This page was generated on 2021-05-06 12:37:19 -0400 (Thu, 06 May 2021).
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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> library(testthat)
> library(velociraptor)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> test_check("velociraptor")
OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
OMP: Warning #96: Cannot form a team with 24 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).
computing neighbors
finished (0:00:06) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0476.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing velocity embedding
finished (0:00:00) --> added
'velocity_target', embedded velocity vectors (adata.obsm)
computing velocity embedding
finished (0:00:00) --> added
'velocity_target', embedded velocity vectors (adata.obsm)
computing velocity embedding
finished (0:00:00) --> added
'velocity_target', embedded velocity vectors (adata.obsm)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0648.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.1483.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0409.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0409.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0648.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0648.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0508.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0508.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
Normalized count data: X, spliced, unspliced.
Logarithmized X.
computing neighbors
finished (0:00:00) --> added
'distances' and 'connectivities', weighted adjacency matrices (adata.obsp)
computing moments based on connectivities
finished (0:00:00) --> added
'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
computing velocities
WARNING: You seem to have very low signal in splicing dynamics.
The correlation threshold has been reduced to -1.0652.
Please be cautious when interpretating results.
finished (0:00:00) --> added
'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph
... 100%
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
finished (0:00:00) --> added
'velocity_graph', sparse matrix with cosine correlations (adata.uns)
computing terminal states
identified 0 region of root cells and 1 region of end points .
finished (0:00:00) --> added
'root_cells', root cells of Markov diffusion process (adata.obs)
'end_points', end points of Markov diffusion process (adata.obs)
--> added 'velocity_length' (adata.obs)
--> added 'velocity_confidence' (adata.obs)
--> added 'velocity_confidence_transition' (adata.obs)
>
> proc.time()
user system elapsed
45.322 2.294 42.697