• using R Under development (unstable) (2019-12-11 r77556)
• using platform: x86_64-pc-linux-gnu (64-bit)
• using session charset: ISO8859-15
• checking for file 'AMAP.Seq/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'AMAP.Seq' version '1.0'
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package 'AMAP.Seq' can be installed ... OK
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking DESCRIPTION meta-information ... NOTE
  Malformed Description field: should contain one or more complete sentences.
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [8s/9s] 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.
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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.
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of 'data' directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [4s/5s] OK
• checking PDF version of manual ... OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 NOTEs