Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2245/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
velociraptor 1.16.0 (landing page) Kevin Rue-Albrecht
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.16.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:velociraptor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings velociraptor_1.16.0.tar.gz |
StartedAt: 2024-12-20 06:31:09 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:37:04 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 355.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: velociraptor.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:velociraptor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings velociraptor_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/velociraptor.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘velociraptor/DESCRIPTION’ ... OK * this is package ‘velociraptor’ version ‘1.16.0’ * 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 ‘/home/biocbuild/bbs-3.20-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 ... WARNING '::' or ':::' import not declared from: ‘basilisk.utils’ 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 ... WARNING '::' or ':::' import not declared from: ‘basilisk.utils’ * 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 18.826 2.136 21.959 plotVelocity 6.103 1.566 7.512 * 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: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/velociraptor.Rcheck/00check.log’ for details.
velociraptor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL velociraptor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)
velociraptor.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 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, saveRDS, 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 -0.926. 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/34 [00:00<?, ?gene/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] 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) 0%| | 0/200 [00:00<?, ?cells/s] /home/biocbuild/.cache/R/basilisk/1.18.0/velociraptor/1.16.0/env/lib/python3.11/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) 0%| | 0/200 [00:00<?, ?cells/s] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 50 ] [ FAIL 0 | WARN 3 | 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 55.197 7.876 60.330
velociraptor.Rcheck/velociraptor-Ex.timings
name | user | system | elapsed | |
embedVelocity | 18.826 | 2.136 | 21.959 | |
gridVectors | 0.085 | 0.000 | 0.086 | |
plotVelocity | 6.103 | 1.566 | 7.512 | |
plotVelocityStream | 3.617 | 0.635 | 4.092 | |
scvelo | 3.864 | 0.992 | 4.494 | |