I tried the following
> my.exp <- RunUMAP(my.exp, dims = 1:30)
UMAP(a=None, angular_rp_forest=False, b=None, init='spectral',
learning_rate=1.0, local_connectivity=1, metric='correlation',
metric_kwds=None, min_dist=0.3, n_components=2, n_epochs=None,
n_neighbors=30, negative_sample_rate=5, random_state=None,
repulsion_strength=1.0, set_op_mix_ratio=1.0, spread=1.0,
target_metric='categorical', target_metric_kwds=None,
target_n_neighbors=-1, target_weight=0.5, transform_queue_size=4.0,
transform_seed=42, verbose=True)
Construct fuzzy simplicial set
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*** caught segfault ***
address 0xfffffffffffffffa, cause 'memory not mapped'
Traceback:
1: py_call_impl(callable, dots$args, dots$keywords)
2: umap$fit_transform(as.matrix(x = object))
3: RunUMAP.default(object = data.use, assay = assay, n.neighbors = n.neighbors, n.components = n.components, metric = metric, n.epochs = n.epochs, learning.rate = learning.rate, min.dist = min.dist, spread = spread, set.op.mix.ratio = set.op.mix.ratio, local.connectivity = local.connectivity, repulsion.strength = repulsion.strength, negative.sample.rate = negative.sample.rate, a = a, b = b, seed.use = seed.use, metric.kwds = metric.kwds, angular.rp.forest = angular.rp.forest, reduction.key = reduction.key, verbose = verbose)
4: RunUMAP(object = data.use, assay = assay, n.neighbors = n.neighbors, n.components = n.components, metric = metric, n.epochs = n.epochs, learning.rate = learning.rate, min.dist = min.dist, spread = spread, set.op.mix.ratio = set.op.mix.ratio, local.connectivity = local.connectivity, repulsion.strength = repulsion.strength, negative.sample.rate = negative.sample.rate, a = a, b = b, seed.use = seed.use, metric.kwds = metric.kwds, angular.rp.forest = angular.rp.forest, reduction.key = reduction.key, verbose = verbose)
5: RunUMAP.Seurat(my.exp, dims = 1:30)
6: RunUMAP(my.exp, dims = 1:30)
I do not see a reason why it should be getting a sigfault here. I have run this function multiple times over last several months. This seems to be happening since about a week.
Any help is appreciated.
UPDATE: I have now restarted the machine one, removed entire older R installation, started with a fresh install. I am still getting exactly same error, including address 0xffffffffffffffffffa ....
Sameet
