CRAN Package Check Results for Package coloc

Last updated on 2017-10-17 01:47:50.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.3-1 3.06 53.39 56.45 NOTE
r-devel-linux-x86_64-debian-gcc 2.3-1 4.34 56.58 60.92 NOTE
r-devel-linux-x86_64-fedora-clang 2.3-1 122.44 NOTE
r-devel-linux-x86_64-fedora-gcc 2.3-1 123.32 NOTE
r-devel-windows-ix86+x86_64 2.3-1 9.00 97.00 106.00 NOTE
r-patched-linux-x86_64 2.3-1 3.48 52.91 56.40 NOTE
r-patched-solaris-x86 2.3-1 157.70 NOTE
r-release-linux-x86_64 2.3-1 3.70 52.33 56.03 NOTE
r-release-windows-ix86+x86_64 2.3-1 14.00 134.00 148.00 NOTE
r-release-osx-x86_64 2.3-1 WARN
r-oldrel-windows-ix86+x86_64 2.3-1 12.00 133.00 145.00 NOTE
r-oldrel-osx-x86_64 2.3-1 NOTE

Check Details

Version: 2.3-1
Check: R code for possible problems
Result: NOTE
    approx.bf.p: no visible global function definition for ‘qnorm’
    coeff.plot: no visible global function definition for ‘polygon’
    coeff.plot: no visible global function definition for ‘abline’
    coeff.plot: no visible global function definition for ‘arrows’
    coeff.plot: no visible global function definition for ‘points’
    coeff.plot: no visible global function definition for ‘segments’
    coloc.abf.snpStats: no visible global function definition for
     ‘single.snp.tests’
    coloc.abf.snpStats: no visible global function definition for
     ‘col.summary’
    coloc.bma: no visible global function definition for ‘as.formula’
    coloc.bma: no visible global function definition for ‘glm’
    coloc.bma: no visible global function definition for ‘coefficients’
    coloc.bma : <anonymous>: no visible global function definition for
     ‘combn’
    coloc.bma: no visible global function definition for ‘vcov’
    coloc.combine: no visible global function definition for ‘var’
    coloc.combine: no visible global function definition for ‘pf’
    coloc.combine: no visible global function definition for ‘pchisq’
    coloc.test: no visible global function definition for ‘coefficients’
    coloc.test: no visible global function definition for ‘vcov’
    coloc.test.summary : findmin: no visible global function definition for
     ‘optimize’
    coloc.test.summary: no visible global function definition for
     ‘integrate’
    coloc.test.summary : pv: no visible global function definition for
     ‘pchisq’
    coloc.test.summary : bf.calc: no visible global function definition for
     ‘integrate’
    credible.interval: no visible global function definition for ‘optimize’
    credible.interval: no visible global function definition for
     ‘integrate’
    extra.plot: no visible global function definition for ‘axis’
    extra.plot: no visible global function definition for ‘box’
    extra.plot: no visible global function definition for ‘abline’
    fillin: no visible global function definition for ‘col.summary’
    fillin: no visible global function definition for ‘snp.imputation’
    fillin: no visible global function definition for ‘impute.snps’
    pcs.model: no visible global function definition for ‘as.formula’
    pcs.model: no visible global function definition for ‘glm’
    pcs.model: no visible global function definition for ‘coefficients’
    pcs.prepare: no visible global function definition for ‘prcomp’
    prepare.df: no visible global function definition for ‘cor’
    sdY.est: no visible global function definition for ‘lm’
    sdY.est: no visible global function definition for ‘coef’
    p.value,coloc: no visible global function definition for ‘pchisq’
    plot,colocPCs-missing: no visible binding for global variable ‘object’
    plot,colocPCs-missing: no visible global function definition for
     ‘abline’
    Undefined global functions or variables:
     abline arrows as.formula axis box coef coefficients col.summary combn
     cor glm impute.snps integrate lm object optimize pchisq pf points
     polygon prcomp qnorm segments single.snp.tests snp.imputation var
     vcov
    Consider adding
     importFrom("graphics", "abline", "arrows", "axis", "box", "points",
     "polygon", "segments")
     importFrom("stats", "as.formula", "coef", "coefficients", "cor", "glm",
     "integrate", "lm", "optimize", "pchisq", "pf", "prcomp",
     "qnorm", "var", "vcov")
     importFrom("utils", "combn")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.3-1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘snpStats’
Flavor: r-release-osx-x86_64

Version: 2.3-1
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘vignette.Rnw’
     ...
     values.against
    values.for c(-0.1, 1) c(0.9, 1.1)
     c(-0.1, 1) 1.00000 0.05150753
     c(0.9, 1.1) 19.41464 1.00000000
    
    > library(snpStats)
    
     When sourcing ‘vignette.R’:
    Error: there is no package called ‘snpStats’
    Execution halted
Flavor: r-release-osx-x86_64

Version: 2.3-1
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Warning in E1ot$app1 - E0ot$app1 :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in E1ot$app1 - E0ot$app1 :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in E1ot$app1 - E0ot$app1 :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in E1ot$app1 - E0ot$app1 :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    Warning in E1ot$app1 - E0ot$app1 :
     Recycling array of length 1 in vector-array arithmetic is deprecated.
     Use c() or as.vector() instead.
    
    
    Error: processing vignette 'vignette.Rnw' failed with diagnostics:
     chunk 7
    Error in library(snpStats) : there is no package called ‘snpStats’
    Execution halted
Flavor: r-release-osx-x86_64