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This page was generated on 2024-07-16 17:43 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2258/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
velociraptor 1.14.3  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/velociraptor
git_branch: RELEASE_3_19
git_last_commit: aa520b4
git_last_commit_date: 2024-06-26 08:49:52 -0400 (Wed, 26 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for velociraptor on kjohnson1

To the developers/maintainers of the velociraptor package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/velociraptor.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: velociraptor
Version: 1.14.3
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_1.14.3.tar.gz
StartedAt: 2024-07-16 12:41:12 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 12:46:46 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 334.8 seconds
RetCode: 0
Status:   OK  
CheckDir: velociraptor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.14.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/velociraptor.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* this is package ‘velociraptor’ version ‘1.14.3’
* 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      28.407  4.696  39.175
plotVelocity        7.305  0.761   8.160
scvelo              4.544  0.904   5.441
plotVelocityStream  4.540  0.509   5.311
* 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.


Installation output

velociraptor.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output

velociraptor.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 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 -0.9523.
Please be cautious when interpreting results.
    finished (0:00:00) --> added 
    'velocity', velocity vectors for each individual cell (adata.layers)
computing velocity graph (using 1/10 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 1/10 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 1/10 cores)
    finished (0:00:03) --> 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 1/10 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)
2024-07-16 12:46:11.555 R[31100:142146420] XType: Using static font registry.
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 1/10 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 1/10 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 1/10 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 1/10 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 1/10 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 1/10 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 1/10 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 1/10 cores)
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.16.0/velociraptor/1.14.3/env/lib/python3.9/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)
WARNING: You’re trying to run this on 2000 dimensions of `.X`, if you really want this, set `use_rep='X'`.
         Falling back to preprocessing with `sc.pp.pca` and default params.
    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 1/10 cores)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
    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 
 68.981   8.034  77.370 

Example timings

velociraptor.Rcheck/velociraptor-Ex.timings

nameusersystemelapsed
embedVelocity28.407 4.69639.175
gridVectors0.0740.0070.082
plotVelocity7.3050.7618.160
plotVelocityStream4.5400.5095.311
scvelo4.5440.9045.441