• using R version 3.4.4 (2018-03-15)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: ISO8859-1
• checking for file 'mseapca/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'mseapca' 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'mseapca' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• 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 ... NOTE
  'library' or 'require' call to 'XML' which was already attached by Depends.
    Please remove these calls from your code.
  Package in Depends field not imported from: 'XML'
    These packages need to be imported from (in the NAMESPACE file)
    for when this namespace is loaded but not attached.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [5s] NOTE
  csv2list: no visible global function definition for 'read.csv'
  kgml_i: no visible global function definition for 'xmlTreeParse'
  kgml_i: no visible global function definition for 'xmlRoot'
  kgml_i: no visible global function definition for 'xmlAttrs'
  list2xml: no visible global function definition for 'xmlNode'
  list2xml: no visible global function definition for 'append.xmlNode'
  msea_ora: no visible global function definition for 'fisher.test'
  msea_ora: no visible global function definition for 'p.adjust'
  msea_sub: no visible global function definition for 'sd'
  msea_sub: no visible global function definition for 'cor.test'
  pathway_class: no visible global function definition for 'untar'
  pca_scaled: no visible binding for global variable 'sd'
  pca_scaled: no visible global function definition for 'cor.test'
  pca_scaled: no visible global function definition for 'p.adjust'
  pca_scaled: no visible binding for global variable 'var'
  read_pathway: no visible global function definition for 'xmlTreeParse'
  read_pathway: no visible global function definition for 'xmlRoot'
  read_pathway: no visible global function definition for 'xmlToList'
  read_pathway: no visible global function definition for 'xmlAttrs'
  Undefined global functions or variables:
    append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
    xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
  Consider adding
    importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
    importFrom("utils", "read.csv", "untar")
  to your NAMESPACE file.
• checking Rd files ... OK
• checking Rd metadata ... OK
• 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 examples ... [1s] OK
• checking PDF version of manual ... OK
• DONE

Status: 2 NOTEs