Error(s) in re-building vignettes:
  ...
--- re-building ‘finemapping.Rmd’ using rmarkdown
--- finished re-building ‘finemapping.Rmd’

--- re-building ‘finemapping_summary_statistics.Rmd’ using rmarkdown
--- finished re-building ‘finemapping_summary_statistics.Rmd’

--- re-building ‘l0_initialization.Rmd’ using rmarkdown
--- finished re-building ‘l0_initialization.Rmd’

--- re-building ‘mwe.Rmd’ using rmarkdown
--- finished re-building ‘mwe.Rmd’

--- re-building ‘sparse_susie_eval.Rmd’ using rmarkdown
--- finished re-building ‘sparse_susie_eval.Rmd’

--- re-building ‘susie_refine.Rmd’ using rmarkdown
--- finished re-building ‘susie_refine.Rmd’

--- re-building ‘susie_rss.Rmd’ using rmarkdown
HINT: For estimate_residual_variance = TRUE, please check that R is the "in-sample" LD matrix; that is, the correlation matrix obtained using the exact same data matrix X that was used for the other summary statistics. Also note, when covariates are included in the univariate regressions that produced the summary statistics, also consider removing these effects from X before computing R.
WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
HINT: For estimate_residual_variance = TRUE, please check that R is the "in-sample" LD matrix; that is, the correlation matrix obtained using the exact same data matrix X that was used for the other summary statistics. Also note, when covariates are included in the univariate regressions that produced the summary statistics, also consider removing these effects from X before computing R.
WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
WARNING: Providing the sample size (n), or even a rough estimate of n, is highly recommended. Without n, the implicit assumption is n is large (Inf) and the effect sizes are small (close to zero).
WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
--- finished re-building ‘susie_rss.Rmd’

--- re-building ‘susierss_diagnostic.Rmd’ using rmarkdown

warning: solve(): system is singular (rcond: 3.28772e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.15883e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.47747e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.36944e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.68099e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.95965e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.86835e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.13856e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.72403e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.89248e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.20664e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.69746e-17); attempting approx solution

warning: solve(): system is singular (rcond: 9.33825e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.1175e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.05731e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.17557e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.6549e-16); attempting approx solution

warning: solve(): system is singular (rcond: 4.11121e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.23716e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.36423e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.85597e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.98797e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.46896e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.59813e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.80754e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.90959e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.12956e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.25035e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.42181e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.29353e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.07456e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.18569e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.17651e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.61851e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.76765e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.88888e-17); attempting approx solution

warning: solve(): system is singular (rcond: 9.18913e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.06316e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.18292e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.19778e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.11312e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.09484e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.30695e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.48843e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.30321e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.57111e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.69838e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.69952e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.91082e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.12963e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.13024e-16); attempting approx solution

warning: solve(): system is singular (rcond: 2.4035e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.76302e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.11813e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.94537e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.6539e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.97756e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.99001e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.8531e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.7062e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.79875e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.08282e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.00771e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.97926e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.62606e-18); attempting approx solution

warning: solve(): system is singular (rcond: 8.63725e-18); attempting approx solution

warning: solve(): system is singular (rcond: 5.89537e-18); attempting approx solution

warning: solve(): system is singular (rcond: 6.21093e-18); attempting approx solution

warning: solve(): system is singular (rcond: 1.63713e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.55432e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.55972e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.57301e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.52289e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.4272e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.45094e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.86378e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.8517e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.72114e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.86057e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.06768e-18); attempting approx solution

warning: solve(): system is singular (rcond: 2.09526e-18); attempting approx solution

warning: solve(): system is singular (rcond: 4.05885e-17); attempting approx solution
--- finished re-building ‘susierss_diagnostic.Rmd’

--- re-building ‘trend_filtering.Rmd’ using rmarkdown
Quitting from lines 86-94 (trend_filtering.Rmd) 
Error: processing vignette ‘trend_filtering.Rmd’ failed with diagnostics:
there is no package called 'genlasso'
--- failed re-building ‘trend_filtering.Rmd’

--- re-building ‘trendfiltering_derivations.Rnw’ using Sweave
--- finished re-building ‘trendfiltering_derivations.Rnw’

SUMMARY: processing the following file failed:
  ‘trend_filtering.Rmd’

Error: Vignette re-building failed.
Execution halted