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This page was generated on 2024-02-28 10:10:44 -0500 (Wed, 28 Feb 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.5 Ventura | arm64 | R Under development (unstable) (2024-02-25 r85988) -- "Unsuffered Consequences" | 4353 |
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 1993/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialFeatureExperiment 1.5.1 (landing page) Lambda Moses
| kjohnson3 | macOS 13.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the SpatialFeatureExperiment package: - 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: 1.5.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.5.1.tar.gz |
StartedAt: 2024-02-28 05:02:58 -0500 (Wed, 28 Feb 2024) |
EndedAt: 2024-02-28 05:26:09 -0500 (Wed, 28 Feb 2024) |
EllapsedTime: 1391.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SpatialFeatureExperiment.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.5.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SpatialFeatureExperiment.Rcheck’ * using R Under development (unstable) (2024-02-25 r85988) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.5.1’ * 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 R 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 removeEmptySpace 1.814 0.08 311.008 * 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: mode = "wb")`: cannot open URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Backtrace: ▆ 1. └─utils::download.file(...) at test-read.R:61:1 ── Error ('test-subset.R:104:1'): (code run outside of `test_that()`) ────────── Error in `download.file("https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5", destfile = file.path("kidney", "outs", "filtered_feature_bc_matrix.h5"), mode = "wb")`: cannot open URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Backtrace: ▆ 1. └─utils::download.file(...) at test-subset.R:104:1 [ FAIL 2 | WARN 2 | SKIP 0 | PASS 530 ] 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, 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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) (2024-02-25 r85988) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 3.11.0, GDAL 3.5.3, PROJ 9.1.0; 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': expand.grid, I, 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 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 The following objects are masked from 'package:testthat': compare, describe 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 Could not check id: EH7561 for updates. Using previously cached version. trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' [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 Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use see ?SFEData and browseVignettes('SFEData') for documentation loading from cache [ FAIL 2 | WARN 2 | SKIP 0 | PASS 530 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-read.R:61:1'): (code run outside of `test_that()`) ───────────── Error in `download.file("https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5", destfile = file.path("kidney", "outs", "filtered_feature_bc_matrix.h5"), mode = "wb")`: cannot open URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Backtrace: ▆ 1. └─utils::download.file(...) at test-read.R:61:1 ── Error ('test-subset.R:104:1'): (code run outside of `test_that()`) ────────── Error in `download.file("https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5", destfile = file.path("kidney", "outs", "filtered_feature_bc_matrix.h5"), mode = "wb")`: cannot open URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5' Backtrace: ▆ 1. └─utils::download.file(...) at test-subset.R:104:1 [ FAIL 2 | WARN 2 | SKIP 0 | PASS 530 ] Error: Test failures Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
name | user | system | elapsed | |
SFE-image | 1.700 | 0.375 | 3.065 | |
SFE-transform | 1.237 | 0.078 | 1.590 | |
SpatialFeatureExperiment-coercion | 0.801 | 0.022 | 0.830 | |
SpatialFeatureExperiment-subset | 0.654 | 0.053 | 0.987 | |
SpatialFeatureExperiment | 0.179 | 0.004 | 0.184 | |
addVisiumSpotPoly | 0.682 | 0.019 | 0.701 | |
annotGeometries | 0.529 | 0.054 | 0.857 | |
annotOp | 0.643 | 0.058 | 0.987 | |
annotPred | 0.550 | 0.053 | 0.874 | |
annotSummary | 0.538 | 0.048 | 0.848 | |
bbox-SpatialFeatureExperiment-method | 0.563 | 0.053 | 0.894 | |
cbind-SpatialFeatureExperiment-method | 1.371 | 0.120 | 2.157 | |
changeSampleIDs | 0.584 | 0.055 | 0.911 | |
crop | 1.095 | 0.074 | 1.533 | |
df2sf | 0.023 | 0.002 | 0.027 | |
dimGeometries | 1.690 | 0.124 | 2.394 | |
findSpatialNeighbors-SpatialFeatureExperiment-method | 1.390 | 0.119 | 2.088 | |
findVisiumGraph | 1.645 | 0.107 | 2.286 | |
localResults | 0.357 | 0.014 | 0.371 | |
read10xVisiumSFE | 0.494 | 0.010 | 0.508 | |
readVizgen | 0.374 | 0.259 | 0.819 | |
removeEmptySpace | 1.814 | 0.080 | 311.008 | |
sampleIDs | 1.022 | 0.064 | 2.007 | |
saveRDS-SpatialFeatureExperiment-method | 0.482 | 0.025 | 0.508 | |
show-SpatialFeatureExperiment-method | 0.630 | 0.061 | 0.990 | |
spatialGraphs | 1.487 | 0.112 | 2.181 | |
st_any_pred | 0.007 | 0.001 | 0.008 | |
unit-SpatialFeatureExperiment-method | 0.590 | 0.065 | 1.028 | |
updateObject | 0.631 | 0.056 | 0.994 | |