CRAN Package Check Results for Package netClass

Last updated on 2017-02-21 20:49:17.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 6.74 91.47 98.22 WARN
r-devel-linux-x86_64-debian-gcc 1.2.1 7.35 91.95 99.31 WARN
r-devel-linux-x86_64-fedora-clang 1.2.1 208.65 WARN --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.2.1 206.08 WARN --no-stop-on-test-error
r-devel-macos-x86_64-clang 1.2.1 155.81 WARN --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.2.1 29.00 201.00 230.00 WARN
r-patched-linux-x86_64 1.2.1 7.35 87.32 94.66 NOTE
r-patched-solaris-sparc 1.2.1 1155.50 NOTE
r-patched-solaris-x86 1.2.1 254.10 NOTE
r-release-linux-x86_64 1.2.1 7.02 86.31 93.33 NOTE
r-release-osx-x86_64-mavericks 1.2.1 ERROR
r-release-windows-ix86+x86_64 1.2.1 29.00 203.00 232.00 NOTE
r-oldrel-windows-ix86+x86_64 1.2.1 31.00 278.00 309.00 NOTE

Check Details

Version: 1.2.1
Check: R code for possible problems
Result: NOTE
    XH: no visible binding for global variable ‘exprs’
    XIs: no visible binding for global variable ‘exprs’
    cv.aep: no visible global function definition for ‘mclapply’
    cv.frsvm: no visible global function definition for ‘mclapply’
    cv.hubc: no visible global function definition for ‘quantile’
    cv.hubc: no visible global function definition for ‘mclapply’
    cv.pac: no visible global function definition for ‘mclapply’
    cv.stsvm: no visible global function definition for ‘mclapply’
    getGeneRanking: no visible global function definition for ‘t.test’
    getGraphRank: no visible global function definition for ‘t.test’
    predictPac: no visible global function definition for ‘predict’
    probeset2pathway: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    probeset2pathwayTrain: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    probeset2pathwayTrain: no visible global function definition for
     ‘t.test’
    probeset2pathwayTrain: no visible global function definition for
     ‘quantile’
    spanbound: no visible global function definition for ‘coef’
    spanbound: no visible global function definition for ‘predict’
    spanbound: no visible global function definition for ‘param’
    spanbound: no visible global function definition for ‘error’
    spanbound: no visible global function definition for ‘kernelf’
    spanbound: no visible global function definition for ‘b’
    svm.fit: no visible global function definition for ‘coef’
    svm.predict: no visible global function definition for ‘coef’
    svm.predict: no visible global function definition for ‘b’
    train.pac: no visible global function definition for ‘glm’
    train.stsvm: no visible global function definition for ‘quantile’
    train.stsvm: no visible global function definition for ‘head’
    Undefined global functions or variables:
     KEGGEXTID2PATHID b coef error exprs glm head kernelf mclapply param
     predict quantile t.test
    Consider adding
     importFrom("stats", "coef", "glm", "predict", "quantile", "t.test")
     importFrom("utils", "head")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, 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: 1.2.1
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory but no files in 'inst/doc':
     ‘Vignettes.pdf’
    Package has no Sweave vignette sources and no VignetteBuilder field.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64

Version: 1.2.1
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    XH: no visible binding for global variable ‘exprs’
    XIs: no visible binding for global variable ‘exprs’
    cv.aep: no visible global function definition for ‘mclapply’
    cv.frsvm: no visible global function definition for ‘mclapply’
    cv.hubc: no visible global function definition for ‘quantile’
    cv.hubc: no visible global function definition for ‘mclapply’
    cv.pac: no visible global function definition for ‘mclapply’
    cv.stsvm: no visible global function definition for ‘mclapply’
    getGeneRanking: no visible global function definition for ‘t.test’
    getGraphRank: no visible global function definition for ‘t.test’
    predictPac: no visible global function definition for ‘predict’
    probeset2pathway: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    probeset2pathwayTrain: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    probeset2pathwayTrain: no visible global function definition for
     ‘t.test’
    probeset2pathwayTrain: no visible global function definition for
     ‘quantile’
    spanbound: no visible global function definition for ‘coef’
    spanbound: no visible global function definition for ‘predict’
    spanbound: no visible global function definition for ‘param’
    spanbound: no visible global function definition for ‘error’
    spanbound: no visible global function definition for ‘kernelf’
    spanbound: no visible global function definition for ‘b’
    svm.fit: no visible global function definition for ‘coef’
    svm.predict: no visible global function definition for ‘coef’
    svm.predict: no visible global function definition for ‘b’
    train.pac: no visible global function definition for ‘glm’
    train.stsvm: no visible global function definition for ‘quantile’
    train.stsvm: no visible global function definition for ‘head’
    Undefined global functions or variables:
     KEGGEXTID2PATHID b coef error exprs glm head kernelf mclapply param
     predict quantile t.test
    Consider adding
     importFrom("stats", "coef", "glm", "predict", "quantile", "t.test")
     importFrom("utils", "head")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.2.1
Flags: --no-stop-on-test-error
Check: files in ‘vignettes’
Result: WARN
    Files in the 'vignettes' directory but no files in 'inst/doc':
     ‘Vignettes.pdf’
    Package has no Sweave vignette sources and no VignetteBuilder field.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.2.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘KEGG.db’
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘netClass-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cv.aep
    > ### Title: Cross validation for aepSVM (aepSVM)
    > ### Aliases: cv.aep
    > ### Keywords: aep
    >
    > ### ** Examples
    >
    > library(netClass)
    > data(expr)
    > data(ad.matrix)
    > x <- expr$genes
    > y <- expr$y
    >
    > library(KEGG.db)
    Error in library(KEGG.db) : there is no package called ‘KEGG.db’
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 1.2.1
Check: R code for possible problems
Result: NOTE
    XH: no visible binding for global variable 'exprs'
    XIs: no visible binding for global variable 'exprs'
    cv.aep: no visible global function definition for 'mclapply'
    cv.frsvm: no visible global function definition for 'mclapply'
    cv.hubc: no visible global function definition for 'mclapply'
    cv.pac: no visible global function definition for 'mclapply'
    cv.stsvm: no visible global function definition for 'mclapply'
    probeset2pathway: no visible binding for global variable
     'KEGGEXTID2PATHID'
    probeset2pathwayTrain: no visible binding for global variable
     'KEGGEXTID2PATHID'
    spanbound: no visible global function definition for 'param'
    spanbound: no visible global function definition for 'error'
    spanbound: no visible global function definition for 'kernelf'
    spanbound: no visible global function definition for 'b'
    svm.predict: no visible global function definition for 'b'
Flavor: r-oldrel-windows-ix86+x86_64