CRAN Package Check Results for Package MAc

Last updated on 2018-05-25 00:46:42 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1 5.49 30.08 35.57 ERROR
r-devel-linux-x86_64-debian-gcc 1.1 3.74 25.65 29.39 ERROR
r-devel-linux-x86_64-fedora-clang 1.1 50.27 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1 48.16 NOTE
r-devel-windows-ix86+x86_64 1.1 9.00 52.00 61.00 NOTE
r-patched-linux-x86_64 1.1 5.74 32.16 37.90 ERROR
r-patched-solaris-x86 1.1 63.80 NOTE
r-release-linux-x86_64 1.1 4.09 32.19 36.28 ERROR
r-release-windows-ix86+x86_64 1.1 11.00 62.00 73.00 NOTE
r-release-osx-x86_64 1.1 NOTE
r-oldrel-windows-ix86+x86_64 1.1 6.00 46.00 52.00 NOTE
r-oldrel-osx-x86_64 1.1 NOTE

Check Details

Version: 1.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘R2wd’
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, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     ‘R2wd’ ‘ggplot2’ ‘metafor’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' 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-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: 1.1
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     mareg.default print.icclist print.macat print.mareg print.omni
     print.summary.mareg r2.mareg summary.mareg wd.default wd.macat
     wd.mareg wd.omni
    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: 1.1
Check: R code for possible problems
Result: NOTE
    CatCompf: no visible global function definition for ‘aov’
    CatCompf: no visible global function definition for ‘TukeyHSD’
    CatCompf: no visible global function definition for ‘pchisq’
    CatCompr: no visible global function definition for ‘aov’
    CatCompr: no visible global function definition for ‘TukeyHSD’
    CatCompr: no visible global function definition for ‘pchisq’
    CatModGraph: no visible global function definition for ‘ggplot’
    CatModGraph: no visible global function definition for ‘aes’
    CatModGraph: no visible binding for global variable ‘z’
    CatModGraph: no visible binding for global variable ‘wi’
    CatModGraph: no visible global function definition for ‘geom_boxplot’
    CatModGraph: no visible global function definition for ‘geom_jitter’
    CatModGraph: no visible binding for global variable ‘wi.tau’
    CatModGraph: no visible global function definition for ‘xlab’
    CatModGraph: no visible global function definition for ‘ylab’
    CatModGraph: no visible global function definition for ‘opts’
    CatModf: no visible global function definition for ‘aggregate’
    CatModf: no visible global function definition for ‘pnorm’
    CatModf: no visible global function definition for ‘pchisq’
    CatModfQ: no visible global function definition for ‘pchisq’
    CatModr: no visible global function definition for ‘aggregate’
    CatModr: no visible global function definition for ‘pnorm’
    CatModr: no visible global function definition for ‘pchisq’
    CatModrQ: no visible global function definition for ‘pchisq’
    ForestPlot: no visible global function definition for ‘ggplot’
    ForestPlot: no visible global function definition for ‘aes’
    ForestPlot: no visible binding for global variable ‘id’
    ForestPlot: no visible binding for global variable ‘r’
    ForestPlot: no visible global function definition for ‘geom_vline’
    ForestPlot: no visible global function definition for ‘geom_point’
    ForestPlot: no visible global function definition for ‘opts’
    ForestPlot: no visible global function definition for ‘geom_errorbarh’
    ForestPlot: no visible binding for global variable ‘l.ci95’
    ForestPlot: no visible binding for global variable ‘u.ci95’
    ForestPlot: no visible global function definition for ‘xlim’
    ForestPlot: no visible global function definition for ‘xlab’
    ForestPlot: no visible global function definition for ‘ylab’
    FunnelPlot: no visible global function definition for ‘ggplot’
    FunnelPlot: no visible global function definition for ‘aes’
    FunnelPlot: no visible binding for global variable ‘se.z’
    FunnelPlot: no visible binding for global variable ‘z’
    FunnelPlot: no visible global function definition for ‘geom_vline’
    FunnelPlot: no visible global function definition for ‘opts’
    FunnelPlot: no visible global function definition for ‘xlim’
    FunnelPlot: no visible global function definition for ‘ylim’
    FunnelPlot: no visible global function definition for ‘xlab’
    FunnelPlot: no visible global function definition for ‘ylab’
    FunnelPlot: no visible global function definition for ‘stat_abline’
    FunnelPlot: no visible global function definition for
     ‘scale_y_continuous’
    FunnelPlot: no visible binding for global variable ‘se.z.tau’
    MAreg1: no visible global function definition for ‘lm’
    MAreg1: no visible global function definition for ‘anova’
    MAreg1: no visible global function definition for ‘qt’
    MAreg1: no visible global function definition for ‘pnorm’
    MAreg2: no visible global function definition for ‘anova’
    MAreg2: no visible global function definition for ‘qt’
    MAreg2: no visible global function definition for ‘pnorm’
    MAregGraph: no visible global function definition for ‘ggplot’
    MAregGraph: no visible global function definition for ‘aes’
    MAregGraph: no visible binding for global variable ‘z’
    MAregGraph: no visible binding for global variable ‘wi’
    MAregGraph: no visible global function definition for ‘geom_point’
    MAregGraph: no visible global function definition for ‘geom_smooth’
    MAregGraph: no visible binding for global variable ‘lm’
    MAregGraph: no visible global function definition for ‘xlab’
    MAregGraph: no visible global function definition for ‘ylab’
    MAregGraph: no visible global function definition for ‘opts’
    MAregGraph: no visible binding for global variable ‘wi.tau’
    MRfit: no visible binding for global variable ‘anova’
    MetaR: no visible global function definition for ‘pnorm’
    MultiModGraph: no visible global function definition for ‘ggplot’
    MultiModGraph: no visible global function definition for ‘aes’
    MultiModGraph: no visible binding for global variable ‘z’
    MultiModGraph: no visible binding for global variable ‘wi’
    MultiModGraph: no visible global function definition for ‘opts’
    MultiModGraph: no visible global function definition for ‘facet_wrap’
    MultiModGraph: no visible global function definition for ‘geom_point’
    MultiModGraph: no visible global function definition for ‘geom_smooth’
    MultiModGraph: no visible binding for global variable ‘lm’
    MultiModGraph: no visible global function definition for ‘ylab’
    MultiModGraph: no visible global function definition for ‘xlab’
    MultiModGraph: no visible binding for global variable ‘wi.tau’
    OmnibusES: no visible global function definition for ‘pnorm’
    OmnibusES: no visible global function definition for ‘pchisq’
    Wifun: no visible global function definition for ‘pnorm’
    icc: no visible global function definition for ‘na.omit’
    icc: no visible global function definition for ‘var’
    icc: no visible binding for global variable ‘var’
    icc: no visible global function definition for ‘pf’
    icc: no visible global function definition for ‘qf’
    macat: no visible global function definition for ‘aggregate’
    macat: no visible global function definition for ‘pnorm’
    macat: no visible global function definition for ‘pchisq’
    macatC: no visible global function definition for ‘pchisq’
    mareg.default: no visible global function definition for
     ‘model.response’
    mareg.default: no visible global function definition for
     ‘model.extract’
    mareg.default: no visible global function definition for ‘model.matrix’
    mareg.default: no visible binding for global variable ‘contrasts’
    mareg.default: no visible global function definition for ‘rma’
    omni: no visible global function definition for ‘pnorm’
    omni: no visible global function definition for ‘pchisq’
    omni: no visible binding for global variable ‘g’
    omni: no visible binding for global variable ‘var.g’
    p.ancova_to_d1: no visible global function definition for ‘qt’
    p.ancova_to_d2: no visible global function definition for ‘qt’
    p_to_d1: no visible global function definition for ‘qt’
    p_to_d2: no visible global function definition for ‘qt’
    plotcat: no visible global function definition for ‘ggplot’
    plotcat: no visible global function definition for ‘aes’
    plotcat: no visible binding for global variable ‘wi’
    plotcat: no visible global function definition for ‘geom_boxplot’
    plotcat: no visible global function definition for ‘geom_jitter’
    plotcat: no visible binding for global variable ‘wi.tau’
    plotcat: no visible global function definition for ‘xlab’
    plotcat: no visible global function definition for ‘ylab’
    plotcat: no visible global function definition for ‘opts’
    plotcon: no visible global function definition for ‘ggplot’
    plotcon: no visible global function definition for ‘aes’
    plotcon: no visible binding for global variable ‘wi’
    plotcon: no visible global function definition for ‘geom_point’
    plotcon: no visible global function definition for ‘geom_smooth’
    plotcon: no visible binding for global variable ‘lm’
    plotcon: no visible global function definition for ‘xlab’
    plotcon: no visible global function definition for ‘ylab’
    plotcon: no visible global function definition for ‘opts’
    plotcon: no visible binding for global variable ‘wi.tau’
    print.summary.mareg: no visible global function definition for
     ‘printCoefmat’
    stat_sum_single1: no visible binding for global variable ‘wi’
    stat_sum_single1: no visible global function definition for
     ‘stat_summary’
    stat_sum_single2: no visible binding for global variable ‘wi.tau’
    stat_sum_single2: no visible global function definition for
     ‘stat_summary’
    wd.default: no visible global function definition for ‘wdGet’
    wd.default: no visible global function definition for ‘wdNewDoc’
    wd.default: no visible global function definition for ‘wdHeading’
    wd.default: no visible global function definition for ‘wdTable’
    wd.macat: no visible global function definition for ‘wdGet’
    wd.macat: no visible global function definition for ‘wdNewDoc’
    wd.macat: no visible global function definition for ‘wdHeading’
    wd.macat: no visible global function definition for ‘wdTable’
    wd.mareg: no visible global function definition for ‘wdGet’
    wd.mareg: no visible global function definition for ‘wdNewDoc’
    wd.mareg: no visible global function definition for ‘wdHeading’
    wd.mareg: no visible global function definition for ‘wdTable’
    wd.omni: no visible global function definition for ‘wdGet’
    wd.omni: no visible global function definition for ‘wdNewDoc’
    wd.omni: no visible global function definition for ‘wdHeading’
    wd.omni: no visible global function definition for ‘wdTable’
    Undefined global functions or variables:
     TukeyHSD aes aggregate anova aov contrasts facet_wrap g geom_boxplot
     geom_errorbarh geom_jitter geom_point geom_smooth geom_vline ggplot
     id l.ci95 lm model.extract model.matrix model.response na.omit opts
     pchisq pf pnorm printCoefmat qf qt r rma scale_y_continuous se.z
     se.z.tau stat_abline stat_summary u.ci95 var var.g wdGet wdHeading
     wdNewDoc wdTable wi wi.tau xlab xlim ylab ylim z
    Consider adding
     importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov",
     "contrasts", "lm", "model.extract", "model.matrix",
     "model.response", "na.omit", "pchisq", "pf", "pnorm",
     "printCoefmat", "qf", "qt", "var")
    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: 1.1
Check: examples
Result: ERROR
    Running examples in ‘MAc-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: MAc-package
    > ### Title: Meta-Analysis with Correlations
    > ### Aliases: MAc-package MAc
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > # Examples for each broad area:
    >
    > id<-c(1:20)
    > n<-c(10,20,13,22,28,12,12,36,19,12,36,75,33,121,37,14,40,16,14,20)
    > r<-c(.68,.56,.23,.64,.49,-.04,.49,.33,.58,.18,-.11,.27,.26,.40,.49,
    + .51,.40,.34,.42,.16)
    > mod1<-c(1,2,3,4,1,2,8,7,5,3,9,7,5,4,3,2,3,5,7,1)
    > dat<-data.frame(id,n,r,mod1)
    > dat$var.r <- var_r(dat$r, dat$n) # MAc function to derive variance
    > dat$z <- r_to_z(dat$r) # MAc function to convert to Fisher's z (z')
    > dat$var.z <- var_z(dat$n) # MAc function for variance of z'
    > dat$mods2 <- factor(rep(1:2, 10))
    > dat
     id n r mod1 var.r z var.z mods2
    1 1 10 0.68 1 0.03211264 0.82911404 0.142857143 1
    2 2 20 0.56 2 0.02479710 0.63283319 0.058823529 2
    3 3 13 0.23 3 0.07474987 0.23418947 0.100000000 1
    4 4 22 0.64 4 0.01659867 0.75817374 0.052631579 2
    5 5 28 0.49 1 0.02138696 0.53606034 0.040000000 1
    6 6 12 -0.04 2 0.09061841 -0.04002135 0.111111111 2
    7 7 12 0.49 8 0.05249527 0.53606034 0.111111111 1
    8 8 36 0.33 7 0.02268741 0.34282825 0.030303030 2
    9 9 19 0.58 5 0.02446472 0.66246271 0.062500000 1
    10 10 12 0.18 3 0.08511361 0.18198269 0.111111111 2
    11 11 36 -0.11 9 0.02788418 -0.11044692 0.030303030 1
    12 12 75 0.27 7 0.01161506 0.27686382 0.013888889 2
    13 13 33 0.26 5 0.02716780 0.26610841 0.033333333 1
    14 14 121 0.40 4 0.00588000 0.42364893 0.008474576 2
    15 15 37 0.49 3 0.01604022 0.53606034 0.029411765 1
    16 16 14 0.51 2 0.04211169 0.56272977 0.090909091 2
    17 17 40 0.40 3 0.01809231 0.42364893 0.027027027 1
    18 18 16 0.34 5 0.05214422 0.35409253 0.076923077 2
    19 19 14 0.42 7 0.05217823 0.44769202 0.090909091 1
    20 20 20 0.16 1 0.04997133 0.16138670 0.058823529 2
    >
    > # Note: for all the examples in this manual, we have made up data and manually
    > # created variables and datasets. If conducting your own meta-analysis,
    > # a more convenient way for using the functions is to import your data from
    > # a .csv file (with relevant variables in the dataset). One way to do this:
    > # dat <- read.csv(file.choose(), header = TRUE)
    > #
    > # Then, you can run the functions with this dataset and you do not need to
    > # manually create your dataset, as we have done above.
    >
    >
    >
    > # 1. Computations to Calculate Correlations:
    >
    > # For example, suppose the primary study reported a t-test value for differences
    > # between 2 groups and the total sample size. Then, running:
    >
    > r_from_t (1.74, 30)
     r var_r
    [1,] 0.3123742 0.02808159
    >
    > # reported t-value (1.74) and sample size (30) will output the
    > # correlation desired for use in the meta-analysis.
    >
    > # 2. Within-Study Aggregation of Effect Sizes:
    >
    > agg(id = id, r = r, n = n, data=dat)
     id r n
    1 1 0.68 10
    2 2 0.56 20
    3 3 0.23 13
    4 4 0.64 22
    5 5 0.49 28
    6 6 -0.04 12
    7 7 0.49 12
    8 8 0.33 36
    9 9 0.58 19
    10 10 0.18 12
    11 11 -0.11 36
    12 12 0.27 75
    13 13 0.26 33
    14 14 0.40 121
    15 15 0.49 37
    16 16 0.51 14
    17 17 0.40 40
    18 18 0.34 16
    19 19 0.42 14
    20 20 0.16 20
    >
    > # where data = data.frame with columns for id, r (correlation coefficient),
    > # and n (sample size) with multiple rows within each study (multiple
    > # correlations reported for each study). Outputs an aggregated data.frame
    > # with 1 effect size per study.
    >
    > # 3. Fixed and Random Effects Omnibus Analysis
    >
    > omni(es = z, var = var.z, data = dat, type="weighted", method = "random", ztor = TRUE)
    $k
    [1] 20
    
    $estimate
    [1] 0.3634356
    
    $var
    [1] 0.002249998
    
    $se
    [1] 0.04743415
    
    $ci.l
    [1] 0.280171
    
    $ci.u
    [1] 0.4412723
    
    $z
    [1] 0.9999998
    
    $p
    [1] 9.992007e-16
    
    $Q
    [1] 20.97445
    
    $df.Q
    [1] 19
    
    $Qp
    [1] 0.3382146
    
    $I2
    [1] "9.4136%"
    
    $call
    omni(es = z, var = var.z, data = dat, type = "weighted", method = "random",
     ztor = TRUE)
    
    attr(,"class")
    [1] "omni"
    >
    > # where data = data.frame with columns for id, es (r or z')
    > # , var (variance of r or z'), n (sample size). ztor = if using z', should
    > # it be converted back to r? see omni documentation for more details.
    >
    > # 4. Moderator Analyses:
    >
    > # Random effects
    > mareg(z~ mod1 + mods2, var = var.z, method = "REML", ztor = TRUE, data = dat)
    Error in UseMethod("mareg") :
     no applicable method for 'mareg' applied to an object of class "formula"
    Calls: mareg
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64