CRAN Package Check Results for Maintainer ‘Yaqing Si <siyaqing at gmail.com>’

Last updated on 2019-09-20 18:48:41 CEST.

Package NOTE
AMAP.Seq 12
MBCluster.Seq 12

Package AMAP.Seq

Current CRAN status:

Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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: 1.0
Check: R code for possible problems
Result: NOTE
    EXP.step: no visible global function definition for 'rgamma'
    EXP.step: no visible global function definition for 'rnorm'
    MAX.step: no visible global function definition for 'uniroot'
    Norm.GMedian: no visible binding for global variable 'median'
    RNASeq.Data.Gene: no visible binding for global variable 'quantile'
    decom.initial: no visible global function definition for 'kmeans'
    decom.initial: no visible global function definition for 'quantile'
    decom.initial: no visible global function definition for 'var'
    dispersion.nb.QL: no visible binding for global variable 'quantile'
    est.mu.nb.mle: no visible global function definition for 'runif'
    est.v.nb.QL: no visible global function definition for 'runif'
    pdf2grid: no visible global function definition for 'dnorm'
    pdf2grid: no visible global function definition for 'dgamma'
    prior.grid: no visible global function definition for 'sd'
    prior.grid: no visible global function definition for 'dnorm'
    test.AMAP: no visible global function definition for 'rgamma'
    test.AMAP: no visible global function definition for 'rnorm'
    test.AMAP: no visible global function definition for 'quantile'
    Undefined global functions or variables:
     dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
    Consider adding
     importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
     "rgamma", "rnorm", "runif", "sd", "uniroot", "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: 1.0
Check: Rd line widths
Result: NOTE
    Rd file 'MGN.EM.Rd':
     \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)
    
    Rd file 'test.AMAP.Rd':
     \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
     \examples lines wider than 100 characters:
     data("SimuHapMap") # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates
    
    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

Package MBCluster.Seq

Current CRAN status:

Version: 1.0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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: 1.0
Check: R code for possible problems
Result: NOTE
    MI.2: no visible global function definition for 'xtabs'
    RNASeq.Data: no visible binding for global variable 'quantile'
    loc.node: no visible global function definition for 'head'
    loc.node: no visible global function definition for 'tail'
    plotHybrid.Tree: no visible global function definition for 'par'
    plotHybrid.Tree: no visible global function definition for 'plot'
    plotHybrid.Tree: no visible global function definition for 'text'
    plotHybrid.Tree: no visible global function definition for 'image'
    plotHybrid.Tree: no visible global function definition for 'grey'
    plotHybrid.Tree: no visible global function definition for
     'heat.colors'
    plotHybrid.Tree: no visible global function definition for 'head'
    plotHybrid.Tree: no visible global function definition for 'segments'
    plotbr: no visible global function definition for 'segments'
    Undefined global functions or variables:
     grey head heat.colors image par plot quantile segments tail text
     xtabs
    Consider adding
     importFrom("grDevices", "grey", "heat.colors")
     importFrom("graphics", "image", "par", "plot", "segments", "text")
     importFrom("stats", "quantile", "xtabs")
     importFrom("utils", "head", "tail")
    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