Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -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 1519/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PDATK 1.14.0 (landing page) Benjamin Haibe-Kains
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the PDATK package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PDATK.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: PDATK |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PDATK_1.14.0.tar.gz |
StartedAt: 2024-12-20 04:06:30 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:12:42 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 371.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PDATK.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PDATK_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘PDATK/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PDATK’ version ‘1.14.0’ * 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 ‘PDATK’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .calculateMSMthresholds: no visible binding for global variable ‘funContext’ .plotNetwork: no visible global function definition for ‘legend’ NCSModel: no visible binding for global variable ‘metric’ NCSModel: no visible binding for global variable ‘comparison’ NCSModel: no visible binding for global variable ‘centroid_K’ NCSModel: no visible binding for global variable ‘assay_K’ NetworkCommunitySearchModel: no visible binding for global variable ‘metric’ NetworkCommunitySearchModel: no visible binding for global variable ‘comparison’ NetworkCommunitySearchModel: no visible binding for global variable ‘centroid_K’ NetworkCommunitySearchModel: no visible binding for global variable ‘assay_K’ predictClasses,ConsensusMetaclusteringModel-ANY: no visible global function definition for ‘.error’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘centroid_cohort’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘centroid_K’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘assay_cohort’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘assay_K’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘tmp’ predictClasses,NCSModel-ANY: no visible binding for global variable ‘cluster_label’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘missignAssays’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature_score’ rankFeatures,MultiAssayExperiment: no visible binding for global variable ‘feature_rank’ trainModel,ConsensusMetaclusteringModel: no visible global function definition for ‘pdf’ trainModel,ConsensusMetaclusteringModel: no visible global function definition for ‘dev.off’ trainModel,NCSModel: no visible binding for global variable ‘ingroup_proportion’ trainModel,NCSModel: no visible binding for global variable ‘cor_threshold’ Undefined global functions or variables: .error assay_K assay_cohort centroid_K centroid_cohort cluster_label comparison cor_threshold dev.off feature feature_rank feature_score funContext ingroup_proportion legend metric missignAssays pdf tmp Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "legend") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'rankFeatures-MultiAssayExperiment-method.Rd': ‘[dplyr:ranking]{dplyr::dense_rank}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'dot-randomSampleIndex.Rd': ‘numSamples’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck/00check.log’ for details.
PDATK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL PDATK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘PDATK’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’ Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’ ** testing if installed package keeps a record of temporary installation path * DONE (PDATK)
PDATK.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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(PDATK) 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, saveRDS, 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 Warning messages: 1: replacing previous import 'survival::brier' by 'verification::brier' when loading 'PDATK' 2: replacing previous import 'limma::logsumexp' by 'mclust::logsumexp' when loading 'genefu' > > test_check("PDATK") [ FAIL 0 | WARN 12 | SKIP 0 | PASS 77 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 77 ] > > proc.time() user system elapsed 26.988 6.850 30.407
PDATK.Rcheck/PDATK-Ex.timings
name | user | system | elapsed | |
CSPC_MAE | 0.004 | 0.000 | 0.004 | |
ClinicalModel-class | 0.073 | 0.000 | 0.072 | |
ClinicalModel | 0.078 | 0.001 | 0.079 | |
CohortList | 0.025 | 0.000 | 0.026 | |
ConsensusMetaclusteringModel | 0.010 | 0.000 | 0.011 | |
CoxModel | 0.993 | 0.000 | 0.995 | |
GeneFuModel | 0.08 | 0.00 | 0.08 | |
ModelComparison | 4.391 | 0.115 | 4.508 | |
PCOSP | 0.081 | 0.017 | 0.098 | |
RandomGeneAssignmentModel | 0.071 | 0.008 | 0.079 | |
RandomLabelShufflingModel | 0.072 | 0.007 | 0.079 | |
SurvivalExperiment | 0.068 | 0.012 | 0.080 | |
SurvivalModel-class | 0.032 | 0.006 | 0.037 | |
SurvivalModel | 0.052 | 0.015 | 0.067 | |
assignColDataColumn | 0.026 | 0.000 | 0.025 | |
assignSubtypes-CohortList-list-method | 0.376 | 0.016 | 0.392 | |
assignSubtypes-SurvivalExperiment-data.frame-method | 0.029 | 0.001 | 0.031 | |
assignSubtypes | 0.029 | 0.001 | 0.031 | |
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method | 0.647 | 0.008 | 0.656 | |
barPlotModelComparison | 0.605 | 0.004 | 0.610 | |
birnbaum | 0.002 | 0.000 | 0.003 | |
chen | 0.001 | 0.001 | 0.002 | |
cohortSubtypeDFs | 0.003 | 0.000 | 0.002 | |
compareModels-ModelComparison-SurvivalModel-method | 0.656 | 0.006 | 0.662 | |
compareModels-SurvivalModel-SurvivalModel-method | 0.584 | 0.027 | 0.611 | |
compareModels | 0.585 | 0.030 | 0.615 | |
dropNotCensored-CohortList-method | 0.383 | 0.002 | 0.385 | |
dropNotCensored-SurvivalExperiment-method | 0.037 | 0.000 | 0.037 | |
dropNotCensored | 0.036 | 0.000 | 0.036 | |
existingClassifierData | 0.001 | 0.001 | 0.003 | |
findCommonGenes-CohortList-method | 0.022 | 0.000 | 0.023 | |
findCommonGenes | 0.022 | 0.000 | 0.023 | |
findCommonSamples-CohortList-method | 0.027 | 0.001 | 0.030 | |
findCommonSamples | 0.027 | 0.001 | 0.028 | |
forestPlot-ModelComparison-method | 0.616 | 0.008 | 0.624 | |
forestPlot-PCOSP_or_ClinicalModel-method | 0.046 | 0.001 | 0.046 | |
forestPlot | 0.111 | 0.000 | 0.110 | |
getModelSeed-SurvivalModel-method | 0.007 | 0.000 | 0.007 | |
getModelSeed | 0.005 | 0.001 | 0.006 | |
getTopFeatures-PCOSP-method | 0.007 | 0.000 | 0.008 | |
getTopFeatures-SummarizedExperiment-method | 0.111 | 0.001 | 0.112 | |
getTopFeatures | 0.007 | 0.000 | 0.007 | |
haiderSigScores | 0.002 | 0.000 | 0.003 | |
hasColDataColumns | 0.010 | 0.000 | 0.011 | |
merge-SurvivalExperiment-SurvivalExperiment-method | 0.107 | 0.000 | 0.108 | |
modelParams-set | 0.013 | 0.000 | 0.013 | |
modelParams | 0.010 | 0.002 | 0.012 | |
models-SurvivalModel-method | 0.006 | 0.001 | 0.007 | |
models-set-SurvivalModel-SimpleList-method | 0.008 | 0.000 | 0.007 | |
models-set | 0.012 | 0.001 | 0.012 | |
models | 0.008 | 0.000 | 0.007 | |
normalsMAE | 0.001 | 0.000 | 0.001 | |
plotROC-PCOSP-method | 0.252 | 0.023 | 0.275 | |
predictClasses-CohortList-ClinicalModel-method | 0.211 | 0.002 | 0.214 | |
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method | 0.271 | 0.004 | 0.276 | |
predictClasses-SurvivalExperiment-ClinicalModel-method | 0.107 | 0.008 | 0.115 | |
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method | 0.102 | 0.011 | 0.112 | |
predictClasses | 0.108 | 0.007 | 0.114 | |
rankFeatures-SummarizedExperiment-method | 0.135 | 0.002 | 0.138 | |
rankFeatures | 0.083 | 0.001 | 0.084 | |
removeColDataFactorColumns | 0.016 | 0.000 | 0.016 | |
removeFactorColumns | 0.002 | 0.000 | 0.003 | |
renameColDataColumns | 0.017 | 0.000 | 0.018 | |
renameColumns | 0.001 | 0.000 | 0.002 | |
sampleClinicalModel | 0.004 | 0.001 | 0.005 | |
sampleCohortList | 0.020 | 0.001 | 0.022 | |
sampleICGCmicro | 0.006 | 0.000 | 0.007 | |
samplePCOSPmodel | 0.006 | 0.000 | 0.007 | |
samplePCOSPpredList | 0.027 | 0.000 | 0.028 | |
samplePCSIsurvExp | 0.004 | 0.001 | 0.006 | |
sampleRGAmodel | 0.005 | 0.001 | 0.007 | |
sampleRLSmodel | 0.006 | 0.000 | 0.007 | |
sampleTrainedPCOSPmodel | 0.006 | 0.001 | 0.007 | |
sampleValPCOSPmodel | 0.029 | 0.001 | 0.029 | |
show-S4Model-method | 0.045 | 0.000 | 0.045 | |
subset-CohortList-method | 0.116 | 0.000 | 0.117 | |
trainData-set | 0.043 | 0.000 | 0.044 | |
trainData | 0.006 | 0.000 | 0.007 | |
trainModel-ClinicalModel-method | 0.038 | 0.001 | 0.039 | |
trainModel-PCOSP-method | 0.974 | 0.051 | 1.026 | |
trainModel-RGAModel-method | 1.029 | 0.000 | 1.029 | |
trainModel-RLSModel-method | 0.984 | 0.000 | 0.985 | |
trainModel | 0.950 | 0.058 | 1.008 | |
validateModel-ClinicalModel-CohortList-method | 0.188 | 0.001 | 0.188 | |
validateModel-ClinicalModel-SurvivalExperiment-method | 0.514 | 0.008 | 0.522 | |
validateModel-GeneFuModel-CohortList-method | 1.055 | 0.008 | 1.063 | |
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method | 0.994 | 0.011 | 1.006 | |
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method | 0.995 | 0.030 | 1.025 | |
validateModel | 0.078 | 0.001 | 0.079 | |
validationData-SurvivalModel-method | 0.007 | 0.000 | 0.007 | |
validationData-set-SurvivalModel-CohortList-method | 0.006 | 0.000 | 0.006 | |
validationData-set | 0.007 | 0.000 | 0.007 | |
validationData | 0.006 | 0.000 | 0.006 | |
validationStats-SurvivalModel-method | 0.005 | 0.001 | 0.006 | |
validationStats-set-SurvivalModel-data.frame-method | 0.007 | 0.000 | 0.007 | |
validationStats-set | 0.007 | 0.000 | 0.007 | |
validationStats | 0.006 | 0.000 | 0.006 | |