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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2
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* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* preparing ‘MOFA2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown
2024-04-16 22:06:53.420 R[91787:449905937] XType: Using static font registry.
--- finished re-building ‘MEFISTO_temporal.Rmd’

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

Quitting from lines 238-241 [unnamed-chunk-15] (downstream_analysis.Rmd)
Error: processing vignette 'downstream_analysis.Rmd' failed with diagnostics:
function 'as_cholmod_sparse' not provided by package 'Matrix'
--- failed re-building ‘downstream_analysis.Rmd’

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

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use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations...

Successfully loaded view='view_0' group='single_group' with N=100 samples and D=1000 features...
Successfully loaded view='view_1' group='single_group' with N=100 samples and D=1000 features...


Model options:
- Automatic Relevance Determination prior on the factors: False
- Automatic Relevance Determination prior on the weights: True
- Spike-and-slab prior on the factors: False
- Spike-and-slab prior on the weights: False
Likelihoods:
- View 0 (view_0): gaussian
- View 1 (view_1): gaussian




######################################
## Training the model with seed 42 ##
######################################


ELBO before training: -1602213.76 

Iteration 1: time=0.05, ELBO=-281808.05, deltaELBO=1320405.703 (82.41133230%), Factors=10
Iteration 2: time=0.04, Factors=10
Iteration 3: time=0.04, Factors=10
Iteration 4: time=0.04, Factors=10
Iteration 5: time=0.04, Factors=10
Iteration 6: time=0.05, ELBO=-237882.87, deltaELBO=43925.181 (2.74153061%), Factors=10
Iteration 7: time=0.05, Factors=10
Iteration 8: time=0.04, Factors=10
Iteration 9: time=0.04, Factors=10
Iteration 10: time=0.06, Factors=10
Iteration 11: time=0.04, ELBO=-237719.43, deltaELBO=163.439 (0.01020081%), Factors=10
Iteration 12: time=0.04, Factors=10
Iteration 13: time=0.04, Factors=10
Iteration 14: time=0.04, Factors=10
Iteration 15: time=0.05, Factors=10
Iteration 16: time=0.05, ELBO=-237643.64, deltaELBO=75.791 (0.00473040%), Factors=10
Iteration 17: time=0.05, Factors=10
Iteration 18: time=0.05, Factors=10
Iteration 19: time=0.05, Factors=10
Iteration 20: time=0.04, Factors=10
Iteration 21: time=0.04, ELBO=-237581.47, deltaELBO=62.173 (0.00388042%), Factors=10
Iteration 22: time=0.04, Factors=10
Iteration 23: time=0.05, Factors=10
Iteration 24: time=0.05, Factors=10
Iteration 25: time=0.05, Factors=10
Iteration 26: time=0.06, ELBO=-237526.93, deltaELBO=54.544 (0.00340429%), Factors=10
Iteration 27: time=0.05, Factors=10
Iteration 28: time=0.04, Factors=10
Iteration 29: time=0.04, Factors=10
Iteration 30: time=0.04, Factors=10
Iteration 31: time=0.04, ELBO=-237478.41, deltaELBO=48.512 (0.00302779%), Factors=10
Iteration 32: time=0.04, Factors=10
Iteration 33: time=0.04, Factors=10
Iteration 34: time=0.04, Factors=10
Iteration 35: time=0.04, Factors=10
Iteration 36: time=0.04, ELBO=-237434.91, deltaELBO=43.504 (0.00271522%), Factors=10
Iteration 37: time=0.05, Factors=10
Iteration 38: time=0.05, Factors=10
Iteration 39: time=0.04, Factors=10
Iteration 40: time=0.04, Factors=10
Iteration 41: time=0.05, ELBO=-237395.76, deltaELBO=39.152 (0.00244361%), Factors=10
Iteration 42: time=0.04, Factors=10
Iteration 43: time=0.05, Factors=10
Iteration 44: time=0.05, Factors=10
Iteration 45: time=0.05, Factors=10
Iteration 46: time=0.06, ELBO=-237360.38, deltaELBO=35.379 (0.00220813%), Factors=10
Iteration 47: time=0.05, Factors=10
Iteration 48: time=0.04, Factors=10
Iteration 49: time=0.04, Factors=10
Iteration 50: time=0.04, Factors=10
Iteration 51: time=0.05, ELBO=-237328.29, deltaELBO=32.093 (0.00200304%), Factors=10
Iteration 52: time=0.04, Factors=10
Iteration 53: time=0.04, Factors=10
Iteration 54: time=0.04, Factors=10
Iteration 55: time=0.04, Factors=10
Iteration 56: time=0.04, ELBO=-237299.19, deltaELBO=29.101 (0.00181631%), Factors=10
Iteration 57: time=0.04, Factors=10
Iteration 58: time=0.04, Factors=10
Iteration 59: time=0.04, Factors=10
Iteration 60: time=0.04, Factors=10
Iteration 61: time=0.05, ELBO=-237272.58, deltaELBO=26.604 (0.00166044%), Factors=10
Iteration 62: time=0.04, Factors=10
Iteration 63: time=0.04, Factors=10
Iteration 64: time=0.04, Factors=10
Iteration 65: time=0.04, Factors=10
Iteration 66: time=0.05, ELBO=-237248.16, deltaELBO=24.421 (0.00152419%), Factors=10
Iteration 67: time=0.04, Factors=10
Iteration 68: time=0.04, Factors=10
Iteration 69: time=0.04, Factors=10
Iteration 70: time=0.04, Factors=10
Iteration 71: time=0.05, ELBO=-237225.71, deltaELBO=22.455 (0.00140148%), Factors=10
Iteration 72: time=0.04, Factors=10
Iteration 73: time=0.04, Factors=10
Iteration 74: time=0.04, Factors=10
Iteration 75: time=0.05, Factors=10
Iteration 76: time=0.05, ELBO=-237204.93, deltaELBO=20.781 (0.00129701%), Factors=10
Iteration 77: time=0.05, Factors=10
Iteration 78: time=0.05, Factors=10
Iteration 79: time=0.04, Factors=10
Iteration 80: time=0.05, Factors=10
Iteration 81: time=0.04, ELBO=-237185.63, deltaELBO=19.293 (0.00120412%), Factors=10
Iteration 82: time=0.04, Factors=10
Iteration 83: time=0.04, Factors=10
Iteration 84: time=0.05, Factors=10
Iteration 85: time=0.05, Factors=10
Iteration 86: time=0.05, ELBO=-237167.59, deltaELBO=18.045 (0.00112624%), Factors=10
Iteration 87: time=0.05, Factors=10
Iteration 88: time=0.04, Factors=10
Iteration 89: time=0.05, Factors=10
Iteration 90: time=0.04, Factors=10
Iteration 91: time=0.05, ELBO=-237150.69, deltaELBO=16.901 (0.00105484%), Factors=10
Iteration 92: time=0.04, Factors=10
Iteration 93: time=0.05, Factors=10
Iteration 94: time=0.05, Factors=10
Iteration 95: time=0.05, Factors=10
Iteration 96: time=0.05, ELBO=-237134.75, deltaELBO=15.943 (0.00099504%), Factors=10
Iteration 97: time=0.05, Factors=10
Iteration 98: time=0.04, Factors=10
Iteration 99: time=0.04, Factors=10
Iteration 100: time=0.04, Factors=10
Iteration 101: time=0.05, ELBO=-237119.68, deltaELBO=15.064 (0.00094020%), Factors=10
Iteration 102: time=0.04, Factors=10
Iteration 103: time=0.04, Factors=10
Iteration 104: time=0.04, Factors=10
Iteration 105: time=0.04, Factors=10
Iteration 106: time=0.04, ELBO=-237105.45, deltaELBO=14.235 (0.00088848%), Factors=10
Iteration 107: time=0.04, Factors=10
Iteration 108: time=0.04, Factors=10
Iteration 109: time=0.04, Factors=10
Iteration 110: time=0.04, Factors=10
Iteration 111: time=0.05, ELBO=-237091.92, deltaELBO=13.522 (0.00084397%), Factors=10
Iteration 112: time=0.04, Factors=10
Iteration 113: time=0.04, Factors=10
Iteration 114: time=0.04, Factors=10
Iteration 115: time=0.04, Factors=10
Iteration 116: time=0.05, ELBO=-237079.08, deltaELBO=12.847 (0.00080184%), Factors=10
Iteration 117: time=0.04, Factors=10
Iteration 118: time=0.04, Factors=10
Iteration 119: time=0.04, Factors=10
Iteration 120: time=0.04, Factors=10
Iteration 121: time=0.05, ELBO=-237066.82, deltaELBO=12.256 (0.00076493%), Factors=10
Iteration 122: time=0.04, Factors=10
Iteration 123: time=0.05, Factors=10
Iteration 124: time=0.04, Factors=10
Iteration 125: time=0.05, Factors=10
Iteration 126: time=0.05, ELBO=-237055.07, deltaELBO=11.752 (0.00073346%), Factors=10
Iteration 127: time=0.04, Factors=10
Iteration 128: time=0.04, Factors=10
Iteration 129: time=0.04, Factors=10
Iteration 130: time=0.04, Factors=10
Iteration 131: time=0.04, ELBO=-237043.83, deltaELBO=11.243 (0.00070169%), Factors=10
Iteration 132: time=0.04, Factors=10
Iteration 133: time=0.04, Factors=10
Iteration 134: time=0.04, Factors=10
Iteration 135: time=0.04, Factors=10
Iteration 136: time=0.04, ELBO=-237033.01, deltaELBO=10.815 (0.00067498%), Factors=10
Iteration 137: time=0.04, Factors=10
Iteration 138: time=0.04, Factors=10
Iteration 139: time=0.04, Factors=10
Iteration 140: time=0.04, Factors=10
Iteration 141: time=0.05, ELBO=-237022.64, deltaELBO=10.369 (0.00064717%), Factors=10
Iteration 142: time=0.04, Factors=10
Iteration 143: time=0.04, Factors=10
Iteration 144: time=0.04, Factors=10
Iteration 145: time=0.05, Factors=10
Iteration 146: time=0.04, ELBO=-237012.63, deltaELBO=10.017 (0.00062520%), Factors=10
Iteration 147: time=0.04, Factors=10
Iteration 148: time=0.04, Factors=10
Iteration 149: time=0.04, Factors=10
Iteration 150: time=0.05, Factors=10
Iteration 151: time=0.05, ELBO=-237003.00, deltaELBO=9.626 (0.00060082%), Factors=10
Iteration 152: time=0.04, Factors=10
Iteration 153: time=0.04, Factors=10
Iteration 154: time=0.04, Factors=10
Iteration 155: time=0.04, Factors=10
Iteration 156: time=0.05, ELBO=-236993.66, deltaELBO=9.341 (0.00058299%), Factors=10
Iteration 157: time=0.04, Factors=10
Iteration 158: time=0.04, Factors=10
Iteration 159: time=0.04, Factors=10
Iteration 160: time=0.04, Factors=10
Iteration 161: time=0.05, ELBO=-236984.69, deltaELBO=8.965 (0.00055952%), Factors=10
Iteration 162: time=0.04, Factors=10
Iteration 163: time=0.04, Factors=10
Iteration 164: time=0.04, Factors=10
Iteration 165: time=0.05, Factors=10
Iteration 166: time=0.04, ELBO=-236975.96, deltaELBO=8.731 (0.00054492%), Factors=10
Iteration 167: time=0.04, Factors=10
Iteration 168: time=0.04, Factors=10
Iteration 169: time=0.04, Factors=10
Iteration 170: time=0.04, Factors=10
Iteration 171: time=0.05, ELBO=-236967.61, deltaELBO=8.352 (0.00052130%), Factors=10
Iteration 172: time=0.04, Factors=10
Iteration 173: time=0.04, Factors=10
Iteration 174: time=0.04, Factors=10
Iteration 175: time=0.05, Factors=10
Iteration 176: time=0.05, ELBO=-236959.52, deltaELBO=8.090 (0.00050492%), Factors=10
Iteration 177: time=0.04, Factors=10
Iteration 178: time=0.04, Factors=10
Iteration 179: time=0.04, Factors=10
Iteration 180: time=0.08, Factors=10
Iteration 181: time=0.05, ELBO=-236951.73, deltaELBO=7.792 (0.00048630%), Factors=10
Iteration 182: time=0.05, Factors=10
Iteration 183: time=0.05, Factors=10
Iteration 184: time=0.04, Factors=10
Iteration 185: time=0.04, Factors=10
Iteration 186: time=0.05, ELBO=-236944.18, deltaELBO=7.549 (0.00047116%), Factors=10

Converged!



#######################
## Training finished ##
#######################


Warning: Output file /tmp/RtmprXqvmq/model.hdf5 already exists, it will be replaced
Saving model in /tmp/RtmprXqvmq/model.hdf5...
--- finished re-building ‘getting_started_R.Rmd’

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

Error: Vignette re-building failed.
Execution halted