CRAN Package Check Results for Package MetaQC

Last updated on 2019-01-26 15:47:38 CET.

Check Details

Version: 0.1.13
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘survival’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘foreach’ ‘iterators’ ‘proto’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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: 0.1.13
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     plot.proto print.proto
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.1.13
Check: R code for possible problems
Result: NOTE
    Download: no visible global function definition for ‘download.file’
    GMT2List: no visible global function definition for ‘%dopar%’
    GMT2List: no visible global function definition for ‘foreach’
    GMT2List: no visible global function definition for ‘iter’
    GMT2List: no visible binding for global variable ‘x’
    GetEWPval: no visible global function definition for ‘pchisq’
    GetPVal : t.test2: no visible global function definition for ‘pt’
    GetPVal : <anonymous>: no visible global function definition for
     ‘t.test’
    GetPVal : <anonymous>: no visible global function definition for ‘lm’
    GetPVal : <anonymous>: no visible global function definition for
     ‘coxph’
    MetaQC: no visible global function definition for ‘proto’
    MetaQC: no visible global function definition for ‘registerDoMC’
    MetaQC: no visible global function definition for ‘registerDoSNOW’
    MetaQC: no visible global function definition for ‘makeCluster’
    MetaQC : .Initialize: no visible global function definition for ‘%do%’
    MetaQC : .Initialize: no visible global function definition for
     ‘foreach’
    MetaQC : .Initialize: no visible global function definition for ‘iter’
    MetaQC : .FilterGenes: no visible global function definition for
     ‘%dopar%’
    MetaQC : .FilterGenes: no visible global function definition for
     ‘foreach’
    MetaQC : .FilterGenes: no visible global function definition for ‘iter’
    MetaQC : .FilterGenes: no visible binding for global variable ‘d’
    MetaQC : .ConvertToGeneSetIdx: no visible global function definition
     for ‘%dopar%’
    MetaQC : .ConvertToGeneSetIdx: no visible global function definition
     for ‘foreach’
    MetaQC : .ConvertToGeneSetIdx: no visible global function definition
     for ‘iter’
    MetaQC : .ConvertToGeneSetIdx: no visible global function definition
     for ‘%do%’
    MetaQC : .ConvertToGeneSetIdx: no visible global function definition
     for ‘na.omit’
    MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
     ‘g’
    MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
     ‘d’
    MetaQC : .CalcPval: no visible global function definition for ‘%do%’
    MetaQC : .CalcPval: no visible global function definition for ‘foreach’
    MetaQC : .CalcPval: no visible binding for global variable ‘i’
    MetaQC : .CalcPval: no visible global function definition for ‘%dopar%’
    MetaQC : .CalcPval: no visible binding for global variable ‘w’
    MetaQC : .CalcPval: no visible global function definition for ‘as.dist’
    MetaQC : .CalcPval: no visible global function definition for ‘cor’
    MetaQC : .CalcPval: no visible global function definition for ‘iter’
    MetaQC : .CalcPval: no visible binding for global variable ‘j’
    MetaQC : .CalcPval : <anonymous>: no visible global function definition
     for ‘as.dist’
    MetaQC : .CalcPval : <anonymous>: no visible global function definition
     for ‘cor’
    MetaQC : .CalcPval: no visible binding for global variable ‘b’
    MetaQC : EQC: no visible global function definition for ‘%do%’
    MetaQC : EQC: no visible global function definition for ‘foreach’
    MetaQC : EQC: no visible global function definition for ‘%dopar%’
    MetaQC : EQC: no visible global function definition for ‘iter’
    MetaQC : EQC: no visible global function definition for ‘as.dist’
    MetaQC : EQC: no visible global function definition for ‘cor’
    MetaQC : EQC: no visible binding for global variable ‘g’
    MetaQC : EQC: no visible global function definition for ‘na.omit’
    MetaQC : EQC: no visible binding for global variable ‘w’
    MetaQC : AQCg: no visible global function definition for ‘%dopar%’
    MetaQC : AQCg: no visible global function definition for ‘foreach’
    MetaQC : AQCg: no visible binding for global variable ‘i’
    MetaQC : AQCg: no visible global function definition for ‘p.adjust’
    MetaQC : AQCg: no visible global function definition for ‘fisher.test’
    MetaQC : AQCp: no visible global function definition for ‘%dopar%’
    MetaQC : AQCp: no visible global function definition for ‘foreach’
    MetaQC : AQCp: no visible binding for global variable ‘i’
    MetaQC : AQCp: no visible global function definition for ‘p.adjust’
    MetaQC : AQCp: no visible global function definition for ‘fisher.test’
    MetaQC : CQCg: no visible global function definition for ‘%dopar%’
    MetaQC : CQCg: no visible global function definition for ‘foreach’
    MetaQC : CQCg: no visible global function definition for ‘iter’
    MetaQC : CQCg: no visible binding for global variable ‘dat’
    MetaQC : CQCg: no visible binding for global variable ‘pv’
    MetaQC : CQCg: no visible binding for global variable ‘i’
    MetaQC : CQCg: no visible global function definition for ‘cor.test’
    MetaQC : CQCp: no visible global function definition for ‘%dopar%’
    MetaQC : CQCp: no visible global function definition for ‘foreach’
    MetaQC : CQCp: no visible global function definition for ‘iter’
    MetaQC : CQCp: no visible binding for global variable ‘dat’
    MetaQC : CQCp: no visible binding for global variable ‘pv’
    MetaQC : CQCp: no visible global function definition for ‘%do%’
    MetaQC : CQCp: no visible binding for global variable ‘ii’
    MetaQC : CQCp: no visible binding for global variable ‘jj’
    MetaQC : CQCp: no visible global function definition for ‘na.omit’
    MetaQC : CQCp: no visible global function definition for ‘ks.test’
    MetaQC : CQCp: no visible binding for global variable ‘i’
    MetaQC : CQCp: no visible global function definition for ‘cor.test’
    MetaQC : IQC: no visible global function definition for ‘%dopar%’
    MetaQC : IQC: no visible global function definition for ‘foreach’
    MetaQC : IQC: no visible binding for global variable ‘i’
    MetaQC : IQC: no visible global function definition for ‘wilcox.test’
    MetaQC : IQC: no visible global function definition for ‘pnorm’
    MetaQC : IQC: no visible global function definition for ‘qnorm’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘%dopar%’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘foreach’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘iter’
    MetaQC : .CalcDistOfStudies: no visible binding for global variable
     ‘ii’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘%do%’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘as.dist’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘cor’
    MetaQC : .CalcDistOfStudies: no visible binding for global variable
     ‘jj’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘na.omit’
    MetaQC : .CalcDistOfStudies: no visible global function definition for
     ‘median’
    MetaQC : .CalcScores: no visible global function definition for ‘%do%’
    MetaQC : .CalcScores: no visible global function definition for
     ‘foreach’
    MetaQC : .CalcScores: no visible global function definition for ‘iter’
    MetaQC : .CalcScores: no visible binding for global variable ‘d’
    MetaQC : Plot : <anonymous>: no visible global function definition for
     ‘sd’
    MetaQC : Plot: no visible global function definition for ‘prcomp’
    MetaQC : Plot: no visible global function definition for ‘plot’
    MetaQC : Plot: no visible global function definition for ‘axis’
    MetaQC : Plot: no visible global function definition for ‘box’
    MetaQC : Plot: no visible global function definition for ‘abline’
    MetaQC : Plot: no visible global function definition for ‘arrows’
    MetaQC : Plot: no visible global function definition for ‘gray’
    MetaQC : Plot: no visible global function definition for ‘text’
    MetaQC : Plot: no visible global function definition for ‘points’
    MetaQC : GetDistOfStudies: no visible global function definition for
     ‘as.dist’
    requireAll: no visible global function definition for
     ‘installed.packages’
    requireAll: no visible binding for global variable ‘biocLite’
    requireAll: no visible global function definition for ‘biocLite’
    Undefined global functions or variables:
     %do% %dopar% abline arrows as.dist axis b biocLite box cor cor.test
     coxph d dat download.file fisher.test foreach g gray i ii
     installed.packages iter j jj ks.test lm makeCluster median na.omit
     p.adjust pchisq plot pnorm points prcomp proto pt pv qnorm
     registerDoMC registerDoSNOW sd t.test text w wilcox.test x
    Consider adding
     importFrom("grDevices", "gray")
     importFrom("graphics", "abline", "arrows", "axis", "box", "plot",
     "points", "text")
     importFrom("stats", "as.dist", "cor", "cor.test", "fisher.test",
     "ks.test", "lm", "median", "na.omit", "p.adjust", "pchisq",
     "pnorm", "prcomp", "pt", "qnorm", "sd", "t.test",
     "wilcox.test")
     importFrom("utils", "download.file", "installed.packages")
    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: 0.1.13
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'doMC'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64