Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 829/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeomxTools 3.9.0 (landing page) Maddy Griswold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | 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: 3.9.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeomxTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeomxTools_3.9.0.tar.gz |
StartedAt: 2024-08-16 01:11:31 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 01:35:56 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 1464.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeomxTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeomxTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeomxTools_3.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GeomxTools/DESCRIPTION' ... OK * this is package 'GeomxTools' version '3.9.0' * 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 whether package 'GeomxTools' can be installed ... OK * checking installed package size ... NOTE installed size is 19.4Mb 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 readNanoStringGeoMxSet 63.57 3.34 66.92 writeNanoStringGeoMxSet 25.92 2.13 28.05 NanoStringGeoMxSet-class 23.73 1.31 25.08 setQCFlags-NanoStringGeoMxSet-method 19.61 0.20 19.81 mixedModelDE 18.94 0.61 103.17 setBioProbeQCFlags 18.28 0.30 18.58 aggregateCounts 15.45 0.24 15.70 readPKCFile 12.72 1.42 14.10 as.SpatialExperiment 6.77 0.95 7.32 plotConcordance 7.30 0.28 7.58 as.Seurat 4.69 0.37 5.13 * 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: 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GeomxTools.Rcheck/00check.log' for details.
GeomxTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeomxTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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% The following object is masked from 'package:grDevices': windows 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 [ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 285 ] > > proc.time() user system elapsed 878.78 48.62 939.53
GeomxTools.Rcheck/GeomxTools-Ex.timings
name | user | system | elapsed | |
NanoStringGeoMxSet-class | 23.73 | 1.31 | 25.08 | |
aggregateCounts | 15.45 | 0.24 | 15.70 | |
as.Seurat | 4.69 | 0.37 | 5.13 | |
as.SpatialExperiment | 6.77 | 0.95 | 7.32 | |
checkQCFlags-NanoStringGeoMxSet-method | 0.06 | 0.07 | 0.07 | |
checkQCFlags | 0.08 | 0.04 | 0.06 | |
computeNormalizationFactors | 0.04 | 0.00 | 0.02 | |
countsShiftedByOne | 0.06 | 0.03 | 0.05 | |
logtBase | 0 | 0 | 0 | |
mixedModelDE | 18.94 | 0.61 | 103.17 | |
ngeoMean | 0 | 0 | 0 | |
ngeoSD | 0 | 0 | 0 | |
normalize-NanoStringGeoMxSet-method | 0.10 | 0.00 | 0.12 | |
plotConcordance | 7.30 | 0.28 | 7.58 | |
plotNormFactorConcordance | 3.08 | 0.05 | 3.13 | |
qcProteinSignal | 0.26 | 0.00 | 0.27 | |
qcProteinSignalNames | 0.03 | 0.00 | 0.03 | |
readDccFile | 0.67 | 0.00 | 0.67 | |
readNanoStringGeoMxSet | 63.57 | 3.34 | 66.92 | |
readPKCFile | 12.72 | 1.42 | 14.10 | |
setBackgroundQCFlags | 0.17 | 0.00 | 0.17 | |
setBioProbeQCFlags | 18.28 | 0.30 | 18.58 | |
setGeoMxQCFlags | 0.11 | 0.00 | 0.11 | |
setQCFlags-NanoStringGeoMxSet-method | 19.61 | 0.20 | 19.81 | |
setSegmentQCFlags | 0.18 | 0.00 | 0.19 | |
setSeqQCFlags | 0.11 | 0.00 | 0.11 | |
shiftCountsOne | 0.07 | 0.02 | 0.07 | |
summarizeNegatives | 0.75 | 0.01 | 0.77 | |
writeNanoStringGeoMxSet | 25.92 | 2.13 | 28.05 | |