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### Running command:
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### rm -rf DOQTL.buildbin-libdir DOQTL.Rcheck && mkdir DOQTL.buildbin-libdir DOQTL.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.6.0.tar.gz >DOQTL.Rcheck\00install.out 2>&1 && cp DOQTL.Rcheck\00install.out DOQTL-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=DOQTL.buildbin-libdir --install="check:DOQTL-install.out" --force-multiarch --no-vignettes --timings DOQTL_1.6.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DOQTL.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.6.0'
* 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 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
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'
* 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.20140803.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.20140803.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.20140803.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.20140803.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 ... 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-3.2-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386/DOQTL.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-3.2-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/x64/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' ... [21s] OK
** running examples for arch 'x64' ... [24s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [50s]
[51s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [49s]
[49s] 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, 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/DOQTL.Rcheck/00check.log'
for details.
