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CHECK report for DOQTL on merida2

This page was generated on 2019-04-09 13:29:55 -0400 (Tue, 09 Apr 2019).

Package 450/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOQTL 1.19.0
Daniel Gatti
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DOQTL
Branch: master
Last Commit: 499bfbe
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: DOQTL
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DOQTL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DOQTL_1.19.0.tar.gz
StartedAt: 2019-04-09 00:34:37 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 00:41:02 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 385.0 seconds
RetCode: 1
Status:  ERROR 
CheckDir: DOQTL.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DOQTL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DOQTL_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.19.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'scanOne(y = pheno, x = addcovar, ': unused argument (intcovar = intcovar) 
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 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 ‘sdps’
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’
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<-’
do.pca: no visible global function definition for ‘impute.knn’
dohap2sanger: no visible global function definition for ‘runValue’
find.overlapping.genes: no visible global function definition for
  ‘subjectHits’
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.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’
impute.genotypes: no visible global function definition for ‘rowRanges’
qtl.qtlrel: possible error in scanOne(y = pheno, x = addcovar, prdat =
  prdat, vc = vc, intcovar = intcovar, numGeno = TRUE, test = "None"):
  unused argument (intcovar = intcovar)
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 ‘subjectHits’
s1.assoc: no visible global function definition for ‘queryHits’
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:
  MM_geno Rle chr i impute.knn makeCluster metadata<- obj org.Hs.egPMID
  org.Mm.egPMID org.Mm.egSYMBOL2EG queryHits rowRanges rowRanges<-
  runValue sdps seqlengths stopCluster subjectHits theta.rho.covars
  theta.rho.means unstrsplit
* 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:
  ‘check.do.coat.color’ ‘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 '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, 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 ... WARNING
Documented arguments not in \usage in documentation object 'plot.genoprobs':
  ‘genome’

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
  FAILURE in test_qtlrel_vs_matrixqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) : 
    Mean relative difference: 3.600419
  
  
  Test files with failing tests
  
     test_qtl.R 
       test_qtlrel_vs_fastqtl 
       test_qtlrel_vs_matrixqtl 
  
  
  Error in BiocGenerics:::testPackage("DOQTL") : 
    unit tests failed for package DOQTL
  Execution halted
* 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: 1 ERROR, 5 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.Rcheck/00check.log’
for details.


Installation output

DOQTL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DOQTL
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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 -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/DOQTL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'scanOne(y = pheno, x = addcovar, ': unused argument (intcovar = intcovar) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DOQTL)

Tests output

DOQTL.Rcheck/tests/runTests.Rout.fail


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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> BiocGenerics:::testPackage("DOQTL")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:Biostrings':

    type

The following objects are masked from 'package:base':

    aperm, apply, rowsum


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

[1] "Retrieved 23114 SNPs."
[1] "Retaining 20706 high quality SNPs."
[1] "Retaining 11156 polymorphic SNPs."
R/QTLRel is loaded

[1] "Mapping with 141 samples."
[1] "Mapping with 537 markers."
[1] "WBC1"
SNP 0
SNP 0
[1] "Mapping with 141 samples."
[1] "Mapping with 537 markers."
[1] "WBC1"
SNP 0
   We now use 'E' (not 'EE') for residual variance matrix; see documentation.
Timing stopped at: 4.19 0.406 5.447
Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq$lod[, 7],  : 
  Mean relative difference: 3.531309

In addition: Warning message:
In .vcf_map_samples(samples(hdr), samples) :
  samples not in file: 'C57BL_6J'
SNP 0
   We now use 'E' (not 'EE') for residual variance matrix; see documentation.
   We now use 'E' (not 'EE') for residual variance matrix; see documentation.
[1] "Time: 0.195999999999998 sec."
Timing stopped at: 5.058 0.667 6.585
Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) : 
  Mean relative difference: 3.600419



RUNIT TEST PROTOCOL -- Tue Apr  9 00:40:54 2019 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
DOQTL RUnit Tests - 7 test functions, 0 errors, 2 failures
FAILURE in test_qtlrel_vs_fastqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq$lod[, 7],  : 
  Mean relative difference: 3.531309

FAILURE in test_qtlrel_vs_matrixqtl: Error in checkEqualsNumeric(target = qt$lod[, 7], current = fq[, 1], tolerance = 0.1) : 
  Mean relative difference: 3.600419


Test files with failing tests

   test_qtl.R 
     test_qtlrel_vs_fastqtl 
     test_qtlrel_vs_matrixqtl 


Error in BiocGenerics:::testPackage("DOQTL") : 
  unit tests failed for package DOQTL
Execution halted

Example timings

DOQTL.Rcheck/DOQTL-Ex.timings

nameusersystemelapsed
add.missing.F1s0.0010.0010.001
add.sig.thr0.0000.0010.001
add.slash0.0050.0010.005
addLog000
addLogVector0.0010.0000.002
assoc.map0.0010.0000.000
assoc.plot0.0000.0010.000
bayesint000
calc.genoprob000
calc.genoprob.alleles0.0000.0000.001
calc.genoprob.intensity000
cc.trans.probs0.0010.0000.000
cluster.strains0.2670.0270.296
coef.doqtl0.6330.3180.957
coefplot0.0000.0010.000
colSumsLog0.0010.0000.001
condense.model.probs0.0010.0000.000
condense.sanger.snps000
convert.allele.calls0.0000.0010.000
convert.genes.to.GRanges000
convert.genotypes000
convert.variants.to.GRanges0.9640.0280.999
convert.variants.to.numeric0.2100.0160.227
create.Rdata.files0.0000.0000.001
create.genotype.states0.0020.0000.003
create.html.page0.0010.0000.001
do.colors0.0020.0000.003
do.states0.0010.0010.001
do.trans.probs000
do2sanger0.0000.0000.001
emission.probs.allele0.0000.0010.000
estimate.cluster.params000
example.genes0.0030.0020.004
example.pheno0.0040.0000.004
example.qtl0.0000.0000.001
example.snps0.0020.0020.004
extract.raw.data000
fast.qtlrel0.0010.0000.001
fill.in.snps000
filter.geno.probs000
filter.samples000
find.overlapping.genes000
gene.plot000
generic.trans.probs0.0010.0000.000
genome.plots000
genome.summary.plots000
get.chr.lengths0.0070.0010.008
get.do.states0.0010.0000.001
get.gene.name000
get.machine.precision0.0000.0000.001
get.max.geno000
get.mgi.features0.0000.0000.001
get.num.auto0.0010.0000.000
get.pattern.variants0.0000.0000.001
get.pgw000
get.sig.thr0.0000.0000.001
get.strains000
get.trans.probs0.0000.0000.001
get.variants000
html.report000
impute.genotypes0.0000.0010.001
intensity.plots0.0010.0000.000
interpolate.markers0.0000.0000.001
kinship000
muga.snps.to.keep0.0840.0280.112
normalize.batches000
plot.doqtl000
pxg.plot000
qtl.LRS000
qtl.heatmap000
qtl.qtlrel000
qtl.simulate000
rankZ0.0010.0000.001
read.vcf000
scanone0.0010.0000.000
scanone.assoc000
scanone.eqtl0.0000.0010.000
scanone.perm000
sdp.plot000
sex.predict0.0000.0000.001
snp.plot0.0000.0000.001
summarize.genotype.transitions0.0000.0000.001
variant.plot0.0000.0000.001
write.founder.genomes0.0000.0000.001