CRAN Package Check Results for Package epicalc

Last updated on 2015-01-28 17:55:16.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.15.1.0 1.73 45.19 46.92 NOTE
r-devel-linux-x86_64-debian-gcc 2.15.1.0 1.66 42.92 44.58 NOTE
r-devel-linux-x86_64-fedora-clang 2.15.1.0 96.44 NOTE
r-devel-linux-x86_64-fedora-gcc 2.15.1.0 83.68 NOTE
r-devel-osx-x86_64-clang 2.15.1.0 85.69 NOTE
r-devel-windows-ix86+x86_64 2.15.1.0 10.00 64.00 74.00 NOTE
r-patched-linux-x86_64 2.15.1.0 1.95 48.21 50.16 NOTE
r-patched-solaris-sparc 2.15.1.0 557.60 NOTE
r-patched-solaris-x86 2.15.1.0 112.10 NOTE
r-release-linux-ix86 2.15.1.0 2.35 57.62 59.97 NOTE
r-release-linux-x86_64 2.15.1.0 1.83 47.81 49.64 NOTE
r-release-osx-x86_64-mavericks 2.15.1.0 NOTE
r-release-windows-ix86+x86_64 2.15.1.0 8.00 79.00 87.00 NOTE
r-oldrel-windows-ix86+x86_64 2.15.1.0 9.00 110.00 119.00 NOTE

Check Details

Version: 2.15.1.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘foreign’ ‘survival’
     Please remove these calls from your code.
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

Version: 2.15.1.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     ci.binomial ci.default ci.numeric ci.poisson kap.2.raters
     kap.ByCategory kap.default kap.m.raters kap.table recode.default
     recode.is.na rename.default rename.pattern rename.var merge.lab
     print.alpha print.cci print.des print.display print.kap.ByCategory
     print.kap.table print.lrtest print.n.for.2means print.n.for.2p
     print.n.for.cluster.2means print.n.for.cluster.2p print.n.for.equi.2p
     print.n.for.lqas print.n.for.noninferior.2p print.n.for.survey
     print.power.for.2means print.power.for.2p print.summ print.tab1
     print.tableStack aggregate.numeric aggregate.plot
    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-devel-osx-x86_64-clang

Version: 2.15.1.0
Check: R code for possible problems
Result: NOTE
    addMissingRecords: no visible binding for global variable ‘.data’
    alpha: no visible binding for global variable ‘.data’
    alphaBest: no visible binding for global variable ‘.data’
    codebook: no visible binding for global variable ‘.data’
    des: no visible binding for global variable ‘.data’
    dotplot: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘Freq’
    keepData: no visible binding for global variable ‘.data’
    label.var: no visible binding for global variable ‘.data’
    pack: no visible binding for global variable ‘.data’
    recode.default: no visible binding for global variable ‘.data’
    recode.is.na: no visible binding for global variable ‘.data’
    ren: no visible binding for global variable ‘.data’
    rename: no visible binding for global variable ‘.data’
    rename.default: no visible binding for global variable ‘.data’
    rename.pattern: no visible binding for global variable ‘.data’
    rename.var: no visible binding for global variable ‘.data’
    sortBy: no visible binding for global variable ‘.data’
    summ: no visible binding for global variable ‘.data’
    tableStack: no visible binding for global variable ‘.data’
    unclassDataframe: no visible binding for global variable ‘.data’
    use: no visible binding for global variable ‘.data’
    
    Found the following assignments to the global environment:
    File ‘epicalc/R/epicalc.R’:
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(nam, (get(y[i]))[order(...)], envir = .GlobalEnv)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(paste(deparse(substitute(x0)), substr(colnames(mod.mat)[i],
     3, nchar(colnames(mod.mat)[i])), sep = ""), mod.mat[, i],
     pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(dataName, data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
    
    Found the following calls to attach():
    File ‘epicalc/R/epicalc.R’:
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = dataName, warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
     attach(data1, name = as.character(substitute(dataFrame)), warn.conflicts = FALSE)
    See section ‘Good practice’ in ‘?attach’.
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

Version: 2.15.1.0
Check: Rd line widths
Result: NOTE
    Rd file 'aggregate.plot.rd':
     \examples lines wider than 100 characters:
     aggregate.plot(x=year, by=list(HOSPITAL = hospital, STAGE = stage), FUN = "median", legend.site = "topleft")
    
    Rd file 'auc.rd':
     \examples lines wider than 100 characters:
     tmp <- by(data=Indometh, INDICES = Indometh$Subject, FUN = function(x) auc(conc=x$conc, time=x$time, id=NULL))
    
    Rd file 'sampsize.rd':
     \usage lines wider than 90 characters:
     n.for.cluster.2means (mu1, mu2, sd1, sd2, alpha = 0.05, power = 0.8, ratio = 1, mean.cluster.size = 10, previous.mean.cluster.size = NU ... [TRUNCATED]
     n.for.cluster.2p (p1, p2, alpha = 0.05, power = 0.8, ratio = 1, mean.cluster.size = 10, previous.mean.cluster.size = NULL, previous.sd. ... [TRUNCATED]
    
    These lines will be truncated in the PDF 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-release-linux-x86_64

Version: 2.15.1.0
Check: R code for possible problems
Result: NOTE
    addMissingRecords: no visible binding for global variable ‘.data’
    alpha: no visible binding for global variable ‘.data’
    alphaBest: no visible binding for global variable ‘.data’
    codebook: no visible binding for global variable ‘.data’
    des: no visible binding for global variable ‘.data’
    dotplot: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘Freq’
    keepData: no visible binding for global variable ‘.data’
    label.var: no visible binding for global variable ‘.data’
    pack: no visible binding for global variable ‘.data’
    recode.default: no visible binding for global variable ‘.data’
    recode.is.na: no visible binding for global variable ‘.data’
    ren: no visible binding for global variable ‘.data’
    rename: no visible binding for global variable ‘.data’
    rename.default: no visible binding for global variable ‘.data’
    rename.pattern: no visible binding for global variable ‘.data’
    rename.var: no visible binding for global variable ‘.data’
    sortBy: no visible binding for global variable ‘.data’
    summ: no visible binding for global variable ‘.data’
    tableStack: no visible binding for global variable ‘.data’
    unclassDataframe: no visible binding for global variable ‘.data’
    use: no visible binding for global variable ‘.data’
    
    Found the following assignments to the global environment:
    File ‘epicalc/R/epicalc.R’:
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(nam, (get(y[i]))[order(...)], envir = .GlobalEnv)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(paste(deparse(substitute(x0)), substr(colnames(mod.mat)[i],
     3, nchar(colnames(mod.mat)[i])), sep = ""), mod.mat[, i],
     pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(dataName, data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
     assign(as.character(substitute(dataFrame)), data1, pos = 1)
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-release-linux-ix86

Version: 2.15.1.0
Check: R code for possible problems
Result: NOTE
    addMissingRecords: no visible binding for global variable ‘.data’
    alpha: no visible binding for global variable ‘.data’
    alphaBest: no visible binding for global variable ‘.data’
    codebook: no visible binding for global variable ‘.data’
    des: no visible binding for global variable ‘.data’
    dotplot: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘.data’
    fillin: no visible binding for global variable ‘Freq’
    keepData: no visible binding for global variable ‘.data’
    label.var: no visible binding for global variable ‘.data’
    pack: no visible binding for global variable ‘.data’
    recode.default: no visible binding for global variable ‘.data’
    recode.is.na: no visible binding for global variable ‘.data’
    ren: no visible binding for global variable ‘.data’
    rename: no visible binding for global variable ‘.data’
    rename.default: no visible binding for global variable ‘.data’
    rename.pattern: no visible binding for global variable ‘.data’
    rename.var: no visible binding for global variable ‘.data’
    sortBy: no visible binding for global variable ‘.data’
    summ: no visible binding for global variable ‘.data’
    tableStack: no visible binding for global variable ‘.data’
    unclassDataframe: no visible binding for global variable ‘.data’
    use: no visible binding for global variable ‘.data’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.15.1.0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘foreign’ ‘survival’
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64