Error(s) in re-building vignettes:
--- re-building ‘MultiPhen.Rnw’ using Sweave
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.2-1).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs
Warning in betasg/normg :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in betasg/normg :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in betasg/normg :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) :
  unable to make heatmap resultsDir/resultsJoint.heatm.pdf all all beta
Warning in max(abs(as.vector(res[, snpinds, , 1]))[pvs < 0.05], na.rm = T) :
  no non-missing arguments to max; returning -Inf
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in .heatm(outC$beta, effPhe, logfun1, opts, TRUE, filek) :
  unable to make heatmap resultsDir/resultsBackwardSelection.heatm.pdf all all beta
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in .manhattan(topl, logfun, beta1 = NULL, paste(opts$mPhen.title,  :
  NAs introduced by coercion
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in plot.window(...) : "na.color" is not a graphical parameter
Warning in plot.window(...) : "dendrogram" is not a graphical parameter
Warning in plot.window(...) :
  "density.info" is not a graphical parameter
Warning in plot.window(...) : "trace" is not a graphical parameter
Warning in plot.window(...) : "key" is not a graphical parameter
Warning in plot.window(...) : "symbreaks" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "na.color" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "dendrogram" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "density.info" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "trace" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "key" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "symbreaks" is not a graphical parameter
Warning in title(...) : "na.color" is not a graphical parameter
Warning in title(...) : "dendrogram" is not a graphical parameter
Warning in title(...) : "density.info" is not a graphical parameter
Warning in title(...) : "trace" is not a graphical parameter
Warning in title(...) : "key" is not a graphical parameter
Warning in title(...) : "symbreaks" is not a graphical parameter
Warning in betag/(betag %*% betag) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error: processing vignette 'MultiPhen.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'MultiPhen.tex' failed.
LaTeX errors:
! LaTeX Error: File `underscore.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘MultiPhen.Rnw’

SUMMARY: processing the following file failed:
  ‘MultiPhen.Rnw’

Error: Vignette re-building failed.
Execution halted