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This page was generated on 2015-08-20 13:22:54 -0700 (Thu, 20 Aug 2015).
| Package 280/1069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| DOQTL 1.1.5 Daniel Gatti
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS |  | |||||
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| Package: DOQTL |
| Version: 1.1.5 |
| Command: 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_1.1.5.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_1.1.5.tar.gz |
| StartedAt: 2015-08-20 03:50:09 -0700 (Thu, 20 Aug 2015) |
| EndedAt: 2015-08-20 04:02:32 -0700 (Thu, 20 Aug 2015) |
| EllapsedTime: 743.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DOQTL.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### 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_1.1.5.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_1.1.5.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/DOQTL.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.1.5'
* 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 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
Package in Depends field not imported from: 'ggplot2'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 'hs.colors'
assoc.map: no visible binding for global variable 'pos'
assoc.map: no visible binding for global variable 'sdps'
assoc.scan1: possible error in scanone(pheno = pheno, pheno.col =
pheno.col, probs = tmp, K = K, addcovar = addcovar, markers =
markers[-nrow(markers), ]): unused argument (markers =
markers[-nrow(markers), ])
call.haps: no visible binding for global variable 'curr.snps'
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'
get.chr.lengths: no visible global function definition for 'seqlengths'
get.snp.patterns: no visible global function definition for
'unstrsplit'
plot.genoprobs: no visible binding for global variable 'hs.colors'
plot.genoprobs2: no visible global function definition for
'seqlengths<-'
pseudophase: no visible binding for global variable 'Rle'
pseudophase : <anonymous>: no visible global function definition for
'runValue'
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' 'get.diplotype2haplotype.matrix'
'get.snp.patterns'
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 '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.v4.snps.dbSNP.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.v4.snps.dbSNP.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 '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 'plot.genoprobs':
plot.genoprobs
Code: function(x, snps, colors = "DO", chrlen = "mm10", ...)
Docs: function(x, snps, colors = "mm10", chrlen = "mm10", ...)
Mismatches in argument default values:
Name: 'colors' Code: "DO" Docs: "mm10"
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
* 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' ... [28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
categorize.variants 1.28 0.03 8
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
categorize.variants 1.89 0.03 8.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [65s]
[66s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [58s]
[59s] 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.
DOQTL.Rcheck/00install.out:
install for i386 * installing *source* package 'DOQTL' ... ** libs gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c transition.c -o transition.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c update.c -o update.o gcc -m32 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o gcc -m32 -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/i386 -lR installing to D:/biocbld/bbs-3.2-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'scanone(pheno = pheno, ': unused argument (markers = markers[-nrow(markers), ]) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded install for x64 * installing *source* package 'DOQTL' ... ** libs gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c transition.c -o transition.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c update.c -o update.o gcc -m64 -I"D:/biocbld/BBS-3˜1.2-B/R/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local320/include" -O2 -Wall -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o gcc -m64 -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LD:/biocbld/BBS-3˜1.2-B/R/bin/x64 -lR installing to D:/biocbld/bbs-3.2-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'DOQTL' as DOQTL_1.1.5.zip * DONE (DOQTL)
DOQTL.Rcheck/examples_i386/DOQTL-Ex.timings:
| name | user | system | elapsed | |
| add.missing.F1s | 0 | 0 | 0 | |
| add.slash | 0 | 0 | 0 | |
| addLog | 0 | 0 | 0 | |
| addLogVector | 0 | 0 | 0 | |
| assoc.map | 0 | 0 | 0 | |
| assoc.plot | 0.02 | 0.00 | 0.01 | |
| bayesint | 0 | 0 | 0 | |
| calc.genoprob | 0 | 0 | 0 | |
| calc.genoprob.alleles | 0 | 0 | 0 | |
| calc.genoprob.intensity | 0 | 0 | 0 | |
| categorize.variants | 1.28 | 0.03 | 8.00 | |
| cc.trans.probs | 0 | 0 | 0 | |
| cluster.strains | 0.82 | 0.00 | 0.81 | |
| coef.doqtl | 0.43 | 0.11 | 0.55 | |
| coefplot | 0 | 0 | 0 | |
| colSumsLog | 0 | 0 | 0 | |
| condense.model.probs | 0 | 0 | 0 | |
| convert.allele.calls | 0 | 0 | 0 | |
| convert.genes.to.GRanges | 0 | 0 | 0 | |
| convert.genotypes | 0 | 0 | 0 | |
| convert.variants.to.GRanges | 0.67 | 0.02 | 0.69 | |
| convert.variants.to.numeric | 0.63 | 0.00 | 0.62 | |
| create.Rdata.files | 0 | 0 | 0 | |
| create.genotype.states | 0 | 0 | 0 | |
| create.html.page | 0 | 0 | 0 | |
| do.colors | 0 | 0 | 0 | |
| do.states | 0 | 0 | 0 | |
| do.trans.probs | 0 | 0 | 0 | |
| do2sanger | 0 | 0 | 0 | |
| emission.probs.allele | 0 | 0 | 0 | |
| estimate.cluster.params | 0 | 0 | 0 | |
| example.genes | 0.00 | 0.01 | 0.01 | |
| example.pheno | 0 | 0 | 0 | |
| example.qtl | 0 | 0 | 0 | |
| example.snps | 0.02 | 0.00 | 0.02 | |
| extract.raw.data | 0 | 0 | 0 | |
| fast.qtlrel | 0 | 0 | 0 | |
| fill.in.snps | 0 | 0 | 0 | |
| filter.geno.probs | 0 | 0 | 0 | |
| filter.samples | 0 | 0 | 0 | |
| find.overlapping.genes | 0 | 0 | 0 | |
| gene.plot | 0 | 0 | 0 | |
| generic.trans.probs | 0 | 0 | 0 | |
| genome.plots | 0 | 0 | 0 | |
| genome.summary.plots | 0 | 0 | 0 | |
| get.chr.lengths | 0.02 | 0.00 | 0.02 | |
| get.do.states | 0 | 0 | 0 | |
| get.gene.name | 0 | 0 | 0 | |
| get.machine.precision | 0 | 0 | 0 | |
| get.max.geno | 0 | 0 | 0 | |
| get.mgi.features | 0 | 0 | 0 | |
| get.num.auto | 0 | 0 | 0 | |
| get.pattern.variants | 0.47 | 0.02 | 0.49 | |
| get.strains | 0 | 0 | 0 | |
| get.trans.probs | 0 | 0 | 0 | |
| get.variants | 0 | 0 | 0 | |
| html.report | 0 | 0 | 0 | |
| intensity.plots | 0 | 0 | 0 | |
| kinship | 0 | 0 | 0 | |
| muga.snps.to.keep | 0.03 | 0.03 | 0.07 | |
| normalize.batches | 0 | 0 | 0 | |
| plot.doqtl | 0 | 0 | 0 | |
| pxg.plot | 0 | 0 | 0 | |
| qtl.LRS | 0 | 0 | 0 | |
| qtl.heatmap | 0 | 0 | 0 | |
| qtl.qtlrel | 0 | 0 | 0 | |
| qtl.simulate | 0 | 0 | 0 | |
| rankZ | 0 | 0 | 0 | |
| read.vcf | 0 | 0 | 0 | |
| scanone | 0 | 0 | 0 | |
| scanone.eqtl | 0 | 0 | 0 | |
| scanone.perm | 0 | 0 | 0 | |
| sdp.plot | 0 | 0 | 0 | |
| sex.predict | 0 | 0 | 0 | |
| snp.plot | 0 | 0 | 0 | |
| summarize.genotype.transitions | 0 | 0 | 0 | |
| variant.plot | 0 | 0 | 0 | |
| write.founder.genomes | 0 | 0 | 0 | |
DOQTL.Rcheck/examples_x64/DOQTL-Ex.timings:
| name | user | system | elapsed | |
| add.missing.F1s | 0 | 0 | 0 | |
| add.slash | 0 | 0 | 0 | |
| addLog | 0 | 0 | 0 | |
| addLogVector | 0 | 0 | 0 | |
| assoc.map | 0 | 0 | 0 | |
| assoc.plot | 0 | 0 | 0 | |
| bayesint | 0 | 0 | 0 | |
| calc.genoprob | 0 | 0 | 0 | |
| calc.genoprob.alleles | 0 | 0 | 0 | |
| calc.genoprob.intensity | 0 | 0 | 0 | |
| categorize.variants | 1.89 | 0.03 | 8.55 | |
| cc.trans.probs | 0 | 0 | 0 | |
| cluster.strains | 0.70 | 0.05 | 0.74 | |
| coef.doqtl | 0.53 | 0.08 | 0.61 | |
| coefplot | 0 | 0 | 0 | |
| colSumsLog | 0 | 0 | 0 | |
| condense.model.probs | 0.02 | 0.00 | 0.02 | |
| convert.allele.calls | 0 | 0 | 0 | |
| convert.genes.to.GRanges | 0 | 0 | 0 | |
| convert.genotypes | 0 | 0 | 0 | |
| convert.variants.to.GRanges | 0.81 | 0.02 | 0.83 | |
| convert.variants.to.numeric | 0.39 | 0.00 | 0.39 | |
| create.Rdata.files | 0 | 0 | 0 | |
| create.genotype.states | 0 | 0 | 0 | |
| create.html.page | 0 | 0 | 0 | |
| do.colors | 0.02 | 0.00 | 0.02 | |
| do.states | 0 | 0 | 0 | |
| do.trans.probs | 0 | 0 | 0 | |
| do2sanger | 0 | 0 | 0 | |
| emission.probs.allele | 0 | 0 | 0 | |
| estimate.cluster.params | 0 | 0 | 0 | |
| example.genes | 0 | 0 | 0 | |
| example.pheno | 0 | 0 | 0 | |
| example.qtl | 0 | 0 | 0 | |
| example.snps | 0 | 0 | 0 | |
| extract.raw.data | 0 | 0 | 0 | |
| fast.qtlrel | 0 | 0 | 0 | |
| fill.in.snps | 0 | 0 | 0 | |
| filter.geno.probs | 0 | 0 | 0 | |
| filter.samples | 0 | 0 | 0 | |
| find.overlapping.genes | 0 | 0 | 0 | |
| gene.plot | 0 | 0 | 0 | |
| generic.trans.probs | 0 | 0 | 0 | |
| genome.plots | 0 | 0 | 0 | |
| genome.summary.plots | 0 | 0 | 0 | |
| get.chr.lengths | 0 | 0 | 0 | |
| get.do.states | 0 | 0 | 0 | |
| get.gene.name | 0 | 0 | 0 | |
| get.machine.precision | 0 | 0 | 0 | |
| get.max.geno | 0 | 0 | 0 | |
| get.mgi.features | 0 | 0 | 0 | |
| get.num.auto | 0 | 0 | 0 | |
| get.pattern.variants | 0.76 | 0.01 | 0.78 | |
| get.strains | 0 | 0 | 0 | |
| get.trans.probs | 0.00 | 0.02 | 0.02 | |
| get.variants | 0 | 0 | 0 | |
| html.report | 0 | 0 | 0 | |
| intensity.plots | 0 | 0 | 0 | |
| kinship | 0 | 0 | 0 | |
| muga.snps.to.keep | 0.05 | 0.01 | 0.06 | |
| normalize.batches | 0 | 0 | 0 | |
| plot.doqtl | 0 | 0 | 0 | |
| pxg.plot | 0 | 0 | 0 | |
| qtl.LRS | 0 | 0 | 0 | |
| qtl.heatmap | 0 | 0 | 0 | |
| qtl.qtlrel | 0 | 0 | 0 | |
| qtl.simulate | 0 | 0 | 0 | |
| rankZ | 0 | 0 | 0 | |
| read.vcf | 0 | 0 | 0 | |
| scanone | 0 | 0 | 0 | |
| scanone.eqtl | 0 | 0 | 0 | |
| scanone.perm | 0 | 0 | 0 | |
| sdp.plot | 0 | 0 | 0 | |
| sex.predict | 0 | 0 | 0 | |
| snp.plot | 0 | 0 | 0 | |
| summarize.genotype.transitions | 0 | 0 | 0 | |
| variant.plot | 0 | 0 | 0 | |
| write.founder.genomes | 0 | 0 | 0 | |