CRAN Package Check Results for Package coloc

Last updated on 2016-08-30 12:46:52.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.3-1 3.19 47.93 51.11 NOTE
r-devel-linux-x86_64-debian-gcc 2.3-1 3.31 46.89 50.20 NOTE
r-devel-linux-x86_64-fedora-clang 2.3-1 107.52 NOTE
r-devel-linux-x86_64-fedora-gcc 2.3-1 101.69 NOTE
r-devel-osx-x86_64-clang 2.3-1 80.94 NOTE
r-devel-windows-ix86+x86_64 2.3-1 14.00 132.00 146.00 NOTE
r-patched-linux-x86_64 2.3-1 3.55 48.20 51.75 NOTE
r-patched-solaris-sparc 2.3-1 622.10 NOTE
r-patched-solaris-x86 2.3-1 132.50 NOTE
r-release-linux-x86_64 2.3-1 3.44 46.38 49.81 NOTE
r-release-osx-x86_64-mavericks 2.3-1 NOTE
r-release-windows-ix86+x86_64 2.3-1 8.00 78.00 86.00 WARN
r-oldrel-windows-ix86+x86_64 2.3-1 17.00 154.00 171.00 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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 2.3-1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: BMA
    Loading required package: survival
    Loading required package: leaps
    Loading required package: robustbase
    
    Attaching package: 'robustbase'
    
    The following object is masked from 'package:survival':
    
     heart
    
    Loading required package: inline
    Loading required package: rrcov
    Scalable Robust Estimators with High Breakdown Point (version 1.3-11)
    
    Loading required package: Matrix
    Processing dataset
    Processing dataset
    Processing dataset
    Processing dataset
    Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "vignette.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.1/share/texmf/bibtex/bst"' had status 1
    Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
     Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'vignette'. The following files exist in directory '.': 'Rplots.pdf', 'vignette-002.pdf', 'vignette-005.pdf', 'vignette.Rnw', 'vignette.org', 'vignette.tex'
    Calls: buildVignettes -> find_vignette_product
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 2.3-1
Check: R code for possible problems
Result: NOTE
    coloc.abf.snpStats: no visible global function definition for
     'single.snp.tests'
    coloc.abf.snpStats: no visible global function definition for
     'col.summary'
    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'
    plot,colocPCs-missing : .local: no visible binding for global variable
     'object'
Flavor: r-oldrel-windows-ix86+x86_64