CRAN Package Check Results for Package lme4

Last updated on 2015-07-27 17:48:02.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-8 42.41 385.87 428.28 NOTE
r-devel-linux-x86_64-debian-gcc 1.1-8 43.70 383.96 427.66 NOTE
r-devel-linux-x86_64-fedora-clang 1.1-8 832.60 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1-8 802.16 NOTE
r-devel-osx-x86_64-clang 1.1-8 601.78 NOTE
r-devel-windows-ix86+x86_64 1.1-8 166.00 646.00 812.00 ERROR
r-patched-linux-x86_64 1.1-8 45.69 389.45 435.14 NOTE
r-patched-solaris-sparc 1.1-8 5192.10 ERROR
r-patched-solaris-x86 1.1-8 1023.00 NOTE
r-release-linux-x86_64 1.1-8 43.51 392.99 436.50 NOTE
r-release-osx-x86_64-mavericks 1.1-8 NOTE
r-release-windows-ix86+x86_64 1.1-8 155.00 621.00 776.00 ERROR
r-oldrel-windows-ix86+x86_64 1.1-8 157.00 622.00 779.00 ERROR

Memtest notes: UBSAN-gcc UBSAN-gcc

Check Details

Version: 1.1-8
Check: installed package size
Result: NOTE
     installed size is 24.5Mb
     sub-directories of 1Mb or more:
     doc 1.8Mb
     libs 19.1Mb
     testdata 1.4Mb
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, r-oldrel-windows-ix86+x86_64

Version: 1.1-8
Check: R code for possible problems
Result: NOTE
    .modelMatrixDrop: no visible global function definition for ‘slotNames’
    .modelMatrixDrop : <anonymous>: no visible global function definition
     for ‘slot’
    .prt.resids: no visible global function definition for ‘setNames’
    .prt.resids: no visible global function definition for ‘quantile’
    .simulateFun: no visible binding for global variable ‘na.pass’
    .simulateFun: no visible global function definition for ‘is’
    .simulateFun: no visible global function definition for ‘runif’
    .simulateFun: no visible global function definition for ‘predict’
    .simulateFun: no visible binding for global variable ‘na.omit’
    .simulateFun: no visible global function definition for ‘reformulate’
    .simulateFun: no visible global function definition for
     ‘update.formula’
    .simulateFun: no visible global function definition for ‘rnorm’
    .simulateFun: no visible global function definition for ‘as’
    .simulateFun: no visible global function definition for
     ‘model.response’
    .simulateFun: no visible global function definition for ‘model.frame’
    .simulateFun : <anonymous>: no visible binding for global variable
     ‘napredict’
    .simulateFun: no visible binding for global variable ‘napredict’
    .simulateFun: no visible global function definition for ‘napredict’
    .simulateFun: no visible global function definition for ‘na.omit’
    GHrule: no visible global function definition for ‘dnorm’
    Gamma_simfun: no visible global function definition for ‘rgamma’
    NelderMead: no visible global function definition for ‘new’
    anova.merMod: no visible binding for global variable ‘is’
    anova.merMod: no visible global function definition for ‘var’
    anova.merMod : <anonymous>: no visible global function definition for
     ‘is’
    anova.merMod: no visible binding for global variable ‘getCall’
    anova.merMod: no visible binding for global variable ‘AIC’
    anova.merMod: no visible binding for global variable ‘BIC’
    anova.merMod: no visible global function definition for ‘pchisq’
    anovaLmer: no visible binding for global variable ‘is’
    anovaLmer: no visible global function definition for ‘var’
    anovaLmer : <anonymous>: no visible global function definition for ‘is’
    anovaLmer: no visible binding for global variable ‘getCall’
    anovaLmer: no visible binding for global variable ‘AIC’
    anovaLmer: no visible binding for global variable ‘BIC’
    anovaLmer: no visible global function definition for ‘pchisq’
    asOneFormula: no visible global function definition for ‘as.formula’
    binomial_simfun: no visible global function definition for
     ‘model.frame’
    binomial_simfun: no visible global function definition for
     ‘model.response’
    binomial_simfun: no visible global function definition for ‘rbinom’
    bootMer: no visible global function definition for ‘runif’
    bootMer: no visible binding for global variable ‘na.exclude’
    bootMer : <local> : <anonymous>: no visible global function definition
     for ‘str’
    checkFormulaData: no visible global function definition for
     ‘as.formula’
    checkScaleX: no visible binding for global variable ‘sd’
    checkScaleX: no visible global function definition for ‘setNames’
    chkRank.drop.cols: no visible global function definition for ‘setNames’
    coef.merMod: no visible global function definition for ‘setNames’
    coefMer: no visible global function definition for ‘setNames’
    confint.lmList4: no visible global function definition for ‘new’
    confint.lmList4: no visible global function definition for ‘qt’
    confint.merMod: no visible global function definition for ‘qnorm’
    confint.merMod : bootFun: no visible global function definition for
     ‘setNames’
    confint.thpr: no visible global function definition for ‘qnorm’
    cont: no visible global function definition for ‘predict’
    dens: no visible global function definition for ‘qnorm’
    dens : <anonymous>: no visible global function definition for ‘qnorm’
    dens: no visible global function definition for ‘dnorm’
    dens: no visible global function definition for ‘predict’
    devcomp: no visible global function definition for ‘is’
    devfun2: no visible global function definition for ‘is’
    dotplot.ranef.mer : f: no visible global function definition for
     ‘stack’
    dotplot.ranef.mer : f: no visible global function definition for
     ‘reorder’
    dotplot.ranef.mer: no visible global function definition for ‘setNames’
    drop1.merMod: no visible global function definition for ‘drop.scope’
    drop1.merMod: no visible global function definition for
     ‘update.formula’
    drop1.merMod : sumFun: no visible global function definition for
     ‘setNames’
    drop1.merMod: no visible global function definition for ‘as.formula’
    est_theta: no visible global function definition for ‘model.response’
    est_theta: no visible global function definition for ‘model.frame’
    expandDoubleVerts : expandDoubleVert: no visible global function
     definition for ‘as.formula’
    family.lmResp: no visible global function definition for ‘gaussian’
    family.nlsResp: no visible global function definition for ‘gaussian’
    famlink: no visible global function definition for ‘is’
    findbars: no visible global function definition for ‘is’
    fitted.merMod: no visible global function definition for ‘model.frame’
    fitted.merMod: no visible global function definition for ‘napredict’
    formatVC : <anonymous>: no visible global function definition for ‘as’
    formula.merMod: no visible global function definition for ‘getCall’
    formula.merMod: no visible global function definition for ‘as.formula’
    fortify.merMod: no visible global function definition for ‘predict’
    fortify.merMod: no visible global function definition for ‘resid’
    gaussian_simfun: no visible global function definition for ‘rnorm’
    getGroupsFormula.default: no visible global function definition for
     ‘asOneSidedFormula’
    getGroupsFormula.default: no visible global function definition for
     ‘as.formula’
    getGroupsFormula.merMod: no visible binding for global variable
     ‘asOneSidedFormula’
    getGroupsFormula.merMod: no visible global function definition for
     ‘asOneSidedFormula’
    getIDLabels: no visible global function definition for ‘model.frame’
    getLlikAIC: no visible global function definition for ‘AIC’
    getLlikAIC: no visible global function definition for ‘BIC’
    getME: no visible global function definition for ‘is’
    getME : Tpfun: no visible global function definition for ‘setNames’
    getME: no visible global function definition for ‘setNames’
    getME: no visible global function definition for ‘getCall’
    getResponseFormula: no visible global function definition for
     ‘as.formula’
    glFormula: no visible binding for global variable ‘gaussian’
    glFormula: no visible global function definition for ‘gaussian’
    glFormula: no visible global function definition for ‘as.formula’
    glmFamily: no visible global function definition for ‘new’
    glmResp: no visible global function definition for ‘new’
    glmer: no visible binding for global variable ‘gaussian’
    glmer: no visible global function definition for ‘gaussian’
    glmer.nb: no visible binding for global variable ‘poisson’
    golden: no visible global function definition for ‘new’
    isGLMlist: no visible global function definition for ‘getDataPart’
    isNested: no visible global function definition for ‘as’
    isNested: no visible global function definition for ‘new’
    lFormula: no visible global function definition for ‘as.formula’
    lmList: no visible global function definition for ‘is’
    lmList : <anonymous>: no visible global function definition for ‘lm’
    lmList : <anonymous>: no visible global function definition for ‘glm’
    lmList: no visible global function definition for ‘as.formula’
    lmList: no visible global function definition for ‘new’
    lmList: no visible global function definition for ‘setNames’
    lmResp: no visible global function definition for ‘new’
    lmerResp: no visible global function definition for ‘new’
    logLik.lmList4 : <anonymous>: no visible global function definition for
     ‘resid’
    merPredD: no visible global function definition for ‘new’
    meth: no visible global function definition for ‘pt’
    mkLmerDevfun: no visible global function definition for
     ‘model.response’
    mkLmerDevfun : <anonymous>: no visible global function definition for
     ‘var’
    mkLmerDevfun : <anonymous>: no visible global function definition for
     ‘ave’
    mkLmerDevfun: no visible global function definition for ‘var’
    mkMerMod: no visible global function definition for ‘is’
    mkMerMod: no visible global function definition for ‘new’
    mkMinimalData: no visible global function definition for ‘setNames’
    mkNewReTrms: no visible binding for global variable ‘na.pass’
    mkNewReTrms: no visible global function definition for ‘model.frame’
    mkNewReTrms: no visible global function definition for
     ‘delete.response’
    mkParsTemplate: no visible global function definition for ‘model.frame’
    mkParsTemplate: no visible global function definition for ‘setNames’
    mkRespMod: no visible global function definition for ‘model.response’
    mkRespMod: no visible global function definition for ‘model.offset’
    mkRespMod: no visible global function definition for ‘model.weights’
    mkRespMod: no visible global function definition for ‘model.extract’
    mkRespMod: no visible binding for global variable ‘new’
    mkdevfun: no visible global function definition for ‘is’
    mmList.formula: no visible global function definition for ‘setNames’
    mmList.merMod: no visible global function definition for ‘model.frame’
    model.frame.merMod: no visible global function definition for
     ‘terms.formula’
    namedList: no visible global function definition for ‘setNames’
    negative.binomial_simfun: no visible global function definition for
     ‘rnbinom’
    nlformula: no visible global function definition for ‘as.formula’
    nlformula: no visible global function definition for ‘is’
    nlminbwrap: no visible global function definition for ‘nlminb’
    nloptwrap: no visible global function definition for ‘packageVersion’
    nloptwrap: no visible global function definition for ‘data’
    nlsResp: no visible global function definition for ‘new’
    noReForm: no visible global function definition for ‘is’
    nobars: no visible global function definition for ‘is’
    nobars: no visible global function definition for ‘reformulate’
    optTheta: no visible global function definition for ‘optimize’
    optimizeLmer: no visible global function definition for ‘new’
    pairs.lmList4: no visible global function definition for ‘na.omit’
    pairs.lmList4: no visible global function definition for ‘var’
    pairs.lmList4: no visible global function definition for ‘qchisq’
    pairs.lmList4: no visible global function definition for
     ‘asOneSidedFormula’
    pairs.lmList4: no visible global function definition for ‘par’
    panel.thpr: no visible global function definition for ‘is’
    panel.thpr: no visible global function definition for ‘predict’
    plot.lmList4: no visible global function definition for ‘par’
    plot.lmList4: no visible global function definition for ‘resid’
    plot.lmList4: no visible global function definition for ‘qnorm’
    plot.lmList4: no visible global function definition for
     ‘asOneSidedFormula’
    plot.lmList4.confint: no visible global function definition for ‘as’
    plot.merMod: no visible global function definition for ‘as.formula’
    plot.merMod: no visible global function definition for ‘par’
    plot.merMod: no visible global function definition for ‘resid’
    plot.merMod: no visible global function definition for ‘qnorm’
    plot.merMod: no visible global function definition for
     ‘asOneSidedFormula’
    poisson_simfun: no visible global function definition for ‘rpois’
    pooledSD: no visible global function definition for ‘is’
    pooledSD : <anonymous>: no visible global function definition for
     ‘resid’
    predict.lmList4: no visible global function definition for ‘predict’
    predict.lmList4 : <anonymous>: no visible global function definition
     for ‘predict’
    predict.merMod: no visible binding for global variable ‘na.pass’
    predict.merMod: no visible global function definition for ‘na.omit’
    predict.merMod: no visible global function definition for ‘model.frame’
    predict.merMod: no visible global function definition for
     ‘delete.response’
    predict.merMod: no visible global function definition for ‘as’
    predict.merMod: no visible global function definition for ‘napredict’
    predy: no visible global function definition for ‘predict’
    print.summary.merMod: no visible global function definition for
     ‘printCoefmat’
    print.summary.merMod: no visible global function definition for
     ‘cov2cor’
    print.summary.merMod: no visible global function definition for ‘as’
    print.summary.merMod: no visible global function definition for
     ‘symnum’
    profile.merMod: no visible global function definition for ‘qchisq’
    profile.merMod : <local> : <anonymous>: no visible global function
     definition for ‘rbind2’
    profile.merMod : <local> : <anonymous>: no visible binding for global
     variable ‘na.omit’
    profile.merMod: no visible global function definition for ‘setNames’
    profile.merMod: no visible global function definition for ‘new’
    profile.merMod: no visible global function definition for ‘rbind2’
    qqmath.merMod: no visible global function definition for ‘qnorm’
    qqmath.merMod: no visible global function definition for
     ‘asOneSidedFormula’
    qqmath.merMod : qqpanel: no visible global function definition for
     ‘setNames’
    qqmath.merMod : qqpanel: no visible global function definition for
     ‘ppoints’
    qqmath.merMod : qqpanel: no visible global function definition for
     ‘qnorm’
    qqmath.ranef.mer : f: no visible global function definition for ‘stack’
    qqnorm.lmList4: no visible global function definition for ‘qqnorm’
    qqnorm.lmList4: no visible global function definition for ‘resid’
    qqnorm.lmList4: no visible global function definition for ‘qnorm’
    qqnorm.lmList4: no visible global function definition for
     ‘asOneSidedFormula’
    qqnorm.lmList4: no visible binding for global variable ‘qqnorm’
    qqnorm.lmList4: no visible global function definition for ‘par’
    quickSimulate: no visible binding for global variable ‘gaussian’
    quickSimulate: no visible binding for global variable ‘rnorm’
    ranef.lmList4 : <anonymous>: no visible global function definition for
     ‘var’
    ranef.merMod: no visible global function definition for ‘is’
    reOnly: no visible global function definition for ‘reformulate’
    rePos: no visible global function definition for ‘new’
    refit.merMod: no visible global function definition for ‘model.frame’
    refit.merMod: no visible global function definition for ‘getCall’
    refitML.merMod: no visible global function definition for ‘is’
    refitML.merMod: no visible global function definition for ‘new’
    residuals.lmList4 : <anonymous>: no visible global function definition
     for ‘resid’
    residuals.merMod: no visible global function definition for
     ‘model.frame’
    residuals.merMod: no visible global function definition for ‘naresid’
    safe_pchisq: no visible global function definition for ‘pchisq’
    simulate.merMod: no visible binding for global variable ‘na.pass’
    splitFormula: no visible global function definition for
     ‘asOneSidedFormula’
    splom.thpr: no visible global function definition for ‘qchisq’
    splom.thpr: no visible global function definition for ‘na.omit’
    splom.thpr : lp: no visible global function definition for ‘predict’
    splom.thpr : up: no visible global function definition for ‘predict’
    summary.lmList4: no visible global function definition for ‘pt’
    summary.merMod: no visible global function definition for ‘pnorm’
    summary.merMod: no visible global function definition for ‘is’
    terms.merMod: no visible global function definition for ‘terms.formula’
    update.lmList4: no visible global function definition for
     ‘update.formula’
    update.merMod: no visible global function definition for ‘getCall’
    update.merMod: no visible global function definition for
     ‘update.formula’
    vcRep: no visible global function definition for ‘new’
    vcov.merMod: no visible global function definition for ‘as’
    xyplot.thpr: no visible global function definition for ‘qchisq’
    xyplot.thpr : mypred: no visible global function definition for
     ‘approx’
    Undefined global functions or variables:
     AIC BIC approx as as.formula asOneSidedFormula ave cov2cor data
     delete.response dnorm drop.scope gaussian getCall getDataPart glm is
     lm model.extract model.frame model.offset model.response
     model.weights na.exclude na.omit na.pass napredict naresid new nlminb
     optimize packageVersion par pchisq pnorm poisson ppoints predict
     printCoefmat pt qchisq qnorm qqnorm qt quantile rbind2 rbinom
     reformulate reorder resid rgamma rnbinom rnorm rpois runif sd
     setNames slot slotNames stack str symnum terms.formula update.formula
     var
    Consider adding
     importFrom("graphics", "par")
     importFrom("methods", "as", "getDataPart", "is", "new", "rbind2",
     "slot", "slotNames")
     importFrom("stats", "AIC", "BIC", "approx", "as.formula",
     "asOneSidedFormula", "ave", "cov2cor", "delete.response",
     "dnorm", "drop.scope", "gaussian", "getCall", "glm", "lm",
     "model.extract", "model.frame", "model.offset",
     "model.response", "model.weights", "na.exclude", "na.omit",
     "na.pass", "napredict", "naresid", "nlminb", "optimize",
     "pchisq", "pnorm", "poisson", "ppoints", "predict",
     "printCoefmat", "pt", "qchisq", "qnorm", "qqnorm", "qt",
     "quantile", "rbinom", "reformulate", "reorder", "resid",
     "rgamma", "rnbinom", "rnorm", "rpois", "runif", "sd",
     "setNames", "symnum", "terms.formula", "update.formula",
     "var")
     importFrom("utils", "data", "packageVersion", "stack", "str")
    to your NAMESPACE.
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

Version: 1.1-8
Check: running tests for arch ‘i386’
Result: ERROR
    Running the tests in 'tests/AAAtest-all.R' failed.
    Last 13 lines of output:
     unname(fixef(mod)) not equal to c(0.5425528, 6.4289962)
     2/2 mismatches (average diff: 5.33e-08).
     First 2:
     pos x y diff
     1 0.543 0.543 1.85e-08
     2 6.429 6.429 -8.81e-08
    
     2. Failure (at test-methods.R#250): predict ------------------------------------
     fmPixS <<- update(fmPix, . ~ . + Side) does not match '(nearly unidentifiable|not uniquely determined)'. Actual values:
     * unable to evaluate scaled gradient
     * Model failed to converge: degenerate Hessian with 1 negative eigenvalues
     Error: Test failures
     Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-8
Check: tests
Result: ERROR
    Running the tests in ‘tests/testOptControl.R’ failed.
    Last 13 lines of output:
     Loading required package: Matrix
     > dat <- read.csv(system.file("testdata","dat20101314.csv",package="lme4"))
     > NMcopy <- lme4:::Nelder_Mead
     >
     > cc <- capture.output(lmer(y ~ (1|Operator)+(1|Part)+(1|Part:Operator), data=dat,
     + control=
     + lmerControl("NMcopy",
     + optCtrl= list(iprint=20))))
     > ## check that printing goes through step 140 twice and up to 240 once
     > findStep <- function(str,n) sum(grepl(paste0("^\\(NM\\) ",n,": "),cc))
     > stopifnot(findStep(cc,140)==2 && findStep(cc,240)==1)
     Error: findStep(cc, 140) == 2 && findStep(cc, 240) == 1 is not TRUE
     Execution halted
Flavor: r-patched-solaris-sparc