Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:38:34 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 2008/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialFeatureExperiment 1.5.2 (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 | ||||||||||
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: 1.5.2 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.5.2.tar.gz |
StartedAt: 2024-03-28 06:55:39 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 07:09:33 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 834.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpatialFeatureExperiment.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck' * using R Under development (unstable) (2024-03-16 r86144 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'SpatialFeatureExperiment/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SpatialFeatureExperiment' version '1.5.2' * 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 ... NOTE Found the following non-portable file path: SpatialFeatureExperiment/inst/extdata/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section 'Package structure' in the 'Writing R Extensions' manual. * checking whether package 'SpatialFeatureExperiment' can be installed ... OK * checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: R 1.4Mb extdata 7.4Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::disableValidity' '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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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 14.97 0.90 18.12 SFE-image 7.96 1.98 10.86 removeEmptySpace 7.42 0.50 12.67 dimGeometries 6.82 0.56 7.52 findSpatialNeighbors-SpatialFeatureExperiment-method 6.21 0.52 6.83 spatialGraphs 5.69 0.73 6.53 cbind-SpatialFeatureExperiment-method 5.69 0.51 7.18 findVisiumGraph 5.28 0.61 5.99 * 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: ── Failure ('test-read.R:574:5'): readCosMX, don't split z, don't split cell compartments ── unclass(st_z_range(txSpots(sfe))) (`actual`) not equal to c(zmin = 0, zmax = 1) (`expected`). `actual` is NULL `expected` is a double vector (0, 1) ── Failure ('test-read.R:626:5'): Format CosMX spots for colGeometry, multiple z-planes ── `cg` (`actual`) not equal to file.path("cosmx", "tx_spots") (`expected`). actual vs expected - "F:\\biocbuild\\bbs-3.19-bioc\\meat\\SpatialFeatureExperiment.Rcheck\\tests\\testthat\\cosmx\\tx_spots" + "cosmx/tx_spots" [ FAIL 9 | WARN 4 | SKIP 5 | PASS 760 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log' for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'SpatialFeatureExperiment' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'saveRDS' 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 Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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) > > test_check("SpatialFeatureExperiment") Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 >>> 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 >>> 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 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 BioFormats library version 6.12.0 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': rotate, translate, transpose 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/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 >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file >>> filtering geometries to match 1023 cells with counts > 0 >>> Reading '.hdf5' files.. >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/detected_transcripts.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/hdf5s_micron_space.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/hdf5s_micron_space.parquet Removing 3 cells with area less than 15 >>> Reading '.hdf5' files.. >>> Reading '.hdf5' files.. >>> Reading '.hdf5' files.. >>> Reading '.hdf5' files.. >>> Reading '.hdf5' files.. >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\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 >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\multi\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\multi\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\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 >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\small\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\small\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\small\vizgen_cellbound/cell_boundaries.parquet >>> Cell segmentations are found in `.parquet` file >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\polyT\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\polyT\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\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 >>> 1 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet >>> Cell segmentations are found in `.parquet` file >>> filtering geometries to match 1023 cells with counts > 0 >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\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 >>> 3 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/cool_cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\vizgen_cellbound/detected_transcripts.parquet >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\test_spots/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\test_spots/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\meat\SpatialFeatureExperiment.Rcheck\tests\testthat\test_spots/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 >>> Total of 26 features/genes with `min_phred` < 20 are removed from SFE object >>> To keep all features -> set `min_phred = NULL` >>> Converting transcript spots to geometry >>> 2 `.parquet` files exist: F:\biocbuild\bbs-3.19-bioc\R\library\SpatialFeatureExperiment\extdata\vizgen_cellbound/cell_boundaries.parquet F:\biocbuild\bbs-3.19-bioc\R\library\SpatialFeatureExperiment\extdata\vizgen_cellbound/detected_transcripts.parquet >>> using -> F:\biocbuild\bbs-3.19-bioc\R\library\SpatialFeatureExperiment\extdata\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% | 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|=============================================================== | 90% | |================================================================ | 92% | |================================================================= | 94% | |=================================================================== | 95% | |==================================================================== | 97% | |===================================================================== | 98% | |======================================================================| 100% >>> Converting transcript spots to geometry >>> Constructing cell polygons >>> File cell_boundaries_sf.parquet found >>> 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` >>> Constructing cell polygons >>> 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` >>> 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` >>> Constructing cell polygons >>> Reading transcript coordinates >>> Converting transcript spots to geometry >>> Writing reformatted transcript spots to disk | | | 0% | |========= | 12% | |================== | 25% | |========================== | 38% | |=================================== | 50% | |============================================ | 62% | |==================================================== | 75% | 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|======================================================================| 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 [ FAIL 9 | WARN 4 | SKIP 5 | PASS 760 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • On Bioconductor (5): 'test-image.R:40:5', 'test-image.R:65:5', 'test-image.R:99:5', 'test-image.R:134:5', 'test-read.R:658:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-image.R:263:1'): (code run outside of `test_that()`) ─────────── <NullPointerException/RuntimeException/Exception/Throwable/Object/error/condition> Error in `.jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;", "getOMEXML"), "S", "dumpXML")`: java.lang.NullPointerException: Cannot invoke "loci.formats.DimensionSwapper.setMetadataFiltered(boolean)" because "RBioFormats.reader" is null ── Error ('test-read.R:373:5'): Message when removing empty polygons ─────────── Error: IOError: Failed to open local file 'F:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/cell_boundaries.parquet'. Detail: [Windows error 1224] The requested operation cannot be performed on a file with a user-mapped section open. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-read.R:373:5 2. │ └─base::withCallingHandlers(...) 3. └─sfarrow::st_write_parquet(parq, file.path(dir_use, "cell_boundaries.parquet")) 4. └─arrow::write_parquet(tbl, sink = dsn, ...) 5. └─arrow:::make_output_stream(sink) 6. └─FileOutputStream$create(x) 7. └─arrow:::io___FileOutputStream__Open(clean_path_abs(path)) ── Failure ('test-read.R:446:5'): Format MERFISH transcript spots for colGeometries ── `cg` (`actual`) not equal to `dir_check` (`expected`). actual vs expected - "F:\\biocbuild\\bbs-3.19-bioc\\meat\\SpatialFeatureExperiment.Rcheck\\tests\\testthat\\cg_vizgen\\tx_in_cells" + "cg_vizgen/tx_in_cells" ── Failure ('test-read.R:540:5'): readCosMX, 2 z-planes, split z, not splitting by cell compartments ── dir.exists(d) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test-read.R:542:5'): readCosMX, 2 z-planes, split z, not splitting by cell compartments ── list.files(d) (`actual`) not equal to `fns_expect` (`expected`). `actual`: `expected`: "tx_spots_z0.parquet" "tx_spots_z1.parquet" ── Failure ('test-read.R:543:5'): readCosMX, 2 z-planes, split z, not splitting by cell compartments ── rowGeometryNames(sfe) (`actual`) not equal to paste0("tx_spots_z", 0:1) (`expected`). `actual`: "txSpots" `expected`: "tx_spots_z0" "tx_spots_z1" ── Error ('test-read.R:544:5'): readCosMX, 2 z-planes, split z, not splitting by cell compartments ── Error in `value[[3L]](cond)`: invalid subscript 'type' in 'dimGeometry(<SpatialFeatureExperiment>, type="character", ...)': 'tx_spots_z0' not in 'rowGeometry(<SpatialFeatureExperiment>)' Backtrace: ▆ 1. ├─testthat::expect_null(st_z_range(rowGeometry(sfe, "tx_spots_z0"))) at test-read.R:544:5 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─sf::st_z_range(rowGeometry(sfe, "tx_spots_z0")) 5. └─SpatialFeatureExperiment::rowGeometry(sfe, "tx_spots_z0") 6. ├─SpatialFeatureExperiment::dimGeometry(...) 7. └─SpatialFeatureExperiment::dimGeometry(...) 8. └─SpatialFeatureExperiment:::.get_internal_id(...) 9. └─SpatialFeatureExperiment (local) .get_internal_fun(...) 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13. └─value[[3L]](cond) ── Failure ('test-read.R:574:5'): readCosMX, don't split z, don't split cell compartments ── unclass(st_z_range(txSpots(sfe))) (`actual`) not equal to c(zmin = 0, zmax = 1) (`expected`). `actual` is NULL `expected` is a double vector (0, 1) ── Failure ('test-read.R:626:5'): Format CosMX spots for colGeometry, multiple z-planes ── `cg` (`actual`) not equal to file.path("cosmx", "tx_spots") (`expected`). actual vs expected - "F:\\biocbuild\\bbs-3.19-bioc\\meat\\SpatialFeatureExperiment.Rcheck\\tests\\testthat\\cosmx\\tx_spots" + "cosmx/tx_spots" [ FAIL 9 | WARN 4 | SKIP 5 | PASS 760 ] Error: Test failures Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
name | user | system | elapsed | |
SFE-image | 7.96 | 1.98 | 10.86 | |
SFE-transform | 3.75 | 0.50 | 4.55 | |
SpatRasterImage | 0 | 0 | 0 | |
SpatialFeatureExperiment-coercion | 2.83 | 0.19 | 3.11 | |
SpatialFeatureExperiment-subset | 2.28 | 0.23 | 2.59 | |
SpatialFeatureExperiment | 0.72 | 0.08 | 0.83 | |
addVisiumSpotPoly | 3.08 | 0.11 | 3.19 | |
annotGeometries | 2.37 | 0.33 | 2.79 | |
annotOp | 2.25 | 0.19 | 2.52 | |
annotPred | 2.97 | 0.20 | 3.23 | |
annotSummary | 2.19 | 0.36 | 2.65 | |
bbox-SpatialFeatureExperiment-method | 2.48 | 0.33 | 2.98 | |
bbox_center | 0 | 0 | 0 | |
callMeta | 2.36 | 0.25 | 2.66 | |
cbind-SpatialFeatureExperiment-method | 5.69 | 0.51 | 7.18 | |
changeSampleIDs | 2.19 | 0.28 | 2.53 | |
colGeometries | 2.34 | 0.38 | 2.80 | |
crop | 3.36 | 0.31 | 4.85 | |
df2sf | 0.06 | 0.00 | 0.06 | |
dimGeometries | 6.82 | 0.56 | 7.52 | |
findSpatialNeighbors-SpatialFeatureExperiment-method | 6.21 | 0.52 | 6.83 | |
findVisiumGraph | 5.28 | 0.61 | 5.99 | |
formatTxSpots | 14.97 | 0.90 | 18.12 | |
localResults | 1.22 | 0.02 | 1.25 | |
read10xVisiumSFE | 2.30 | 0.05 | 2.49 | |
readCosMX | 1.48 | 0.04 | 1.64 | |
readVizgen | 2.30 | 0.05 | 2.48 | |
readXenium | 0 | 0 | 0 | |
removeEmptySpace | 7.42 | 0.50 | 12.67 | |
rowGeometries | 0 | 0 | 0 | |
sampleIDs | 3.45 | 0.31 | 3.83 | |
saveRDS-SpatialFeatureExperiment-method | 2.28 | 0.05 | 2.37 | |
show-SpatialFeatureExperiment-method | 2.52 | 0.30 | 2.88 | |
spatialGraphs | 5.69 | 0.73 | 6.53 | |
st_any_pred | 0.01 | 0.00 | 0.01 | |
unit-SpatialFeatureExperiment-method | 2.03 | 0.31 | 2.39 | |
updateObject | 3.22 | 0.24 | 3.53 | |