CRAN Package Check Results for Package MetaDE

Last updated on 2017-12-13 23:14:28 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.5 4.00 90.13 94.13 WARN
r-devel-linux-x86_64-debian-gcc 1.0.5 3.20 78.73 81.93 WARN
r-devel-linux-x86_64-fedora-clang 1.0.5 119.47 WARN
r-devel-linux-x86_64-fedora-gcc 1.0.5 130.82 WARN
r-devel-windows-ix86+x86_64 1.0.5 11.00 102.00 113.00 NOTE
r-patched-linux-x86_64 1.0.5 3.97 102.33 106.30 NOTE
r-patched-solaris-x86 1.0.5 180.00 NOTE
r-release-linux-x86_64 1.0.5 3.85 104.07 107.92 NOTE
r-release-windows-ix86+x86_64 1.0.5 9.00 138.00 147.00 NOTE
r-release-osx-x86_64 1.0.5 ERROR
r-oldrel-windows-ix86+x86_64 1.0.5 8.00 128.00 136.00 NOTE
r-oldrel-osx-x86_64 1.0.5 NOTE

Check Details

Version: 1.0.5
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘Biobase’ ‘combinat’ ‘impute’ ‘tools’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘Biobase’ ‘combinat’ ‘impute’ ‘survival’ ‘tools’
     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-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0.5
Check: R code for possible problems
Result: NOTE
    CDF.rop : <anonymous> : <anonymous>: no visible global function
     definition for ‘dmnom’
    CDF.rop: no visible global function definition for ‘pbinom’
    Match.gene : IQR.f: no visible binding for global variable ‘IQR’
    MetaDE.Read: no visible global function definition for ‘read.table’
    MetaDE.Read: no visible global function definition for ‘read.csv’
    MetaDE.filter: no visible global function definition for ‘quantile’
    MetaDE.impute: no visible global function definition for ‘impute.knn’
    MetaDE.rawdata: no visible binding for global variable ‘data’
    cal.logrank : get.stat: no visible global function definition for
     ‘coxph’
    cal.minMCC: no visible global function definition for ‘combn’
    cal.modt: no visible global function definition for ‘median’
    cal.p.logrank : get.p: no visible global function definition for
     ‘coxph’
    count.DEnumber : <anonymous>: no visible global function definition for
     ‘p.adjust’
    draw.DEnumber : <anonymous>: no visible global function definition for
     ‘p.adjust’
    draw.DEnumber : get.c: no visible global function definition for ‘dist’
    draw.DEnumber: no visible global function definition for ‘plot’
    draw.DEnumber: no visible global function definition for ‘points’
    draw.DEnumber: no visible global function definition for ‘lines’
    draw.DEnumber: no visible global function definition for ‘legend’
    get.AW: no visible global function definition for ‘runif’
    get.AW: no visible global function definition for ‘p.adjust’
    get.AW.OC: no visible global function definition for ‘runif’
    get.AW.OC: no visible global function definition for ‘p.adjust’
    get.FEM: no visible global function definition for ‘pnorm’
    get.FEM: no visible global function definition for ‘p.adjust’
    get.FEM2: no visible global function definition for ‘pnorm’
    get.FEM2: no visible global function definition for ‘p.adjust’
    get.PR: no visible global function definition for ‘p.adjust’
    get.PR: no visible global function definition for ‘runif’
    get.REM: no visible global function definition for ‘pchisq’
    get.REM: no visible global function definition for ‘pnorm’
    get.REM: no visible global function definition for ‘p.adjust’
    get.REM2: no visible global function definition for ‘pchisq’
    get.REM2: no visible global function definition for ‘pnorm’
    get.REM2: no visible global function definition for ‘p.adjust’
    get.RP: no visible binding for global variable ‘na.rm’
    get.RP: no visible global function definition for ‘NaReplace2’
    get.RP: no visible global function definition for ‘p.adjust’
    get.SR: no visible global function definition for ‘p.adjust’
    get.SR: no visible global function definition for ‘runif’
    get.Stouff : <anonymous>: no visible global function definition for
     ‘qnorm’
    get.Stouff: no visible global function definition for ‘p.adjust’
    get.Stouff : <anonymous>: no visible global function definition for
     ‘pnorm’
    get.Stouff.OC : <anonymous>: no visible global function definition for
     ‘qnorm’
    get.Stouff.OC: no visible global function definition for ‘p.adjust’
    get.Stouff.OC : <anonymous>: no visible global function definition for
     ‘pnorm’
    get.fisher: no visible global function definition for ‘p.adjust’
    get.fisher : <anonymous>: no visible global function definition for
     ‘pchisq’
    get.fisher.OC: no visible global function definition for ‘runif’
    get.fisher.OC: no visible global function definition for ‘p.adjust’
    get.maxP: no visible global function definition for ‘p.adjust’
    get.maxP : <anonymous>: no visible global function definition for
     ‘pbeta’
    get.maxP.OC: no visible global function definition for ‘p.adjust’
    get.minMCC: no visible global function definition for ‘p.adjust’
    get.minP: no visible global function definition for ‘p.adjust’
    get.minP : <anonymous>: no visible global function definition for
     ‘pbeta’
    get.minP.OC: no visible global function definition for ‘p.adjust’
    get.p.F: no visible global function definition for ‘pf’
    get.p.pairedt: no visible global function definition for ‘pt’
    get.p.pearsonr: no visible global function definition for ‘pt’
    get.p.regt: no visible global function definition for ‘p.adjust’
    get.p.regt: no visible global function definition for ‘pt’
    get.p.spearmanr: no visible global function definition for ‘pt’
    get.roP: no visible global function definition for ‘p.adjust’
    get.roP : <anonymous>: no visible global function definition for
     ‘pbeta’
    get.roP.OC: no visible global function definition for ‘p.adjust’
    order.genes.AW: no visible global function definition for ‘hclust’
    order.genes.AW: no visible global function definition for ‘dist’
    order.genes.simple: no visible global function definition for ‘hclust’
    order.genes.simple: no visible global function definition for ‘dist’
    perm.lab: no visible global function definition for ‘rbinom’
    plot.matrix: no visible global function definition for
     ‘colorRampPalette’
    plot.matrix: no visible global function definition for ‘layout’
    plot.matrix: no visible global function definition for ‘par’
    plot.matrix: no visible global function definition for ‘image’
    plot.matrix: no visible global function definition for ‘axis’
    plot.matrix: no visible global function definition for ‘abline’
    Undefined global functions or variables:
     IQR NaReplace2 abline axis colorRampPalette combn coxph data dist
     dmnom hclust image impute.knn layout legend lines median na.rm
     p.adjust par pbeta pbinom pchisq pf plot pnorm points pt qnorm
     quantile rbinom read.csv read.table runif
    Consider adding
     importFrom("grDevices", "colorRampPalette")
     importFrom("graphics", "abline", "axis", "image", "layout", "legend",
     "lines", "par", "plot", "points")
     importFrom("stats", "IQR", "dist", "hclust", "median", "p.adjust",
     "pbeta", "pbinom", "pchisq", "pf", "pnorm", "pt", "qnorm",
     "quantile", "rbinom", "runif")
     importFrom("utils", "combn", "data", "read.csv", "read.table")
    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-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0.5
Check: Rd line widths
Result: NOTE
    Rd file 'MetaDE.filter.Rd':
     \examples lines wider than 100 characters:
     meta.res<-MetaDE.rawdata(mydata.filtered,ind.method=c("regt","regt"),meta.method="Fisher",ind.tail="abs",nperm=10,paired=rep(FALSE,2))
    
    Rd file 'MetaDE.pvalue.Rd':
     \examples lines wider than 100 characters:
     #--then you can use meta analysis method to combine the above p-values:here I used the Fisher's method
    
    Rd file 'MetaDE.rawdata.Rd':
     \examples lines wider than 100 characters:
     test2 <-list(list(x=exp1,y=time1,censoring.status=event1),list(x=exp2,y=time2,censoring.status=event2))
    
    Rd file 'ind.analysis.Rd':
     \examples lines wider than 100 characters:
     test3<-list(list(x=exp1,y=time1,censoring.status=event1),list(x=exp2,y=time2,censoring.status=event2),
    
    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: 1.0.5
Check: examples
Result: WARN
    Found the following significant warnings:
     Warning: working directory was changed to ‘/tmp/Rtmpod5T5Q’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpod5T5Q’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpod5T5Q’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpod5T5Q’, resetting
    Examples with CPU or elapsed time > 5s
     user system elapsed
    ind.analysis 24.480 0.072 24.610
    MetaDE.rawdata 5.984 0.032 6.029
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.5
Check: examples
Result: WARN
    Found the following significant warnings:
     Warning: working directory was changed to ‘/tmp/RtmpkEUE3E’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpkEUE3E’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpkEUE3E’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpkEUE3E’, resetting
    Examples with CPU or elapsed time > 5s
     user system elapsed
    ind.analysis 20.847 0.054 32.473
    MetaDE.rawdata 4.840 0.056 7.807
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.5
Check: examples
Result: WARN
    Found the following significant warnings:
     Warning: working directory was changed to ‘/tmp/RtmpsuGkiD’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpsuGkiD’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpsuGkiD’, resetting
     Warning: working directory was changed to ‘/tmp/RtmpsuGkiD’, resetting
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.0.5
Check: examples
Result: WARN
    Found the following significant warnings:
     Warning: working directory was changed to ‘/tmp/Rtmpl21zGW’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpl21zGW’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpl21zGW’, resetting
     Warning: working directory was changed to ‘/tmp/Rtmpl21zGW’, resetting
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.5
Check: package dependencies
Result: ERROR
    Package required but not available: ‘impute’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64