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: 2.56377e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.70416e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.88334e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.09527e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.27277e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.81271e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.22396e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.33779e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.18471e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.08355e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.63438e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.37742e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.85768e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.09635e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.08654e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.47807e-16); attempting approx solution

warning: solve(): system is singular (rcond: 3.79853e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.89134e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.15807e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.15649e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.28451e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.22485e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.43151e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.38823e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.02336e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.12746e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.43674e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.55583e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.77743e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.88222e-17); attempting approx solution

warning: solve(): system is singular (rcond: 6.57353e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.12794e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.80137e-17); attempting approx solution

warning: solve(): system is singular (rcond: 7.9903e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.10645e-17); attempting approx solution

warning: solve(): system is singular (rcond: 8.27978e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.06967e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.07965e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.09466e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.1251e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.13066e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.3055e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.37585e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.37611e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.40483e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.52526e-16); attempting approx solution

warning: solve(): system is singular (rcond: 1.5171e-16); attempting approx solution

warning: solve(): system is singular (rcond: 5.33822e-18); attempting approx solution

warning: solve(): system is singular (rcond: 6.13508e-18); attempting approx solution

warning: solve(): system is singular (rcond: 4.47041e-18); attempting approx solution

warning: solve(): system is singular (rcond: 1.26187e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.19851e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.7337e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.67373e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.39351e-17); attempting approx solution

warning: solve(): system is singular (rcond: 5.33138e-17); attempting approx solution

warning: solve(): system is singular (rcond: 4.69373e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.40385e-18); attempting approx solution

warning: solve(): system is singular (rcond: 2.58177e-18); attempting approx solution

warning: solve(): system is singular (rcond: 3.70066e-18); attempting approx solution

warning: solve(): system is singular (rcond: 3.79148e-18); attempting approx solution

warning: solve(): system is singular (rcond: 3.75665e-18); attempting approx solution

warning: solve(): system is singular (rcond: 3.66815e-18); attempting approx solution

warning: solve(): system is singular (rcond: 1.12858e-18); attempting approx solution

warning: solve(): system is singular (rcond: 9.48657e-18); attempting approx solution

warning: solve(): system is singular (rcond: 9.60838e-18); attempting approx solution

warning: solve(): system is singular (rcond: 9.30958e-18); attempting approx solution

warning: solve(): system is singular (rcond: 9.23361e-18); attempting approx solution

warning: solve(): system is singular (rcond: 1.36481e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.59888e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.58214e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.60849e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.58313e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.44953e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.38059e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.84673e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.85097e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.70653e-17); attempting approx solution

warning: solve(): system is singular (rcond: 1.83213e-17); attempting approx solution

warning: solve(): system is singular (rcond: 2.37093e-17); attempting approx solution

warning: solve(): system is singular (rcond: 3.08293e-18); attempting approx solution

warning: solve(): system is singular (rcond: 4.13514e-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