* using log directory 'd:/Rcompile/CRANpkg/local/3.3/MEGENA.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 'MEGENA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEGENA' version '1.3.5-2'
* 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 'MEGENA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
plot_module: possible error in theme(panel.background =
  element_blank(), axis.title.x = element_blank(), axis.title.y =
  element_blank(), panel.background = element_rect(fill = "white",
  colour = NA), axis.line = element_blank(), axis.ticks =
  element_blank(), axis.text = element_blank(), panel.grid.minor =
  element_blank(), panel.grid.major = element_blank(), plot.title =
  element_text(size = title.size), legend.position = "bottom",
  legend.direction = "horizontal"): formal argument "panel.background"
  matched by multiple actual arguments
plot_module_hierarchy: possible error in theme(panel.background =
  element_blank(), axis.title.x = element_blank(), axis.title.y =
  element_blank(), panel.background = element_rect(fill = "white",
  colour = NA), axis.line = element_blank(), axis.ticks =
  element_blank(), axis.text = element_blank(), panel.grid.minor =
  element_blank(), panel.grid.major = element_blank(), legend.position
  = "bottom", legend.direction = "horizontal"): formal argument
  "panel.background" matched by multiple actual arguments
plot_subgraph: possible error in theme(panel.background =
  element_blank(), axis.title.x = element_blank(), axis.title.y =
  element_blank(), panel.background = element_rect(fill = "white",
  colour = NA), axis.line = element_blank(), axis.ticks =
  element_blank(), axis.text = element_blank(), panel.grid.minor =
  element_blank(), panel.grid.major = element_blank(), plot.title =
  element_text(size = title.size), legend.position = "bottom",
  legend.direction = "horizontal"): formal argument "panel.background"
  matched by multiple actual arguments
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...

The following object is masked from 'package:base':

    union

Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Warning in vattrs[[name]][index] <- value :
  number of items to replace is not a multiple of replacement length
Quitting from lines 119-127 (MEGENA_pipeline_10062016.Rmd) 
Error: processing vignette 'MEGENA_pipeline_10062016.Rmd' failed with diagnostics:
formal argument "panel.background" matched by multiple actual arguments
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE