Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:51 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the SpatialFeatureExperiment package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1921/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialFeatureExperiment 1.1.3 (landing page) Lambda Moses
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: SpatialFeatureExperiment |
Version: 1.1.3 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpatialFeatureExperiment_1.1.3.tar.gz |
StartedAt: 2023-02-28 16:11:00 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 16:20:28 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 567.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpatialFeatureExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpatialFeatureExperiment_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialFeatureExperiment.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SpatialFeatureExperiment’ version ‘1.1.3’ * 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 SpatialFeatureExperiment-subset 7.609 0.655 12.664 dimGeometries 7.507 0.180 13.205 removeEmptySpace 6.583 0.248 10.302 spatialGraphs 6.139 0.132 11.058 cbind-SpatialFeatureExperiment-method 5.980 0.228 12.013 findVisiumGraph 5.948 0.228 10.871 findSpatialNeighbors-SpatialFeatureExperiment-method 5.331 0.191 11.305 crop 5.000 0.160 7.524 annotPred 3.345 0.168 5.923 annotSummary 2.859 0.124 5.336 annotOp 2.715 0.155 5.247 bbox-SpatialFeatureExperiment-method 2.701 0.137 6.760 show-SpatialFeatureExperiment-method 2.631 0.092 5.110 annotGeometries 2.457 0.181 7.852 changeSampleIDs 2.540 0.091 5.075 sampleIDs 2.229 0.060 5.912 * 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 ... ‘SFE.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’ for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpatialFeatureExperiment)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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 3.10.2, 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, 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 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 snapshotDate(): 2023-02-14 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache snapshotDate(): 2023-02-14 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache snapshotDate(): 2023-02-14 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache snapshotDate(): 2023-02-14 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 snapshotDate(): 2023-02-14 see ?SFEData and browseVignettes('SFEData') for documentation loading from cache [ FAIL 0 | WARN 0 | SKIP 0 | PASS 435 ] > > proc.time() user system elapsed 94.888 5.133 116.629
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
name | user | system | elapsed | |
SpatialFeatureExperiment-coercion | 4.113 | 0.113 | 4.227 | |
SpatialFeatureExperiment-subset | 7.609 | 0.655 | 12.664 | |
SpatialFeatureExperiment | 1.040 | 0.020 | 1.059 | |
addVisiumSpotPoly | 3.733 | 0.312 | 4.045 | |
annotGeometries | 2.457 | 0.181 | 7.852 | |
annotOp | 2.715 | 0.155 | 5.247 | |
annotPred | 3.345 | 0.168 | 5.923 | |
annotSummary | 2.859 | 0.124 | 5.336 | |
bbox-SpatialFeatureExperiment-method | 2.701 | 0.137 | 6.760 | |
cbind-SpatialFeatureExperiment-method | 5.980 | 0.228 | 12.013 | |
changeSampleIDs | 2.540 | 0.091 | 5.075 | |
crop | 5.000 | 0.160 | 7.524 | |
df2sf | 0.094 | 0.004 | 0.102 | |
dimGeometries | 7.507 | 0.180 | 13.205 | |
findSpatialNeighbors-SpatialFeatureExperiment-method | 5.331 | 0.191 | 11.305 | |
findVisiumGraph | 5.948 | 0.228 | 10.871 | |
localResults | 1.679 | 0.007 | 1.687 | |
read10xVisiumSFE | 2.350 | 0.016 | 2.373 | |
removeEmptySpace | 6.583 | 0.248 | 10.302 | |
sampleIDs | 2.229 | 0.060 | 5.912 | |
show-SpatialFeatureExperiment-method | 2.631 | 0.092 | 5.110 | |
spatialGraphs | 6.139 | 0.132 | 11.058 | |
st_any_pred | 0.024 | 0.000 | 0.024 | |