Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 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" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 849/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeomxTools 3.8.0 (landing page) Maddy Griswold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 3.8.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeomxTools_3.8.0.tar.gz |
StartedAt: 2024-07-10 23:28:16 -0400 (Wed, 10 Jul 2024) |
EndedAt: 2024-07-10 23:50:36 -0400 (Wed, 10 Jul 2024) |
EllapsedTime: 1340.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeomxTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GeomxTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GeomxTools_3.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GeomxTools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * this is package ‘GeomxTools’ version ‘3.8.0’ * 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 13.5Mb sub-directories of 1Mb or more: extdata 12.7Mb * 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 loading without being on the library search path ... 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 61.263 1.328 64.637 normalize-NanoStringGeoMxSet-method 49.865 1.220 0.131 readNanoStringGeoMxSet 43.035 1.004 44.041 NanoStringGeoMxSet-class 17.884 0.543 18.469 writeNanoStringGeoMxSet 16.903 0.220 17.123 setQCFlags-NanoStringGeoMxSet-method 13.262 0.060 13.316 setBioProbeQCFlags 13.103 0.140 13.237 aggregateCounts 11.406 0.188 11.596 readPKCFile 9.198 0.072 9.270 as.SpatialExperiment 5.229 0.172 5.402 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/GeomxTools.Rcheck/00check.log’ for details.
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > 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, 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 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 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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) 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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') 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 0 | WARN 1 | SKIP 0 | PASS 290 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 290 ] > > proc.time() user system elapsed 558.906 9.322 594.974
GeomxTools.Rcheck/GeomxTools-Ex.timings
name | user | system | elapsed | |
NanoStringGeoMxSet-class | 17.884 | 0.543 | 18.469 | |
aggregateCounts | 11.406 | 0.188 | 11.596 | |
as.Seurat | 3.037 | 0.080 | 3.116 | |
as.SpatialExperiment | 5.229 | 0.172 | 5.402 | |
checkQCFlags-NanoStringGeoMxSet-method | 0.060 | 0.000 | 0.061 | |
checkQCFlags | 0.074 | 0.003 | 0.078 | |
computeNormalizationFactors | 0.013 | 0.000 | 0.014 | |
countsShiftedByOne | 0.06 | 0.00 | 0.06 | |
logtBase | 0.001 | 0.000 | 0.001 | |
mixedModelDE | 61.263 | 1.328 | 64.637 | |
ngeoMean | 0.001 | 0.000 | 0.001 | |
ngeoSD | 0.001 | 0.000 | 0.001 | |
normalize-NanoStringGeoMxSet-method | 49.865 | 1.220 | 0.131 | |
plotConcordance | 4.227 | 0.476 | 4.704 | |
plotNormFactorConcordance | 2.121 | 0.072 | 2.230 | |
qcProteinSignal | 0.238 | 0.008 | 0.245 | |
qcProteinSignalNames | 0.011 | 0.000 | 0.011 | |
readDccFile | 0.396 | 0.024 | 0.420 | |
readNanoStringGeoMxSet | 43.035 | 1.004 | 44.041 | |
readPKCFile | 9.198 | 0.072 | 9.270 | |
setBackgroundQCFlags | 0.112 | 0.004 | 0.116 | |
setBioProbeQCFlags | 13.103 | 0.140 | 13.237 | |
setGeoMxQCFlags | 0.077 | 0.000 | 0.076 | |
setQCFlags-NanoStringGeoMxSet-method | 13.262 | 0.060 | 13.316 | |
setSegmentQCFlags | 0.143 | 0.000 | 0.143 | |
setSeqQCFlags | 0.102 | 0.000 | 0.101 | |
shiftCountsOne | 0.072 | 0.012 | 0.084 | |
summarizeNegatives | 0.583 | 0.004 | 0.587 | |
writeNanoStringGeoMxSet | 16.903 | 0.220 | 17.123 | |