Package: wrGraph
Check: examples
New result: ERROR
  Running examples in ‘wrGraph-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: MAplotW
  > ### Title: MA-plot (differential intensity versus average intensity)
  > ### Aliases: MAplotW
  > 
  > ### ** Examples
  > 
  > library(wrMisc)
  > set.seed(2005); mat <- matrix(round(runif(600),2), ncol=6)
  > rownames(mat) <- c(rep(letters[1:25],each=3), letters[2:26])
  > MAplotW(mat[,2] -mat[,1], A=rowMeans(mat))
  > ## assume 2 groups with 3 samples each
  > matMeans <- rowGrpMeans(mat, gr=gl(2,3,labels=LETTERS[3:4]))
  > MAplotW(M=matMeans[,2] -matMeans[,1], A=matMeans) 
  MAplotW :  Note, matMeans has 2 columns, using last column
  > ## assume 2 groups with 3 samples each and run moderated t-test (from package 'limma')
  > tRes <- moderTest2grp(mat, gl(2,3))
  moderTest2grp : Package 'fdrtool' not found, omitting .. Please install from CRAN for enabeling 'lfdr'
  moderTest2grp : Detected 74 non-unique rownames of 'dat' !
  > MAplotW(tRes$Mval, tRes$Amean)                          
  > MAplotW(M=tRes$Mval, A=tRes$means, FCth=1.3) 
  MAplotW :  Note, tRes$means has 2 columns, using last column
  > MAplotW(tRes)
  Error in wrMisc::sampNoDeMArrayLM(Mvalue, useComp, lstMeans = "means",  : 
    unused arguments (lstMeans = "means", lstP = names(Mvalue)[FDRcol[1]])
  Calls: MAplotW
  Execution halted

Package: wrGraph
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘wrGraphVignette1.Rmd’ using rmarkdown
  
  Quitting from wrGraphVignette1.Rmd:452-455 [MA5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `wrMisc::sampNoDeMArrayLM()`:
  ! unused arguments (lstMeans = "means", lstP = names(Mvalue)[FDRcol[1]])
  ---
  Backtrace:
      ▆
   1. └─wrGraph::MAplotW(tRes, FCth = 2, namesNBest = "passFC")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'wrGraphVignette1.Rmd' failed with diagnostics:
  unused arguments (lstMeans = "means", lstP = names(Mvalue)[FDRcol[1]])
  --- failed re-building ‘wrGraphVignette1.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘wrGraphVignette1.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: wrProteo
Check: examples
New result: ERROR
  Running examples in ‘wrProteo-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: extractTestingResults
  > ### Title: Extract Results From Moderated t-tests
  > ### Aliases: extractTestingResults
  > 
  > ### ** Examples
  > 
  > grp <- factor(rep(LETTERS[c(3,1,4)],c(2,3,3)))
  > set.seed(2017); t8 <- matrix(round(rnorm(208*8,10,0.4),2), ncol=8,
  +   dimnames=list(paste(letters[],rep(1:8,each=26),sep=""), paste(grp,c(1:2,1:3,1:3),sep="")))
  > t8[3:6,1:2] <- t8[3:6,1:2] +3                    # augment lines 3:6 (c-f) 
  > t8[5:8,c(1:2,6:8)] <- t8[5:8,c(1:2,6:8)] -1.5    # lower lines 
  > t8[6:7,3:5] <- t8[6:7,3:5] +2.2                  # augment lines 
  > ## expect to find C/A in c,d,g, (h)
  > ## expect to find C/D in c,d,e,f
  > ## expect to find A/D in f,g,(h) 
  > library(wrMisc)     # for testing we'll use this package
  > test8 <- moderTestXgrp(t8, grp) 
  > extractTestingResults(test8)
  extractTestingResults : Cannot find list-element 'annot' in test8
  Error in wrMisc::sampNoDeMArrayLM(stat, compNo, lstP = useFdrTy) : 
    unused argument (lstP = useFdrTy)
  Calls: extractTestingResults
  Execution halted

Package: wrProteo
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘wrProteoVignette1.Rmd’ using rmarkdown
  
  Quitting from wrProteoVignette1.Rmd:751-754 [MAplot1]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `wrMisc::sampNoDeMArrayLM()`:
  ! unused arguments (lstMeans = "means", lstP = names(Mvalue)[FDRcol[1]])
  ---
  Backtrace:
      ▆
   1. └─wrGraph::MAplotW(testMQ)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'wrProteoVignette1.Rmd' failed with diagnostics:
  unused arguments (lstMeans = "means", lstP = names(Mvalue)[FDRcol[1]])
  --- failed re-building ‘wrProteoVignette1.Rmd’
  
  --- re-building ‘wrProteoVignetteUPS1.Rmd’ using rmarkdown
  
  Quitting from wrProteoVignetteUPS1.Rmd:576-580 [check2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `wrMisc::sampNoDeMArrayLM()`:
  ! unused argument (lstP = useFdrTy)
  ---
  Backtrace:
      ▆
   1. └─wrProteo::extractTestingResults(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'wrProteoVignetteUPS1.Rmd' failed with diagnostics:
  unused argument (lstP = useFdrTy)
  --- failed re-building ‘wrProteoVignetteUPS1.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘wrProteoVignette1.Rmd’ ‘wrProteoVignetteUPS1.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted