Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:08 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 2313/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
visiumStitched 1.1.2 (landing page) Nicholas J. Eagles
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the visiumStitched package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/visiumStitched.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: visiumStitched |
Version: 1.1.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:visiumStitched.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings visiumStitched_1.1.2.tar.gz |
StartedAt: 2025-10-17 14:52:39 -0000 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 15:07:31 -0000 (Fri, 17 Oct 2025) |
EllapsedTime: 892.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: visiumStitched.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:visiumStitched.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings visiumStitched_1.1.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/visiumStitched.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘visiumStitched/DESCRIPTION’ ... OK * this is package ‘visiumStitched’ version ‘1.1.2’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘visiumStitched’ 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 ... NOTE Namespace in Imports field not imported from: ‘GenomeInfoDb’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .fit_to_array_lsap: no visible binding for global variable ‘key’ .fit_to_array_lsap: no visible binding for global variable ‘capture_area’ .fit_to_array_lsap: no visible binding for global variable ‘pxl_row_in_fullres’ .fit_to_array_lsap: no visible binding for global variable ‘pxl_col_in_fullres’ .map_lsap: no visible binding for global variable ‘pxl_col_in_fullres’ .map_lsap: no visible binding for global variable ‘pxl_row_in_fullres’ .map_lsap: no visible binding for global variable ‘pxl_col_in_fullres_rounded’ .map_lsap: no visible binding for global variable ‘pxl_row_in_fullres_rounded’ Undefined global functions or variables: capture_area key pxl_col_in_fullres pxl_col_in_fullres_rounded pxl_row_in_fullres pxl_row_in_fullres_rounded * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_SpatialExperiment 85.657 6.296 95.990 add_array_coords 29.660 5.160 41.134 merge_overlapping 22.903 0.610 25.512 prep_fiji 19.038 3.898 26.569 rescale_fiji_inputs 16.556 2.751 22.896 as.Seurat 15.486 0.679 20.126 add_overlap_info 6.025 0.395 8.347 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/visiumStitched.Rcheck/00check.log’ for details.
visiumStitched.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL visiumStitched ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘visiumStitched’ ... ** this is package ‘visiumStitched’ version ‘1.1.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (visiumStitched)
visiumStitched.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(visiumStitched) Loading required package: SpatialExperiment Loading required package: SingleCellExperiment 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 Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo 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 > > test_check("visiumStitched") 2025-10-17 15:04:02.476588 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f466c5cb1_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 2025-10-17 15:04:11.732164 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f58119169_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 2025-10-17 15:04:16.211143 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f38d7bdf1_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1 2025-10-17 15:04:39.421889 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f466c5cb1_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 2025-10-17 15:04:49.039131 loading file /home/biocbuild/.cache/R/BiocFileCache/21c2e97c2b5f16_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1 Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it. 2025-10-17 15:05:03.915649 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f58119169_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 2025-10-17 15:05:08.783642 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f38d7bdf1_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1 Building SpatialExperiment using capture area as sample ID 2025-10-17 15:05:20.870024 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger 2025-10-17 15:05:26.142496 read10xVisiumAnalysis: reading analysis output from SpaceRanger 2025-10-17 15:05:27.038289 add10xVisiumAnalysis: adding analysis output from SpaceRanger 2025-10-17 15:05:27.651872 rtracklayer::import: reading the reference GTF file 2025-10-17 15:06:22.251958 adding gene information to the SPE object 2025-10-17 15:06:22.775032 adding information used by spatialLIBD Overwriting imgData(spe) with merged images (one per group) Adding array coordinates and overlap info 2025-10-17 15:06:30.445697 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f466c5cb1_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1 'sample_id's are duplicated across 'SpatialExperiment' objects to cbind; appending sample indices. 2025-10-17 15:06:56.00218 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f58119169_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 2025-10-17 15:07:01.173445 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f38d7bdf1_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1 2025-10-17 15:07:17.352137 loading file /home/biocbuild/.cache/R/BiocFileCache/8a4f58119169_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1 [ FAIL 0 | WARN 3 | SKIP 0 | PASS 36 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 36 ] > > proc.time() user system elapsed 199.816 11.546 232.419
visiumStitched.Rcheck/visiumStitched-Ex.timings
name | user | system | elapsed | |
add_array_coords | 29.660 | 5.160 | 41.134 | |
add_overlap_info | 6.025 | 0.395 | 8.347 | |
as.Seurat | 15.486 | 0.679 | 20.126 | |
build_SpatialExperiment | 85.657 | 6.296 | 95.990 | |
merge_overlapping | 22.903 | 0.610 | 25.512 | |
prep_fiji | 19.038 | 3.898 | 26.569 | |
rescale_fiji_inputs | 16.556 | 2.751 | 22.896 | |