Benjamin Haibe-Kains
| Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/PDATK |
| git_branch: RELEASE_3_19 |
| git_last_commit: 857690d |
| git_last_commit_date: 2024-04-30 11:31:36 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| 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 1533/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PDATK 1.12.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | 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: 1.12.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PDATK.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings PDATK_1.12.0.tar.gz |
| StartedAt: 2024-06-13 08:23:43 -0400 (Thu, 13 Jun 2024) |
| EndedAt: 2024-06-13 08:37:22 -0400 (Thu, 13 Jun 2024) |
| EllapsedTime: 818.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PDATK.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PDATK.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings PDATK_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/PDATK.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'PDATK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PDATK' version '1.12.0'
* 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 'PDATK' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'survival::brier' by 'verification::brier' when loading 'PDATK'
See 'F:/biocbuild/bbs-3.19-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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method 1.44 5.13 6.73
validateModel-GeneFuModel-CohortList-method 1.24 5.20 6.66
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method 1.34 5.03 6.61
* 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: 2 WARNINGs, 3 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/PDATK.Rcheck/00check.log'
for details.
PDATK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL PDATK ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
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(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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 1 | SKIP 0 | PASS 77 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]
>
> proc.time()
user system elapsed
29.00 26.15 55.95
PDATK.Rcheck/PDATK-Ex.timings
| name | user | system | elapsed | |
| CSPC_MAE | 0.02 | 0.00 | 0.02 | |
| ClinicalModel-class | 0.08 | 0.06 | 0.14 | |
| ClinicalModel | 0.09 | 0.08 | 0.17 | |
| CohortList | 0.01 | 0.05 | 0.06 | |
| ConsensusMetaclusteringModel | 0.02 | 0.00 | 0.02 | |
| CoxModel | 0.23 | 0.10 | 0.38 | |
| GeneFuModel | 0.15 | 0.11 | 0.26 | |
| ModelComparison | 2.65 | 0.97 | 3.68 | |
| PCOSP | 0.10 | 0.20 | 0.29 | |
| RandomGeneAssignmentModel | 0.08 | 0.17 | 0.25 | |
| RandomLabelShufflingModel | 0.06 | 0.17 | 0.24 | |
| SurvivalExperiment | 0.06 | 0.05 | 0.11 | |
| SurvivalModel-class | 0.07 | 0.06 | 0.12 | |
| SurvivalModel | 0.03 | 0.08 | 0.11 | |
| assignColDataColumn | 0.03 | 0.00 | 0.03 | |
| assignSubtypes-CohortList-list-method | 0.47 | 0.48 | 0.96 | |
| assignSubtypes-SurvivalExperiment-data.frame-method | 0.04 | 0.02 | 0.06 | |
| assignSubtypes | 0.04 | 0.03 | 0.06 | |
| barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method | 0.87 | 1.15 | 2.05 | |
| barPlotModelComparison | 0.83 | 1.08 | 1.90 | |
| birnbaum | 0.00 | 0.02 | 0.02 | |
| chen | 0.00 | 0.01 | 0.02 | |
| cohortSubtypeDFs | 0.00 | 0.02 | 0.01 | |
| compareModels-ModelComparison-SurvivalModel-method | 0.86 | 0.98 | 1.84 | |
| compareModels-SurvivalModel-SurvivalModel-method | 0.69 | 1.05 | 1.74 | |
| compareModels | 0.61 | 0.98 | 1.59 | |
| dropNotCensored-CohortList-method | 0.35 | 0.04 | 0.39 | |
| dropNotCensored-SurvivalExperiment-method | 0.04 | 0.01 | 0.05 | |
| dropNotCensored | 0.03 | 0.02 | 0.05 | |
| existingClassifierData | 0.00 | 0.01 | 0.01 | |
| findCommonGenes-CohortList-method | 0.01 | 0.02 | 0.03 | |
| findCommonGenes | 0.02 | 0.00 | 0.02 | |
| findCommonSamples-CohortList-method | 0.03 | 0.01 | 0.05 | |
| findCommonSamples | 0.02 | 0.02 | 0.03 | |
| forestPlot-ModelComparison-method | 0.73 | 0.95 | 1.75 | |
| forestPlot-PCOSP_or_ClinicalModel-method | 0.08 | 0.00 | 0.08 | |
| forestPlot | 0.15 | 0.02 | 0.17 | |
| getModelSeed-SurvivalModel-method | 0.02 | 0.00 | 0.01 | |
| getModelSeed | 0.00 | 0.01 | 0.02 | |
| getTopFeatures-PCOSP-method | 0.02 | 0.00 | 0.02 | |
| getTopFeatures-SummarizedExperiment-method | 0.10 | 0.00 | 0.11 | |
| getTopFeatures | 0.00 | 0.02 | 0.02 | |
| haiderSigScores | 0.00 | 0.01 | 0.00 | |
| hasColDataColumns | 0.02 | 0.00 | 0.02 | |
| merge-SurvivalExperiment-SurvivalExperiment-method | 0.13 | 0.05 | 0.18 | |
| modelParams-set | 0.01 | 0.04 | 0.07 | |
| modelParams | 0.03 | 0.00 | 0.03 | |
| models-SurvivalModel-method | 0.02 | 0.00 | 0.01 | |
| models-set-SurvivalModel-SimpleList-method | 0.00 | 0.02 | 0.02 | |
| models-set | 0.01 | 0.05 | 0.06 | |
| models | 0.00 | 0.01 | 0.02 | |
| normalsMAE | 0.00 | 0.02 | 0.01 | |
| plotROC-PCOSP-method | 0.30 | 0.06 | 0.36 | |
| predictClasses-CohortList-ClinicalModel-method | 0.25 | 0.05 | 0.30 | |
| predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method | 0.31 | 0.06 | 0.37 | |
| predictClasses-SurvivalExperiment-ClinicalModel-method | 0.11 | 0.03 | 0.14 | |
| predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method | 0.11 | 0.00 | 0.13 | |
| predictClasses | 0.13 | 0.00 | 0.12 | |
| rankFeatures-SummarizedExperiment-method | 0.11 | 0.02 | 0.13 | |
| rankFeatures | 0.07 | 0.01 | 0.09 | |
| removeColDataFactorColumns | 0.00 | 0.02 | 0.01 | |
| removeFactorColumns | 0.02 | 0.00 | 0.02 | |
| renameColDataColumns | 0.01 | 0.01 | 0.03 | |
| renameColumns | 0 | 0 | 0 | |
| sampleClinicalModel | 0.00 | 0.02 | 0.02 | |
| sampleCohortList | 0.02 | 0.02 | 0.03 | |
| sampleICGCmicro | 0.00 | 0.01 | 0.01 | |
| samplePCOSPmodel | 0.00 | 0.02 | 0.02 | |
| samplePCOSPpredList | 0.01 | 0.01 | 0.03 | |
| samplePCSIsurvExp | 0.00 | 0.02 | 0.02 | |
| sampleRGAmodel | 0.02 | 0.00 | 0.01 | |
| sampleRLSmodel | 0.00 | 0.01 | 0.02 | |
| sampleTrainedPCOSPmodel | 0.00 | 0.02 | 0.01 | |
| sampleValPCOSPmodel | 0.03 | 0.00 | 0.03 | |
| show-S4Model-method | 0.03 | 0.01 | 0.05 | |
| subset-CohortList-method | 0.13 | 0.02 | 0.14 | |
| trainData-set | 0.02 | 0.03 | 0.05 | |
| trainData | 0.00 | 0.01 | 0.01 | |
| trainModel-ClinicalModel-method | 0.04 | 0.00 | 0.05 | |
| trainModel-PCOSP-method | 0.94 | 0.05 | 1.05 | |
| trainModel-RGAModel-method | 0.95 | 0.02 | 0.96 | |
| trainModel-RLSModel-method | 0.94 | 0.01 | 0.96 | |
| trainModel | 1.14 | 0.02 | 1.15 | |
| validateModel-ClinicalModel-CohortList-method | 0.24 | 0.04 | 0.30 | |
| validateModel-ClinicalModel-SurvivalExperiment-method | 0.76 | 1.02 | 1.84 | |
| validateModel-GeneFuModel-CohortList-method | 1.24 | 5.20 | 6.66 | |
| validateModel-PCOSP_or_RLS_or_RGA-CohortList-method | 1.34 | 5.03 | 6.61 | |
| validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method | 1.44 | 5.13 | 6.73 | |
| validateModel | 0.11 | 0.05 | 0.16 | |
| validationData-SurvivalModel-method | 0.01 | 0.00 | 0.02 | |
| validationData-set-SurvivalModel-CohortList-method | 0.00 | 0.01 | 0.01 | |
| validationData-set | 0.00 | 0.02 | 0.02 | |
| validationData | 0.00 | 0.01 | 0.01 | |
| validationStats-SurvivalModel-method | 0.02 | 0.00 | 0.02 | |
| validationStats-set-SurvivalModel-data.frame-method | 0.00 | 0.02 | 0.01 | |
| validationStats-set | 0.01 | 0.00 | 0.02 | |
| validationStats | 0.00 | 0.02 | 0.01 | |