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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:velociraptor.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings velociraptor_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/velociraptor.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* this is package ‘velociraptor’ version ‘1.19.1’
* 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 ‘/home/biocbuild/bbs-3.22-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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  embedVelocity.Rd: SingleCellExperiment-class, reducedDims
  gridVectors.Rd: SingleCellExperiment-class, reducedDims
  plotVelocity.Rd: SingleCellExperiment-class, reducedDims
  plotVelocityStream.Rd: SingleCellExperiment-class, reducedDims
  scvelo.Rd: SummarizedExperiment-class, librarySizeFactors,
    BiocParallelParam-class, BiocSingularParam-class, reducedDims,
    normalizeCounts, SingleCellExperiment-class, colData, assays
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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      15.002  1.547  16.625
plotVelocity        8.591  0.811   7.835
plotVelocityStream  4.828  0.472   3.830
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/velociraptor.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL velociraptor
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘velociraptor’ ...
** this is package ‘velociraptor’ version ‘1.19.1’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo
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 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 -0.8785.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
WARNING: Unable to create progress bar. Consider installing `tqdm` as `pip install tqdm` and `ipywidgets` as `pip install ipywidgets`,
or disable the progress bar using `show_progress_bar=False`.
    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 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 -0.915.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 moments based on connectivities
    finished (0:00:00) --> added 
    'Ms' and 'Mu', moments of un/spliced abundances (adata.layers)
recovering dynamics (using 1/72 cores)
    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 (using 1/72 cores)
    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)
computing velocity embedding
    finished (0:00:00) --> added
    'velocity_target', embedded velocity vectors (adata.obsm)
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 -0.9308.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.9343.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.891.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.891.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.9308.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)

 *** caught segfault ***
address 0x17ba, cause 'memory not mapped'
Warning: stack imbalance in 'c', 79 then 76
Warning: stack imbalance in '$', 54 then 47
    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 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 -0.9308.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.8939.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
    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 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 -0.8939.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
/var/cache/basilisk/1.21.5/velociraptor/1.19.1/env/lib/python3.12/site-packages/scvelo/preprocessing/utils.py:705: DeprecationWarning: `log1p` is deprecated since scVelo v0.3.0 and will be removed in a future version. Please use `log1p` from `scanpy.pp` instead.
  log1p(adata)
    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 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 -0.9394.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/72 cores)
/home/biocbuild/.pyenv/versions/3.12.10/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=2644776) is multi-threaded, use of fork() may lead to deadlocks in the child.
  self.pid = os.fork()
    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)
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 50 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
 57.408   5.605  56.403