Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:21 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 2012/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialFeatureExperiment 1.4.0 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.4.0 |
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.4.0.tar.gz |
StartedAt: 2024-03-28 05:25:03 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 05:35:33 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 630.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpatialFeatureExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SpatialFeatureExperiment.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.4.0' * 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 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 SFE-image 6.54 1.70 8.45 dimGeometries 6.41 0.65 7.17 readVizgen 5.14 1.75 7.18 spatialGraphs 5.97 0.53 6.59 removeEmptySpace 5.61 0.42 6.37 findSpatialNeighbors-SpatialFeatureExperiment-method 5.45 0.54 6.22 cbind-SpatialFeatureExperiment-method 4.91 0.53 5.61 findVisiumGraph 4.34 0.58 5.32 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.18-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log' for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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 3.11.2, GDAL 3.8.2, 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, sort, 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 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 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 [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 0 | WARN 0 | SKIP 0 | PASS 548 ] > > proc.time() user system elapsed 194.25 23.85 209.60
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
name | user | system | elapsed | |
SFE-image | 6.54 | 1.70 | 8.45 | |
SFE-transform | 4.19 | 0.39 | 4.80 | |
SpatialFeatureExperiment-coercion | 3.31 | 0.11 | 3.50 | |
SpatialFeatureExperiment-subset | 2.48 | 0.30 | 2.85 | |
SpatialFeatureExperiment | 0.86 | 0.04 | 0.90 | |
addVisiumSpotPoly | 3.07 | 0.07 | 3.18 | |
annotGeometries | 2.26 | 0.28 | 2.62 | |
annotOp | 2.46 | 0.23 | 2.77 | |
annotPred | 2.43 | 0.28 | 2.78 | |
annotSummary | 2.19 | 0.24 | 2.48 | |
bbox-SpatialFeatureExperiment-method | 2.14 | 0.25 | 2.47 | |
cbind-SpatialFeatureExperiment-method | 4.91 | 0.53 | 5.61 | |
changeSampleIDs | 2.06 | 0.29 | 2.42 | |
crop | 4.20 | 0.25 | 4.61 | |
df2sf | 0.06 | 0.00 | 0.06 | |
dimGeometries | 6.41 | 0.65 | 7.17 | |
findSpatialNeighbors-SpatialFeatureExperiment-method | 5.45 | 0.54 | 6.22 | |
findVisiumGraph | 4.34 | 0.58 | 5.32 | |
localResults | 1.45 | 0.05 | 1.50 | |
read10xVisiumSFE | 2.10 | 0.01 | 2.14 | |
readVizgen | 5.14 | 1.75 | 7.18 | |
removeEmptySpace | 5.61 | 0.42 | 6.37 | |
sampleIDs | 3.04 | 0.33 | 3.44 | |
saveRDS-SpatialFeatureExperiment-method | 2.21 | 0.10 | 2.31 | |
show-SpatialFeatureExperiment-method | 2.78 | 0.23 | 3.08 | |
spatialGraphs | 5.97 | 0.53 | 6.59 | |
st_any_pred | 0.03 | 0.00 | 0.03 | |
unit-SpatialFeatureExperiment-method | 2.12 | 0.39 | 2.58 | |
updateObject | 2.00 | 0.22 | 2.38 | |