* using log directory 'd:/Rcompile/CRANpkg/local/3.3/PIGE.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'PIGE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PIGE' version '0.9'
* 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 'PIGE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 ... NOTE
Packages in Depends field not imported from:
  'ARTP' 'snowfall' 'survival' 'xtable'
  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 ... NOTE
ARTP.GE: no visible global function definition for 'read.table'
ARTP.GE: no visible global function definition for 'write.table'
ARTP.GE: no visible global function definition for 'ARTP_pathway'
LR.cont: no visible global function definition for 'glm'
LR.cont: no visible global function definition for 'update'
LR.cont: no visible global function definition for 'binomial'
LR.cont.surv: no visible global function definition for 'coxph'
LR.cont.surv: no visible global function definition for 'update'
LR.inter.cat: no visible global function definition for 'glm'
LR.inter.cat: no visible global function definition for 'update'
LR.inter.cat: no visible global function definition for 'binomial'
LR.inter.cat: no visible global function definition for 'pchisq'
LR.inter.cat: no visible global function definition for 'anova'
LR.inter.cat.surv: no visible global function definition for 'coxph'
LR.inter.cat.surv: no visible global function definition for 'update'
LR.inter.cat.surv: no visible global function definition for 'anova'
LR.inter.cont: no visible global function definition for 'glm'
LR.inter.cont: no visible global function definition for 'update'
LR.inter.cont: no visible global function definition for 'binomial'
LR.inter.cont.surv: no visible global function definition for 'coxph'
LR.inter.cont.surv: no visible global function definition for 'update'
compute.p.snp.obs: no visible global function definition for
  'write.table'
data.to.list.gene.snp: no visible global function definition for
  'read.table'
permutation.snp: no visible global function definition for 'sfInit'
permutation.snp: no visible global function definition for 'sfLibrary'
permutation.snp: no visible global function definition for
  'sfExportAll'
permutation.snp: no visible global function definition for 'sfLapply'
permutation.snp: no visible global function definition for 'sfStop'
permutation.snp: no visible global function definition for
  'write.table'
permutation.wrapper.cat.inter: no visible global function definition
  for 'update'
permutation.wrapper.cont: no visible global function definition for
  'update'
permutation.wrapper.cont.inter: no visible global function definition
  for 'update'
Undefined global functions or variables:
  ARTP_pathway anova binomial coxph glm pchisq read.table sfExportAll
  sfInit sfLapply sfLibrary sfStop update write.table
Consider adding
  importFrom("stats", "anova", "binomial", "glm", "pchisq", "update")
  importFrom("utils", "read.table", "write.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [22s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs