Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2239/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Voyager 1.9.2 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
To the developers/maintainers of the Voyager package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Voyager.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: Voyager |
Version: 1.9.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Voyager.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Voyager_1.9.2.tar.gz |
StartedAt: 2024-12-24 03:15:50 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:29:40 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 829.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Voyager.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Voyager.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Voyager_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘Voyager/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Voyager’ version ‘1.9.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘Voyager’ can be installed ... OK * 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: ‘spatialreg’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .get_tx_df: no visible binding for global variable ‘cell_col’ .get_tx_df: no visible global function definition for ‘getTechTxFields’ .get_tx_df: no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : <anonymous>: no visible global function definition for ‘gdalParquetAvailable’ .get_tx_df : <anonymous>: no visible global function definition for ‘rowGeometryNames’ .get_tx_df : <anonymous>: no visible global function definition for ‘st_is_empty’ .get_tx_df : <anonymous>: no visible global function definition for ‘readSelectTx’ .plot_var_sf: no visible binding for global variable ‘gene’ plotTxBin2D: no visible binding for global variable ‘X’ plotTxBin2D: no visible binding for global variable ‘Y’ Undefined global functions or variables: X Y cell_col gdalParquetAvailable gene getTechTxFields readSelectTx rowGeometryNames st_is_empty * 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: calculateBivariate.Rd: lee, lee.mc, lee.test, localmoran_bv, BiocParallelParam, colGraphNames, colGeometryNames, localResults calculateMultivariate.Rd: localC, colGraphNames, BiocParallelParam, reducedDim calculateUnivariate.Rd: BiocParallelParam, colGeometry, annotGeometry, colGraphNames, colGeometryNames, annotGeometryNames, annotGraphNames, reducedDimNames, geometryFeatureData, colFeatureData clusterCorrelograms.Rd: BlusterParam-class, reducedDimNames clusterMoranPlot.Rd: BlusterParam-class clusterVariograms.Rd: BlusterParam-class, reducedDimNames moranPlot.Rd: colGeometryNames, geom_bin2d, geom_hex, geom_density2d plotCellBin2D.Rd: geom_bin2d, geom_hex, wrap_plots plotColDataHistogram.Rd: facet_grid plotColGraph.Rd: colGeometryNames, wrap_plots plotCorrelogram.Rd: colFeatureData, colGeometryNames, reducedDimNames, moran.test, geary.test plotGeometry.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData plotImage.Rd: wrap_plots plotLocalResult.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex plotMoranMC.Rd: colGeometryNames, reducedDimNames, geom_density, geom_histogram, geom_freqpoly plotSpatialFeature.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex plotTxBin2D.Rd: geom_bin2d, geom_hex, wrap_plots, formatTxSpots plotVariogram.Rd: colFeatureData, colGeometryNames, reducedDimNames plotVariogramMap.Rd: colGeometryNames, reducedDimNames spatialReducedDim.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData, geom_bin2d, geom_hex 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculateMultivariate 53.938 1.197 55.410 plotImage 18.502 1.725 16.464 calculateBivariate 11.883 0.409 12.545 clusterVariograms 9.935 0.191 10.354 plotGeometry 7.546 0.230 8.235 plotCellBin2D 7.061 0.414 7.707 ElbowPlot 5.997 0.411 6.765 plotVariogram 5.889 0.505 6.617 moranPlot 5.683 0.236 6.148 calculateUnivariate 4.379 0.439 5.058 plotLocalResult 4.438 0.375 5.041 * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/00check.log’ for details.
Voyager.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Voyager ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Voyager’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Voyager)
Voyager.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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(Voyager) Loading required package: SpatialFeatureExperiment Attaching package: 'SpatialFeatureExperiment' The following object is masked from 'package:base': scale > > test_check("Voyager") Loading required package: spData To access larger datasets in this package, install the spDataLarge package with: `install.packages('spDataLarge', repos='https://nowosad.github.io/drat/', type='source')` Loading required package: sf Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE Loading required package: SingleCellExperiment 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 object is masked from 'package:SpatialFeatureExperiment': saveRDS 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: 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 Loading required package: scuttle Loading required package: ggplot2 Attaching package: 'ggplot2' The following object is masked from 'package:SpatialFeatureExperiment': unit Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following object is masked from 'package:SpatialFeatureExperiment': scale The following objects are masked from 'package:base': apply, scale, sweep see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache BioFormats library version 7.3.0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' The downloaded files are in /tmp/Rtmp3QxlIU/file3415b7388a8b17/xenium2/xenium2 >>> Cell segmentations are found in `.parquet` file(s) >>> Reading cell and nucleus segmentations >>> Making MULTIPOLYGON nuclei geometries >>> Making POLYGON cell geometries Sanity checks on cell segmentation polygons: >>> ..found 132 cells with (nested) polygon lists >>> ..applying filtering >>> Checking polygon validity >>> Saving geometries to parquet files >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 >>> Preprocessed sf segmentations found >>> Reading cell and nucleus segmentations >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache gstat does not fit anisotropic variograms. Variogram model is fitted to the whole dataset. Only one cluster is present. Not using color_by. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' The downloaded files are in /tmp/Rtmp3QxlIU/file3415b74ed6e312/xenium2 >>> Must use gene symbols as row names when adding transcript spots. >>> Cell segmentations are found in `.parquet` file(s) >>> Reading cell and nucleus segmentations >>> Making MULTIPOLYGON nuclei geometries >>> Making POLYGON cell geometries Sanity checks on cell segmentation polygons: >>> ..found 132 cells with (nested) polygon lists >>> ..applying filtering >>> Checking polygon validity >>> Saving geometries to parquet files >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> Must use gene symbols as row names when adding transcript spots. >>> Preprocessed sf segmentations found >>> Reading cell and nucleus segmentations >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 >>> Reading transcript coordinates >>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` see ?SFEData and browseVignettes('SFEData') for documentation loading from cache >>> Preprocessed sf segmentations found >>> Reading cell and nucleus segmentations >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 Attaching package: 'EBImage' The following object is masked from 'package:SparseArray': abind The following object is masked from 'package:S4Arrays': abind The following object is masked from 'package:abind': abind The following object is masked from 'package:SummarizedExperiment': resize The following object is masked from 'package:Biobase': channel The following objects are masked from 'package:GenomicRanges': resize, tile The following objects are masked from 'package:IRanges': resize, tile The following objects are masked from 'package:SpatialFeatureExperiment': affine, rotate, translate, transpose see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache Coordinate system already present. Adding new coordinate system, which will replace the existing one. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache beginning bbox testssee ?SFEData and browseVignettes('SFEData') for documentation loading from cache trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5' Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB) ================================================== downloaded 7.2 MB trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz' Content type 'application/x-tar' length 7806681 bytes (7.4 MB) ================================================== downloaded 7.4 MB >>> 10X Visium data will be loaded: outs >>> Adding spatial neighborhood graph to sample01 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file >>> Checking polygon validity see ?SFEData and browseVignettes('SFEData') for documentation loading from cache /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' /usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance' The downloaded files are in /home/biocbuild/bbs-3.21-bioc/meat/Voyager.Rcheck/tests/testthat/xenium_test/xenium2 >>> Cell segmentations are found in `.parquet` file(s) >>> Reading cell and nucleus segmentations >>> Making MULTIPOLYGON nuclei geometries >>> Making POLYGON cell geometries Sanity checks on cell segmentation polygons: >>> ..found 132 cells with (nested) polygon lists >>> ..applying filtering >>> Checking polygon validity >>> Saving geometries to parquet files >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 >>> Preprocessed sf segmentations found >>> Reading cell and nucleus segmentations >>> Reading cell metadata -> `cells.parquet` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 6272 cells with counts > 0 >>> filtering nucSeg geometries to match 6158 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache [ FAIL 0 | WARN 0 | SKIP 18 | PASS 651 ] ══ Skipped tests (18) ══════════════════════════════════════════════════════════ • On CRAN (17): 'test-bivariate.R:130:5', 'test-bivariate.R:151:5', 'test-gstat.R:187:5', 'test-plot.R:358:5', 'test-plot.R:404:5', 'test-plot.R:441:5', 'test-plot.R:459:5', 'test-plot.R:473:5', 'test-plot.R:477:5', 'test-plot.R:527:5', 'test-plot.R:605:5', 'test-plot.R:638:5', 'test-plot.R:660:5', 'test-plot.R:820:5', 'test-plot.R:855:5', 'test-plot.R:866:5', 'test-plot.R:926:5' • gdalParquetAvailable() is not TRUE (1): 'test-plot-transcripts.R:65:5' [ FAIL 0 | WARN 0 | SKIP 18 | PASS 651 ] Deleting unused snapshots: • bivariate/plot-cross-variograms-no-np.svg • bivariate/plot-cross-variograms-with-anisotropy.svg • gstat/multiple-samples-multiple-features.svg • gstat/multiple-samples-one-feature.svg • gstat/plot-np.svg • plot/both-positive-and-negative.svg • plot/change-the-number-of-columns.svg • plot/cluster-by-gene-instead.svg • plot/coldata-freqpoly-multiple-variables.svg • plot/coldata-histogram-multiple-variables.svg • plot/correlograms-for-multispati-pcs-one-component.svg • plot/elbowplot-more-pcs-than-available.svg • plot/elbowplot-with-10-of-the-20-pcs.svg • plot/facetting-by-sample.svg • plot/illegal-symbol-freqpoly.svg • plot/illegal-symbol.svg • plot/moran-plot-don-t-plot-influential.svg • plot/moran-plot-hex-bin.svg • plot/multiple-samples.svg • plot/multiple-variables-color-by.svg • plot/multiple-variables-facetting.svg • plot/multiple-variables-fill-by.svg • plot/not-facetting-multispati-elbow-negative-only.svg • plot/one-variable-color-by.svg • plot/one-variable-facetting.svg • plot/one-variable-fill-by.svg • plot/plotcorrelogram-categorical-color-by.svg • plot/plotcorrelogram-coldata-i.svg • plot/plotcorrelogram-continuous-color-by.svg • plot/plotcorrelogram-one-gene-c.svg • plot/plotcorrelogram-one-gene-corr.svg • plot/plotcorrelogram-specify-gene-and-coldata-i.svg • plot/plotdimloadings-not-balanced.svg • plot/with-subset-freqpoly.svg • plot/with-subset.svg > > proc.time() user system elapsed 256.222 15.707 271.257
Voyager.Rcheck/Voyager-Ex.timings
name | user | system | elapsed | |
ElbowPlot | 5.997 | 0.411 | 6.765 | |
SFEMethod | 0.002 | 0.001 | 0.002 | |
calculateBivariate | 11.883 | 0.409 | 12.545 | |
calculateMultivariate | 53.938 | 1.197 | 55.410 | |
calculateUnivariate | 4.379 | 0.439 | 5.058 | |
clusterCorrelograms | 2.491 | 0.120 | 2.841 | |
clusterMoranPlot | 2.612 | 0.136 | 2.975 | |
clusterVariograms | 9.935 | 0.191 | 10.354 | |
getDivergeRange | 0.000 | 0.000 | 0.001 | |
listSFEMethods | 0.001 | 0.000 | 0.001 | |
moranBounds | 2.294 | 0.114 | 2.652 | |
moranPlot | 5.683 | 0.236 | 6.148 | |
multispati_rsp | 2.671 | 0.122 | 3.019 | |
plotCellBin2D | 7.061 | 0.414 | 7.707 | |
plotColDataFreqpoly | 3.783 | 0.105 | 4.216 | |
plotColDataHistogram | 3.740 | 0.175 | 4.143 | |
plotColGraph | 2.985 | 0.116 | 3.376 | |
plotCorrelogram | 4.318 | 0.167 | 4.719 | |
plotCrossVariogram | 4.061 | 0.168 | 4.458 | |
plotCrossVariogramMap | 4.391 | 0.135 | 4.754 | |
plotDimLoadings | 3.016 | 0.105 | 3.348 | |
plotGeometry | 7.546 | 0.230 | 8.235 | |
plotImage | 18.502 | 1.725 | 16.464 | |
plotLocalResult | 4.438 | 0.375 | 5.041 | |
plotMoranMC | 2.932 | 0.262 | 3.423 | |
plotSpatialFeature | 3.945 | 0.328 | 4.518 | |
plotVariogram | 5.889 | 0.505 | 6.617 | |
plotVariogramMap | 3.576 | 0.340 | 4.143 | |
spatialReducedDim | 3.855 | 0.333 | 4.416 | |