Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:37:13 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 2035/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialFeatureExperiment 1.6.0 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SpatialFeatureExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.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: SpatialFeatureExperiment |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialFeatureExperiment_1.6.0.tar.gz |
StartedAt: 2024-05-04 03:55:08 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 04:11:50 -0400 (Sat, 04 May 2024) |
EllapsedTime: 1001.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpatialFeatureExperiment.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialFeatureExperiment_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.6.0’ * 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 ‘SpatialFeatureExperiment’ 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: ‘Biobase’ Unexported objects imported by ':::' calls: ‘S4Vectors:::disableValidity’ ‘SpatialExperiment:::.get_img_idx’ ‘spdep:::minmax.listw’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to ‘assays_sfe_out’ .seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to ‘sfe_out’ .seu_to_sfe : <anonymous>: no visible global function definition for ‘reducedDim<-’ .seu_to_sfe : <anonymous>: no visible global function definition for ‘slot<-’ .seu_to_sfe : <anonymous>: no visible global function definition for ‘altExp<-’ .seu_to_sfe: no visible binding for '<<-' assignment to ‘obj_list_test’ reducedDimFeatureData<-: no visible global function definition for ‘reducedDim<-’ showAsCell,SpatRasterImage: no visible binding for global variable ‘d’ Undefined global functions or variables: altExp<- d reducedDim<- slot<- Consider adding importFrom("methods", "slot<-") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 formatTxSpots 15.000 0.636 16.114 removeEmptySpace 6.964 0.688 7.911 spatialGraphs 5.505 0.424 6.439 dimGeometries 5.557 0.327 6.404 findSpatialNeighbors-SpatialFeatureExperiment-method 4.780 0.252 5.539 findVisiumGraph 4.612 0.256 5.388 cbind-SpatialFeatureExperiment-method 4.317 0.216 5.041 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 2. └─sfe1[, integer(0)] 3. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 4. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) ── Error ('test-subset.R:198:5'): Still works when using logical vector of all FALSE ── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─sfe1[, rep(FALSE, ncol(sfe1))] at test-subset.R:198:5 2. └─sfe1[, rep(FALSE, ncol(sfe1))] 3. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 4. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) [ FAIL 7 | WARN 0 | SKIP 2 | PASS 990 ] Error: Test failures Execution halted * 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 ERROR, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘toSpatialFeatureExperiment’ with signature ‘"Seurat"’: no definition for class “Seurat” Creating a generic function for ‘NROW’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘readRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ ** 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 (SpatialFeatureExperiment)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 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(SpatialFeatureExperiment) Attaching package: 'SpatialFeatureExperiment' The following object is masked from 'package:base': scale > > test_check("SpatialFeatureExperiment") Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE 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 objects are masked from 'package:Matrix': expand, unname 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: spData To access larger datasets in this package, install the spDataLarge package with: `install.packages('spDataLarge', repos='https://nowosad.github.io/drat/', type='source')` 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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 212 features/genes with `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 see ?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 terra 1.7.71 Attaching package: 'terra' The following objects are masked from 'package:SummarizedExperiment': distance, nearest, shift, trim, values, values<-, width The following objects are masked from 'package:GenomicRanges': distance, gaps, nearest, shift, trim, values, values<-, width The following objects are masked from 'package:IRanges': distance, gaps, nearest, shift, trim, width The following objects are masked from 'package:S4Vectors': values, values<-, width The following object is masked from 'package:BiocGenerics': width The following objects are masked from 'package:SpatialFeatureExperiment': centroids, crop, origin, rotate The following objects are masked from 'package:testthat': compare, describe see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` BioFormats library version 7.3.0 Attaching package: 'EBImage' The following objects are masked from 'package:terra': flip, rotate 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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/xenium_test/xenium_lr Error in .jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;", : java.lang.NullPointerException >>> Must use gene symbols as row names when adding transcript spots. >>> Cell segmentations are found in `.csv` file(s) >>> Reading cell and nucleus segmentations >>> Making POLYGON geometries >>> Checking polygon validity >>> Saving geometries to parquet files >>> Reading cell metadata -> `cells.csv` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 16324 cells with counts > 0 >>> filtering nucSeg geometries to match 16324 cells with counts > 0 >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 484 features/genes with `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 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache Testing dist_type none style W Testing dist_type idw style W Testing dist_type exp style W Testing dist_type dpd style W Testing dist_type idw style raw Testing dist_type idw style W Testing dist_type idw style B Testing dist_type idw style C Testing dist_type idw style U Testing dist_type idw style minmax Testing dist_type idw style S Testing dist_type none style W Testing dist_type idw style W Testing dist_type exp style W Testing dist_type dpd style W Testing dist_type idw style raw Testing dist_type idw style W Testing dist_type idw style B Testing dist_type idw style C Testing dist_type idw style U Testing dist_type idw style minmax Testing dist_type idw style S see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/xenium_test/xenium_lr see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound see ?SFEData and browseVignettes('SFEData') for documentation loading from cache trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Content type 'binary/octet-stream' length 10785331 bytes (10.3 MB) ================================================== downloaded 10.3 MB trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_spatial.tar.gz' Content type 'application/x-tar' length 8531653 bytes (8.1 MB) ================================================== downloaded 8.1 MB see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Reading '.hdf5' files.. >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet Removing 3 cells with area less than 15 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Reading '.hdf5' files.. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Reading '.hdf5' files.. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Reading '.hdf5' files.. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Reading '.hdf5' files.. >>> Reading '.hdf5' files.. see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 35 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file >>> filtering geometries to match 3 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 35 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound_Cellpose >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet >>> Cell segmentations are found in `.parquet` file >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 34 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 35 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> 2 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cool_cell_boundaries.parquet see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/vizgen_cellbound >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 35 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 26 features/genes with `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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound >>> Converting transcript spots to geometry >>> 1 `.parquet` files exist: /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound/cell_boundaries.parquet >>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file Removing 35 cells with area less than 15 >>> filtering geometries to match 1023 cells with counts > 0 >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk | | | 0% | |= | 2% | |== | 3% | |=== | 5% | |===== | 6% | |====== | 8% | |======= | 10% | |======== | 11% | |========= | 13% | |========== | 15% | |=========== | 16% | |============ | 18% | |============== | 19% | |=============== | 21% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |==================== | 29% | |===================== | 31% | |======================= | 32% | |======================== | 34% | |========================= | 35% | |========================== | 37% | |=========================== | 39% | |============================ | 40% 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|==================================================================== | 97% | |===================================================================== | 98% | |======================================================================| 100% see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound >>> Converting transcript spots to geometry see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> File cell_boundaries_sf.parquet found see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 258 features/genes with `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> File cell_boundaries_sf.parquet found >>> Reading transcript coordinates >>> Total of 258 features/genes with `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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk | | | 0% | |=================================== | 50% | |======================================================================| 100% >>> Total of 212 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> File cell_boundaries_sf.parquet found >>> Reading transcript coordinates >>> Total of 212 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> File cell_boundaries_sf.parquet found >>> Reading transcript coordinates >>> Total of 576 features/genes with `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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk >>> Total of 212 features/genes with `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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | |============================================================= | 88% | |======================================================================| 100% >>> Total of 212 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> File cell_boundaries_sf.parquet found >>> Reading transcript coordinates >>> Total of 212 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> File cell_boundaries_sf.parquet found >>> Reading transcript coordinates >>> Total of 576 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 The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | 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|===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK updateObject(object="ANY") default for object of class 'dgCMatrix' updateObjectFromSlots(object = 'dgCMatrix' class = 'dgCMatrix') updateObject(object="ANY") default for object of class 'integer' [updateObject] Validating the updated object ... OK updateObject(object="ANY") default for object of class 'integer' [updateObject] Validating the updated object ... OK updateObject(object="ANY") default for object of class 'integer' [updateObject] Validating the updated object ... OK updateObject(object = 'list') updateObject(object="ANY") default for object of class 'character' [updateObject] Validating the updated object ... OK updateObject(object="ANY") default for object of class 'character' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK updateObject(object="ANY") default for object of class 'numeric' [updateObject] Validating the updated object ... OK updateObject(object = 'list') [updateObject] Validating the updated object ... OK heuristic updateObjectFromSlots, method 1 [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] CompressedGRangesList object is current. [updateObject] Nothing to update. [updateObject] Internal representation of GRanges object is current. [updateObject] Nothing to update. [updateObject] Internal representation of IRanges object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Internal representation of GRanges object is current. [updateObject] Nothing to update. [updateObject] Internal representation of IRanges object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Internal representation of PartitioningByEnd object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] DFrame object is current. [updateObject] Nothing to update. updateObject(object="ANY") default for object of class 'NULL' [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK see ?SFEData and browseVignettes('SFEData') for documentation loading from cache see ?SFEData and browseVignettes('SFEData') for documentation loading from cache The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/xenium_test/xenium_lr >>> Cell segmentations are found in `.csv` file(s) >>> Reading cell and nucleus segmentations >>> Making POLYGON geometries >>> Checking polygon validity >>> Saving geometries to parquet files >>> Reading cell metadata -> `cells.csv` >>> Reading h5 gene count matrix >>> filtering cellSeg geometries to match 16324 cells with counts > 0 >>> filtering nucSeg geometries to match 16324 cells with counts > 0 [ FAIL 7 | WARN 0 | SKIP 2 | PASS 990 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test-read.R:627:5' • empty test (1): 'test-read.R:637:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-geometry_operation.R:139:5'): When a sample is removed by cropping ── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-geometry_operation.R:139:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─SpatialFeatureExperiment::crop(sfe_visium, m) 8. ├─x[, preds] 9. └─x[, preds] 10. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 11. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) ── Error ('test-geometry_operation.R:319:5'): bbox when 0 rows or columns ────── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─sfe_visium[, logical(0)] at test-geometry_operation.R:319:5 2. └─sfe_visium[, logical(0)] 3. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 4. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) ── Error ('test-geometry_operation.R:531:5'): When no cells/spots left after cropping ── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-geometry_operation.R:531:5 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─SpatialFeatureExperiment::crop(sfe, bbox0) 8. ├─x[, preds] 9. └─x[, preds] 10. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 11. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) ── Error ('test-read.R:434:5'): Format MERFISH transcript spots for colGeometries ── <Rcpp::exception/C++Error/error/condition> Error: Cannot open "/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound/tx_in_cells/NCAM1_spots.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats. Backtrace: ▆ 1. ├─sf::st_read(fn) at test-read.R:434:5 2. └─sf:::st_read.character(fn) 3. └─sf:::CPL_read_ogr(...) ── Error ('test-read.R:606:5'): Format CosMX spots for colGeometry, multiple z-planes ── <Rcpp::exception/C++Error/error/condition> Error: Cannot open "/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx/tx_spots/6330403K07Rik_spots_z0.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats. Backtrace: ▆ 1. ├─sf::st_read(fn) at test-read.R:606:5 2. └─sf:::st_read.character(fn) 3. └─sf:::CPL_read_ogr(...) ── Error ('test-subset.R:186:5'): Returning 0 columns ────────────────────────── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─sfe1[, integer(0)] at test-subset.R:186:5 2. └─sfe1[, integer(0)] 3. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 4. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) ── Error ('test-subset.R:198:5'): Still works when using logical vector of all FALSE ── Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object. Backtrace: ▆ 1. ├─sfe1[, rep(FALSE, ncol(sfe1))] at test-subset.R:198:5 2. └─sfe1[, rep(FALSE, ncol(sfe1))] 3. └─SpatialFeatureExperiment::`rowGeometries<-`(...) 4. └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE) [ FAIL 7 | WARN 0 | SKIP 2 | PASS 990 ] Error: Test failures Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
name | user | system | elapsed | |
SFE-image | 3.882 | 0.184 | 4.486 | |
SFE-transform | 3.931 | 0.293 | 4.475 | |
SpatRasterImage | 0.000 | 0.001 | 0.000 | |
SpatialFeatureExperiment-coercion | 2.423 | 0.043 | 2.465 | |
SpatialFeatureExperiment-subset | 2.019 | 0.112 | 2.384 | |
SpatialFeatureExperiment | 0.605 | 0.004 | 0.611 | |
addVisiumSpotPoly | 2.290 | 0.032 | 2.322 | |
annotGeometries | 1.853 | 0.127 | 2.277 | |
annotOp | 1.866 | 0.148 | 2.269 | |
annotPred | 1.928 | 0.104 | 2.338 | |
annotSummary | 1.923 | 0.148 | 2.320 | |
bbox-SpatialFeatureExperiment-method | 1.977 | 0.064 | 2.333 | |
bbox_center | 0.001 | 0.000 | 0.000 | |
cbind-SpatialFeatureExperiment-method | 4.317 | 0.216 | 5.041 | |
changeSampleIDs | 1.931 | 0.115 | 2.307 | |
colFeatureData | 2.774 | 0.141 | 3.183 | |
colGeometries | 2.918 | 0.264 | 3.440 | |
crop | 3.034 | 0.107 | 3.414 | |
df2sf | 0.008 | 0.004 | 0.013 | |
dimGeometries | 5.557 | 0.327 | 6.404 | |
findSpatialNeighbors-SpatialFeatureExperiment-method | 4.780 | 0.252 | 5.539 | |
findVisiumGraph | 4.612 | 0.256 | 5.388 | |
formatTxSpots | 15.000 | 0.636 | 16.114 | |
getParams | 2.651 | 0.136 | 3.072 | |
localResults | 1.270 | 0.053 | 1.322 | |
read10xVisiumSFE | 2.449 | 0.231 | 2.683 | |
readCosMX | 3.146 | 0.297 | 3.705 | |
readVizgen | 3.601 | 0.136 | 3.985 | |
readXenium | 0.000 | 0.000 | 0.001 | |
removeEmptySpace | 6.964 | 0.688 | 7.911 | |
rowGeometries | 0.001 | 0.000 | 0.000 | |
sampleIDs | 1.979 | 0.169 | 2.484 | |
saveRDS-SpatialFeatureExperiment-method | 2.334 | 0.113 | 2.447 | |
show-SpatialFeatureExperiment-method | 2.263 | 0.152 | 2.671 | |
spatialGraphs | 5.505 | 0.424 | 6.439 | |
st_any_pred | 0.028 | 0.000 | 0.028 | |
unit-SpatialFeatureExperiment-method | 2.167 | 0.136 | 2.559 | |
updateObject | 2.158 | 0.224 | 2.639 | |