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This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1533/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.12.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for PDATK on palomino3

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.

raw results


Summary

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: 2024-06-17 08:38:48 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 08:52:06 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 798.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PDATK.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### 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-GeneFuModel-CohortList-method                 1.57   5.25    6.96
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method         1.39   5.14    6.72
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method 1.32   5.03    6.44
* 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.


Installation output

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)

Tests output

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 
  28.06   24.59   53.15 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.000.020.01
ClinicalModel-class0.080.060.14
ClinicalModel0.090.110.24
CohortList0.010.050.06
ConsensusMetaclusteringModel0.020.010.03
CoxModel0.410.080.53
GeneFuModel0.120.110.24
ModelComparison2.490.933.44
PCOSP0.060.200.28
RandomGeneAssignmentModel0.090.140.23
RandomLabelShufflingModel0.060.220.29
SurvivalExperiment0.080.030.11
SurvivalModel-class0.050.060.12
SurvivalModel0.060.070.13
assignColDataColumn0.050.000.04
assignSubtypes-CohortList-list-method0.530.461.08
assignSubtypes-SurvivalExperiment-data.frame-method0.050.040.08
assignSubtypes0.040.010.06
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method0.791.051.83
barPlotModelComparison0.761.091.86
birnbaum000
chen0.000.010.02
cohortSubtypeDFs0.020.000.01
compareModels-ModelComparison-SurvivalModel-method0.750.971.72
compareModels-SurvivalModel-SurvivalModel-method0.780.881.70
compareModels0.760.871.66
dropNotCensored-CohortList-method0.470.020.48
dropNotCensored-SurvivalExperiment-method0.040.000.05
dropNotCensored0.040.010.04
existingClassifierData0.000.020.02
findCommonGenes-CohortList-method0.010.010.03
findCommonGenes0.020.000.02
findCommonSamples-CohortList-method0.030.020.04
findCommonSamples0.050.020.06
forestPlot-ModelComparison-method0.900.981.93
forestPlot-PCOSP_or_ClinicalModel-method0.080.000.07
forestPlot0.170.000.18
getModelSeed-SurvivalModel-method0.020.000.01
getModelSeed0.000.020.02
getTopFeatures-PCOSP-method0.010.000.02
getTopFeatures-SummarizedExperiment-method0.160.020.17
getTopFeatures0.020.000.01
haiderSigScores0.000.010.02
hasColDataColumns0.020.000.01
merge-SurvivalExperiment-SurvivalExperiment-method0.120.050.18
modelParams-set0.000.050.06
modelParams0.020.000.01
models-SurvivalModel-method0.030.000.03
models-set-SurvivalModel-SimpleList-method0.010.000.02
models-set0.030.030.06
models0.020.000.02
normalsMAE000
plotROC-PCOSP-method0.340.060.40
predictClasses-CohortList-ClinicalModel-method0.320.030.35
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.400.020.44
predictClasses-SurvivalExperiment-ClinicalModel-method0.170.000.17
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.150.030.18
predictClasses0.150.020.17
rankFeatures-SummarizedExperiment-method0.170.010.18
rankFeatures0.110.000.11
removeColDataFactorColumns0.020.020.04
removeFactorColumns0.010.000.01
renameColDataColumns0.040.000.03
renameColumns000
sampleClinicalModel0.010.000.02
sampleCohortList0.020.000.01
sampleICGCmicro0.000.020.01
samplePCOSPmodel0.000.010.02
samplePCOSPpredList0.030.020.05
samplePCSIsurvExp0.000.010.01
sampleRGAmodel0.000.020.02
sampleRLSmodel0.000.010.01
sampleTrainedPCOSPmodel0.000.020.02
sampleValPCOSPmodel0.020.020.03
show-S4Model-method0.050.010.06
subset-CohortList-method0.110.020.13
trainData-set0.010.040.06
trainData0.030.000.03
trainModel-ClinicalModel-method0.030.020.05
trainModel-PCOSP-method1.070.051.20
trainModel-RGAModel-method1.110.001.11
trainModel-RLSModel-method0.900.000.91
trainModel1.030.001.03
validateModel-ClinicalModel-CohortList-method0.210.010.22
validateModel-ClinicalModel-SurvivalExperiment-method0.821.021.90
validateModel-GeneFuModel-CohortList-method1.575.256.96
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method1.395.146.72
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method1.325.036.44
validateModel0.060.030.11
validationData-SurvivalModel-method0.000.020.01
validationData-set-SurvivalModel-CohortList-method0.000.000.02
validationData-set0.010.000.02
validationData0.000.010.01
validationStats-SurvivalModel-method0.000.020.02
validationStats-set-SurvivalModel-data.frame-method0.000.010.01
validationStats-set0.020.000.02
validationStats0.010.000.01