Error(s) in re-building vignettes:
  ...
--- re-building ‘glmmSeq.rmd’ using rmarkdown
Using classic mode.
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0204233 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.247208 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0110666 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00913615 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0367411 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0139193 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 2 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0159605 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0327284 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0581862 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model is nearly unidentifiable: very large eigenvalue
 - Rescale variables?
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0117918 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00844109 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0269439 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.097074 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00538513 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.011127 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00755446 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.026424 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00569523 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.016357 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0154493 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0572743 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model is nearly unidentifiable: very large eigenvalue
 - Rescale variables?
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00373728 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0167601 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00843445 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0242556 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0367193 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 2 negative eigenvalues
Warning in vcov.merMod(mod, complete = FALSE) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in vcov.merMod(fit) :
  variance-covariance matrix computed from finite-difference Hessian is
not positive definite or contains NA values: falling back to var-cov estimated from RX
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0204233 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0204233 (tol = 0.002, component 1)
Warning in pairedPlot(glmmResult = results, geneName = "IGHV3-23", x1Label = "Timepoint",  :
  PAT300 has multiple entries for: Timepoint=6; EULAR_6m=Good responder. These will all be removed from plotting.
Warning in pairedPlot(glmmResult = results2, geneName = "FGF14", x1Label = "Timepoint",  :
  PAT300 has multiple entries for: Timepoint=6; EULAR_binary=responder. These will all be removed from plotting.
Warning in pairedPlot(glmmResult = results, geneName = "EMILIN3", x1Label = "Timepoint",  :
  PAT300 has multiple entries for: Timepoint=6; EULAR_6m=Good responder. These will all be removed from plotting.
Warning in par(oldpar) : graphical parameter "cin" cannot be set
Warning in par(oldpar) : graphical parameter "cra" cannot be set
Warning in par(oldpar) : graphical parameter "csi" cannot be set
Warning in par(oldpar) : graphical parameter "cxy" cannot be set
Warning in par(oldpar) : graphical parameter "din" cannot be set
Warning in par(oldpar) : graphical parameter "page" cannot be set
Loading required package: ggplot2
Warning in pairedPlot(glmmResult = results, geneName = "ADAM12", x1Label = "Timepoint",  :
  PAT300 has multiple entries for: Timepoint=6; EULAR_6m=Good responder. These will all be removed from plotting.
Warning in pairedPlot(glmmResult = results, geneName = "IGHJ6", x1Label = "Timepoint",  :
  PAT300 has multiple entries for: Timepoint=6; EULAR_6m=Good responder. These will all be removed from plotting.
Could not fetch https://img.shields.io/travis/KatrionaGoldmann/glmmSeq.svg
HttpExceptionRequest Request {
  host                 = "img.shields.io"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/travis/KatrionaGoldmann/glmmSeq.svg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'glmmSeq.rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘glmmSeq.rmd’

SUMMARY: processing the following file failed:
  ‘glmmSeq.rmd’

Error: Vignette re-building failed.
Execution halted