Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:43 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1026/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
imcRtools 1.10.0 (landing page) Daniel Schulz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the imcRtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/imcRtools.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: imcRtools |
Version: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imcRtools_1.10.0.tar.gz |
StartedAt: 2024-08-12 23:02:12 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 23:24:31 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 1339.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: imcRtools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imcRtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imcRtools_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/imcRtools.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘imcRtools/DESCRIPTION’ ... OK * this is package ‘imcRtools’ version ‘1.10.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘imcRtools’ 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 dependencies in R code ... OK * 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 ... NOTE checkRd: (-1) aggregateNeighbors.Rd:52: Lost braces; missing escapes or markup? 52 | \code{summarize_by = "metadata"} or "{statistic}_aggregatedExpression" when | ^ checkRd: (-1) testInteractions.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) testInteractions.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly * 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 testInteractions 156.816 1.834 158.771 read_steinbock 26.102 4.637 24.495 buildSpatialGraph 11.878 0.421 12.180 plotSpatial 6.189 0.134 6.326 * 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: `actual`: FALSE `expected`: TRUE ── Failure ('test_countInteractions.R:396:5'): countInteractions function works ── all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ── dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)]. 1/22 mismatches [8] 0.881 - 0.901 == -0.0198 [ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ] 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/meat/imcRtools.Rcheck/00check.log’ for details.
imcRtools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL imcRtools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘imcRtools’ ... ** using staged installation ** R ** 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 (imcRtools)
imcRtools.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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(imcRtools) 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 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 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: 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 > > test_check("imcRtools") [ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_aggregateNeighbors.R:36:5'): aggregateNeighbors function works ── all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_aggregateNeighbors.R:116:5'): aggregateNeighbors function works ── all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_aggregateNeighbors.R:545:5'): aggregateNeighbors function works ── all(rowSums(as.matrix(cur_sce$aggregatedNeighbors)) == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_countInteractions.R:396:5'): countInteractions function works ── all(cur_out$ct[!is.na(cur_out$ct)] == 1) is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_integration_interactions.R:351:5'): testInteractions gives same results as neighbouRhood ── dat_p$p_gt[!is.na(imcRtools_classic$ct)] not equal to imcRtools_classic_perm$p_gt[!is.na(imcRtools_classic$ct)]. 1/22 mismatches [8] 0.881 - 0.901 == -0.0198 [ FAIL 5 | WARN 2 | SKIP 0 | PASS 2238 ] Error: Test failures Execution halted
imcRtools.Rcheck/imcRtools-Ex.timings
name | user | system | elapsed | |
aggregateNeighbors | 1.219 | 0.080 | 1.300 | |
binAcrossPixels | 1.277 | 0.105 | 1.361 | |
buildSpatialGraph | 11.878 | 0.421 | 12.180 | |
countInteractions | 0.771 | 0.014 | 0.785 | |
detectCommunity | 2.001 | 0.032 | 2.033 | |
detectSpatialContext | 1.514 | 0.024 | 1.549 | |
filterPixels | 3.930 | 0.201 | 4.119 | |
filterSpatialContext | 3.008 | 0.073 | 3.083 | |
findBorderCells | 0.419 | 0.010 | 0.428 | |
minDistToCells | 2.548 | 0.053 | 2.595 | |
patchDetection | 2.463 | 0.035 | 2.490 | |
patchSize | 1.302 | 0.019 | 1.306 | |
plotSpatial | 6.189 | 0.134 | 6.326 | |
plotSpatialContext | 2.964 | 0.052 | 3.027 | |
plotSpotHeatmap | 0.742 | 0.041 | 0.765 | |
readImagefromTXT | 0.364 | 0.088 | 0.358 | |
readSCEfromTXT | 0.506 | 0.042 | 0.529 | |
read_cpout | 1.274 | 0.173 | 1.350 | |
read_steinbock | 26.102 | 4.637 | 24.495 | |
show_cpout_features | 0.200 | 0.079 | 0.278 | |
testInteractions | 156.816 | 1.834 | 158.771 | |