Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 840/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeomxTools 3.10.0 (landing page) Maddy Griswold
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 GeomxTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeomxTools.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: GeomxTools |
Version: 3.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeomxTools_3.10.0.tar.gz |
StartedAt: 2024-12-20 20:47:41 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 21:06:51 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1149.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeomxTools.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeomxTools_3.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * this is package ‘GeomxTools’ version ‘3.10.0’ * 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 ‘GeomxTools’ can be installed ... OK * checking installed package size ... NOTE installed size is 19.3Mb sub-directories of 1Mb or more: extdata 18.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... NOTE aggregateCounts: no visible binding for global variable ‘TargetName’ hkNorm: no visible binding for global variable ‘TargetName’ mixedModelDE: multiple local function definitions for ‘deFunc’ with different formal arguments qgrubbs: no visible global function definition for ‘qtable’ readPKCFile: no visible binding for global variable ‘RTS_ID’ readPKCFile: no visible binding for global variable ‘Module’ setGrubbsFlags: no visible binding for global variable ‘TargetName’ setGrubbsFlags : <anonymous>: no visible binding for global variable ‘Module’ setProbeRatioFlags: no visible binding for global variable ‘TargetName’ setTargetFlags: no visible global function definition for ‘analtye’ subtractBackground : <anonymous>: no visible binding for global variable ‘Module’ setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global function definition for ‘setSigFuncs<-’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘assayDataElement2’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘.sigCalc’ Undefined global functions or variables: .sigCalc Module RTS_ID TargetName analtye assayDataElement2 qtable setSigFuncs<- * 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 mixedModelDE 62.679 1.461 65.550 readNanoStringGeoMxSet 49.629 5.601 55.429 writeNanoStringGeoMxSet 23.262 1.772 25.118 NanoStringGeoMxSet-class 22.748 1.727 24.652 setBioProbeQCFlags 15.652 0.387 15.895 setQCFlags-NanoStringGeoMxSet-method 14.483 0.208 14.505 readPKCFile 10.324 1.184 11.563 aggregateCounts 10.503 0.212 10.766 as.SpatialExperiment 6.128 0.244 6.385 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_GeoMxSet_probeCollapse.R:61:3'): test that collapsed probe count is equal to the geomean of probes for each target ── sum(matches) == nrow(aggTestData@assayData$exprs) * numDCC is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_GeoMxSet_probeCollapse.R:100:3'): test that the geomean and geosd of negatives is correct ── sum(matches) == length(unique(PKC$Module)) * numDCC * 2 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 1 | SKIP 0 | PASS 288 ] 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck/00check.log’ for details.
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘GeomxTools’ ... ** 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 (GeomxTools)
GeomxTools.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(GeomxTools) Loading required package: Biobase 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: NanoStringNCTools Loading required package: S4Vectors Loading required package: stats4 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: ggplot2 > > test_check("GeomxTools") Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm Coercing raw data, it is NOT recommended to use Seurat's normalization for GeoMx data. Loading required package: SeuratObject Loading required package: sp 'SeuratObject' was built under R 4.4.0 but the current version is 4.4.2; it is recomended that you reinstall 'SeuratObject' as the ABI for R may have changed 'SeuratObject' was built with package 'Matrix' 1.7.0 but the current version is 1.7.1; it is recomended that you reinstall 'SeuratObject' as the ABI for 'Matrix' may have changed Attaching package: 'SeuratObject' The following object is masked from 'package:S4Vectors': intersect The following object is masked from 'package:BiocGenerics': intersect The following objects are masked from 'package:base': intersect, t Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following object is masked from 'package:EnvStats': iqr The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians Loading required package: GenomicRanges Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:sp': %over% Loading required package: GenomeInfoDb Attaching package: 'SummarizedExperiment' The following object is masked from 'package:Seurat': Assays The following object is masked from 'package:SeuratObject': Assays Attaching package: 'SingleCellExperiment' The following object is masked from 'package:NanoStringNCTools': weights<- Loading required package: lme4 Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'lmerTest' The following object is masked from 'package:lme4': lmer The following object is masked from 'package:stats': step boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary 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fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary 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help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') [ FAIL 2 | WARN 1 | SKIP 0 | PASS 288 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_GeoMxSet_probeCollapse.R:61:3'): test that collapsed probe count is equal to the geomean of probes for each target ── sum(matches) == nrow(aggTestData@assayData$exprs) * numDCC is not TRUE `actual`: FALSE `expected`: TRUE ── Failure ('test_GeoMxSet_probeCollapse.R:100:3'): test that the geomean and geosd of negatives is correct ── sum(matches) == length(unique(PKC$Module)) * numDCC * 2 is not TRUE `actual`: FALSE `expected`: TRUE [ FAIL 2 | WARN 1 | SKIP 0 | PASS 288 ] Error: Test failures Execution halted
GeomxTools.Rcheck/GeomxTools-Ex.timings
name | user | system | elapsed | |
NanoStringGeoMxSet-class | 22.748 | 1.727 | 24.652 | |
aggregateCounts | 10.503 | 0.212 | 10.766 | |
as.Seurat | 3.436 | 0.114 | 3.556 | |
as.SpatialExperiment | 6.128 | 0.244 | 6.385 | |
checkQCFlags-NanoStringGeoMxSet-method | 0.084 | 0.002 | 0.086 | |
checkQCFlags | 0.101 | 0.003 | 0.104 | |
computeNormalizationFactors | 0.016 | 0.002 | 0.018 | |
countsShiftedByOne | 0.081 | 0.002 | 0.082 | |
logtBase | 0.000 | 0.000 | 0.001 | |
mixedModelDE | 62.679 | 1.461 | 65.550 | |
ngeoMean | 0.000 | 0.001 | 0.001 | |
ngeoSD | 0 | 0 | 0 | |
normalize-NanoStringGeoMxSet-method | 0.119 | 0.049 | 0.167 | |
plotConcordance | 4.395 | 0.396 | 4.813 | |
plotNormFactorConcordance | 2.283 | 0.017 | 2.300 | |
qcProteinSignal | 0.202 | 0.015 | 0.217 | |
qcProteinSignalNames | 0.014 | 0.002 | 0.015 | |
readDccFile | 0.642 | 0.030 | 0.672 | |
readNanoStringGeoMxSet | 49.629 | 5.601 | 55.429 | |
readPKCFile | 10.324 | 1.184 | 11.563 | |
setBackgroundQCFlags | 0.179 | 0.004 | 0.182 | |
setBioProbeQCFlags | 15.652 | 0.387 | 15.895 | |
setGeoMxQCFlags | 0.101 | 0.005 | 0.105 | |
setQCFlags-NanoStringGeoMxSet-method | 14.483 | 0.208 | 14.505 | |
setSegmentQCFlags | 0.174 | 0.004 | 0.179 | |
setSeqQCFlags | 0.128 | 0.003 | 0.131 | |
shiftCountsOne | 0.098 | 0.013 | 0.111 | |
summarizeNegatives | 0.672 | 0.014 | 0.686 | |
writeNanoStringGeoMxSet | 23.262 | 1.772 | 25.118 | |