs:
gr
Mismatches in argument names (first 3):
Position: 2 Code: gr Docs: chr
Position: 3 Code: chr Docs: start
Position: 4 Code: start Docs: end
Codoc mismatches from documentation object 'scanone.perm':
scanone.perm
Code: function(pheno, pheno.col = 1, probs, 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:
return.val
* checking Rd \usage sections ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [24s/26s]
[24s/27s] 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: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/DOQTL.Rcheck/00check.log’
for details.
