Back to Multiple platform build/check report for BioC 3.19: simplified long 

This page was generated on 20240716 17:43 0400 (Tue, 16 Jul 2024).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo1  Linux (Ubuntu 22.04.3 LTS)  x86_64  4.4.1 (20240614)  "Race for Your Life"  4742 
palomino7  Windows Server 2022 Datacenter  x64  4.4.1 (20240614 ucrt)  "Race for Your Life"  4484 
merida1  macOS 12.7.4 Monterey  x86_64  4.4.1 (20240614)  "Race for Your Life"  4513 
kjohnson1  macOS 13.6.6 Ventura  arm64  4.4.1 (20240614)  "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 2258/2300  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
velociraptor 1.14.3 (landing page) Kevin RueAlbrecht
 nebbiolo1  Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  OK  OK  
palomino7  Windows Server 2022 Datacenter / x64  OK  ERROR  skipped  skipped  
merida1  macOS 12.7.4 Monterey / x86_64  OK  OK  OK  OK  
kjohnson1  macOS 13.6.6 Ventura / arm64  OK  OK  OK  OK  
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. 
Package: velociraptor 
Version: 1.14.3 
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check install=check:velociraptor.installout.txt library=/Library/Frameworks/R.framework/Resources/library novignettes timings velociraptor_1.14.3.tar.gz 
StartedAt: 20240716 12:41:12 0400 (Tue, 16 Jul 2024) 
EndedAt: 20240716 12:46:46 0400 (Tue, 16 Jul 2024) 
EllapsedTime: 334.8 seconds 
RetCode: 0 
Status: OK 
CheckDir: velociraptor.Rcheck 
Warnings: 0 
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check install=check:velociraptor.installout.txt library=/Library/Frameworks/R.framework/Resources/library novignettes timings velociraptor_1.14.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs3.19bioc/meat/velociraptor.Rcheck’ * using R version 4.4.1 (20240614) * using platform: aarch64appledarwin20 * R was compiled by Apple clang version 14.0.0 (clang1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF8 * using option ‘novignettes’ * checking for file ‘velociraptor/DESCRIPTION’ ... OK * this is package ‘velociraptor’ version ‘1.14.3’ * package encoding: UTF8 * 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: Nonstaged installation was used See ‘/Users/biocbuild/bbs3.19bioc/meat/velociraptor.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION metainformation ... OK * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for nonASCII 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 crossreferences ... 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 rebuilding of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs3.19bioc/meat/velociraptor.Rcheck/00check.log’ for details.
velociraptor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL velociraptor ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library’ * installing *source* package ‘velociraptor’ ... ** using nonstaged installation via StagedInstall field ** R ** inst ** bytecompile 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)
velociraptor.Rcheck/tests/testthat.Rout
R version 4.4.1 (20240614)  "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64appledarwin20 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 online 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) 20240716 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.Rproject.R/R/basilisk/1.16.0/velociraptor/1.14.3/env/lib/python3.9/sitepackages/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
velociraptor.Rcheck/velociraptorEx.timings
name  user  system  elapsed  
embedVelocity  28.407  4.696  39.175  
gridVectors  0.074  0.007  0.082  
plotVelocity  7.305  0.761  8.160  
plotVelocityStream  4.540  0.509  5.311  
scvelo  4.544  0.904  5.441  