DOQTL 1.3.1
Daniel Gatti
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DOQTL | | Last Changed Rev: 107674 / Revision: 107696 | | Last Changed Date: 2015-08-21 14:17:35 -0700 (Fri, 21 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| 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 | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DOQTL_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DOQTL.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOQTL/DESCRIPTION’ ... OK
* this is package ‘DOQTL’ version ‘1.3.1’
* 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 ... [56s/62s] 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
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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/33s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
categorize.variants 2.794 0.071 9.905
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [53s/61s]
[53s/61s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/DOQTL.Rcheck/00check.log’
for details.