Last updated on 2022-08-15 08:50:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.12.16 | 16.08 | 380.32 | 396.40 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.12.16 | 14.96 | 230.31 | 245.27 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.12.16 | 412.58 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.12.16 | 417.75 | ERROR | |||
| r-devel-windows-x86_64 | 0.12.16 | 54.00 | 457.00 | 511.00 | OK | |
| r-patched-linux-x86_64 | 0.12.16 | 15.05 | 300.41 | 315.46 | ERROR | |
| r-release-linux-x86_64 | 0.12.16 | 14.47 | 301.59 | 316.06 | ERROR | |
| r-release-macos-arm64 | 0.12.16 | 166.00 | OK | |||
| r-release-macos-x86_64 | 0.12.16 | 200.00 | OK | |||
| r-release-windows-x86_64 | 0.12.16 | 59.00 | 623.00 | 682.00 | OK | |
| r-oldrel-macos-arm64 | 0.12.16 | 160.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.12.16 | 219.00 | OK | |||
| r-oldrel-windows-ix86+x86_64 | 0.12.16 | 34.00 | 513.00 | 547.00 | OK |
Version: 0.12.16
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘genlasso’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.12.16
Check: re-building of vignette outputs
Result: ERROR
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.12.16
Check: re-building of vignette outputs
Result: ERROR
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
OMP: Warning #96: Cannot form a team with 8 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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: 4.01843e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.11394e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.25252e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.36048e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.19142e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.24038e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.94777e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.58907e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.20789e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.02055e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.531e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.60974e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.36857e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.90301e-17); attempting approx solution
warning: solve(): system is singular (rcond: 7.20692e-17); attempting approx solution
warning: solve(): system is singular (rcond: 6.42453e-17); attempting approx solution
warning: solve(): system is singular (rcond: 7.68976e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.008e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.2439e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.44558e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.79767e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.15118e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.16821e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.25576e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.267e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.30885e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.41519e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.41311e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.49332e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.61273e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.60351e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.93909e-16); attempting approx solution
warning: solve(): system is singular (rcond: 2.17591e-16); attempting approx solution
warning: solve(): system is singular (rcond: 6.27113e-18); attempting approx solution
warning: solve(): system is singular (rcond: 8.57803e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.15501e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.43319e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.9016e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.83793e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.76722e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.30378e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.60957e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.81536e-18); attempting approx solution
warning: solve(): system is singular (rcond: 3.81565e-18); attempting approx solution
warning: solve(): system is singular (rcond: 6.24995e-17); attempting approx solution
warning: solve(): system is singular (rcond: 6.16545e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.79258e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.51524e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.07442e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.10006e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.48049e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.07773e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.67863e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.48111e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.52692e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.94584e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.92048e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.7091e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.73652e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.30398e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.84885e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.70851e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.82447e-17); attempting approx solution
warning: solve(): system is singular (rcond: 3.54818e-18); attempting approx solution
warning: solve(): system is singular (rcond: 4.24499e-19); attempting approx solution
warning: solve(): system is singular (rcond: 4.17232e-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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.12.16
Check: re-building of vignette outputs
Result: ERROR
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: 4.01843e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.11394e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.25252e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.36048e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.19142e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.24038e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.94777e-17); attempting approx solution
warning: solve(): system is singular (rcond: 4.58907e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.20789e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.02055e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.531e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.60974e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.36857e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.90301e-17); attempting approx solution
warning: solve(): system is singular (rcond: 7.20692e-17); attempting approx solution
warning: solve(): system is singular (rcond: 6.42453e-17); attempting approx solution
warning: solve(): system is singular (rcond: 7.68976e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.008e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.2439e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.44558e-17); attempting approx solution
warning: solve(): system is singular (rcond: 8.79767e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.15118e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.16821e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.25576e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.267e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.30885e-16); attempting approx solution
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warning: solve(): system is singular (rcond: 1.41311e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.49332e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.61273e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.60351e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.93909e-16); attempting approx solution
warning: solve(): system is singular (rcond: 2.17591e-16); attempting approx solution
warning: solve(): system is singular (rcond: 6.27113e-18); attempting approx solution
warning: solve(): system is singular (rcond: 8.57803e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.15501e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.43319e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.9016e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.83793e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.76722e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.30378e-17); attempting approx solution
warning: solve(): system is singular (rcond: 5.60957e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.81536e-18); attempting approx solution
warning: solve(): system is singular (rcond: 3.81565e-18); attempting approx solution
warning: solve(): system is singular (rcond: 6.24995e-17); attempting approx solution
warning: solve(): system is singular (rcond: 6.16545e-17); attempting approx solution
warning: solve(): system is singular (rcond: 2.79258e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.51524e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.07442e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.10006e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.48049e-16); attempting approx solution
warning: solve(): system is singular (rcond: 1.07773e-16); attempting approx solution
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warning: solve(): system is singular (rcond: 1.92048e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.7091e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.73652e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.30398e-18); attempting approx solution
warning: solve(): system is singular (rcond: 1.84885e-17); attempting approx solution
warning: solve(): system is singular (rcond: 1.70851e-17); attempting approx solution
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warning: solve(): system is singular (rcond: 3.54818e-18); attempting approx solution
warning: solve(): system is singular (rcond: 4.24499e-19); attempting approx solution
warning: solve(): system is singular (rcond: 4.17232e-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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.12.16
Check: re-building of vignette outputs
Result: ERROR
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
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64