##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:velociraptor.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings velociraptor_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/velociraptor.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* this is package ‘velociraptor’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘velociraptor’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/velociraptor.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make_np_friendly’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
embedVelocity      17.078  2.750  21.274
plotVelocity        7.403  0.205   7.108
scvelo              5.370  0.206   4.759
plotVelocityStream  4.960  0.082   4.857
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/velociraptor.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL velociraptor
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘velociraptor’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (velociraptor)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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

Attaching package: 'BiocGenerics'

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

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")
computing neighbors
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
OMP: Warning #96: Cannot form a team with 48 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).
    finished (0:00:04) --> 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 -1.055.
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 1 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)
recovering dynamics

... 100%
    finished (0:00:02) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)
computing velocities
    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)
WARNING: No root cells detected. Consider specifying root cells to improve latent time prediction.
computing latent time using root_cells as prior
    finished (0:00:00) --> added 
    'latent_time', shared time (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)
2024-06-09 23:50:03.752 R[5987:35546148] XType: com.apple.fonts is not accessible.
2024-06-09 23:50:03.752 R[5987:35546148] XType: XTFontStaticRegistry is enabled.
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 -1.0162.
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 -1.137.
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 -1.0059.
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 -1.0059.
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 -1.0162.
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 -1.0162.
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 -1.0136.
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 -1.0136.
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 -1.017.
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)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
--> added 'velocity_confidence_transition' (adata.obs)
> 
> proc.time()
   user  system elapsed 
 59.608   4.081  58.683