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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 1490/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.13.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: devel
git_last_commit: e15f1cf
git_last_commit_date: 2024-04-30 11:31:36 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for PDATK on nebbiolo2

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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2024-06-15 02:02:21 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 02:08:40 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 379.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PDATK.Rcheck
Warnings: 2

Command output

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### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.13.0’
* 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.


Installation output

PDATK.Rcheck/00install.out

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##############################################################################
###
### 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)

Tests output

PDATK.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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, 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 
 28.028   7.424  32.078 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0050.0000.005
ClinicalModel-class0.0770.0520.129
ClinicalModel0.1090.0160.125
CohortList0.0320.0030.036
ConsensusMetaclusteringModel0.0130.0040.017
CoxModel0.3130.0210.332
GeneFuModel0.1080.0110.119
ModelComparison4.2480.4884.736
PCOSP0.0780.0200.098
RandomGeneAssignmentModel0.0610.0040.064
RandomLabelShufflingModel0.0610.0000.061
SurvivalExperiment0.0640.0000.064
SurvivalModel-class0.0280.0040.032
SurvivalModel0.0320.0000.032
assignColDataColumn0.0260.0000.025
assignSubtypes-CohortList-list-method0.4000.0160.415
assignSubtypes-SurvivalExperiment-data.frame-method0.0450.0040.049
assignSubtypes0.0270.0040.031
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method0.6500.0240.674
barPlotModelComparison0.6530.0240.676
birnbaum0.0020.0000.002
chen0.0020.0000.002
cohortSubtypeDFs0.0020.0000.003
compareModels-ModelComparison-SurvivalModel-method0.6330.0040.638
compareModels-SurvivalModel-SurvivalModel-method0.5660.0120.578
compareModels0.5760.0240.601
dropNotCensored-CohortList-method0.3880.0400.428
dropNotCensored-SurvivalExperiment-method0.0340.0000.033
dropNotCensored0.0340.0000.034
existingClassifierData0.0020.0000.003
findCommonGenes-CohortList-method0.0180.0040.022
findCommonGenes0.0220.0000.022
findCommonSamples-CohortList-method0.0300.0000.029
findCommonSamples0.0280.0000.027
forestPlot-ModelComparison-method0.6260.0240.649
forestPlot-PCOSP_or_ClinicalModel-method0.0430.0040.047
forestPlot0.1100.0000.111
getModelSeed-SurvivalModel-method0.0070.0000.007
getModelSeed0.0020.0040.007
getTopFeatures-PCOSP-method0.0080.0000.008
getTopFeatures-SummarizedExperiment-method0.1060.0120.117
getTopFeatures0.0070.0000.006
haiderSigScores0.0020.0000.002
hasColDataColumns0.0120.0000.011
merge-SurvivalExperiment-SurvivalExperiment-method0.1130.0120.125
modelParams-set0.0080.0030.011
modelParams0.0110.0000.011
models-SurvivalModel-method0.0070.0000.006
models-set-SurvivalModel-SimpleList-method0.0070.0000.007
models-set0.0120.0000.011
models0.0070.0000.006
normalsMAE0.0020.0000.001
plotROC-PCOSP-method0.2300.0080.238
predictClasses-CohortList-ClinicalModel-method0.2100.0080.218
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.2840.0040.289
predictClasses-SurvivalExperiment-ClinicalModel-method0.1000.0000.101
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.0890.0080.097
predictClasses0.1020.0040.105
rankFeatures-SummarizedExperiment-method0.0990.0200.119
rankFeatures0.0760.0120.088
removeColDataFactorColumns0.0160.0000.016
removeFactorColumns0.0010.0030.003
renameColDataColumns0.0140.0010.016
renameColumns0.0010.0000.001
sampleClinicalModel0.0060.0000.005
sampleCohortList0.0220.0000.022
sampleICGCmicro0.0060.0000.006
samplePCOSPmodel0.0060.0000.007
samplePCOSPpredList0.0270.0000.027
samplePCSIsurvExp0.0050.0000.005
sampleRGAmodel0.0060.0000.006
sampleRLSmodel0.0060.0000.006
sampleTrainedPCOSPmodel0.0070.0000.006
sampleValPCOSPmodel0.0290.0000.029
show-S4Model-method0.0620.0000.062
subset-CohortList-method0.1150.0000.115
trainData-set0.0130.0000.012
trainData0.0060.0000.006
trainModel-ClinicalModel-method0.040.000.04
trainModel-PCOSP-method0.9760.0971.076
trainModel-RGAModel-method0.9540.0080.962
trainModel-RLSModel-method0.8950.0640.958
trainModel0.9840.0000.984
validateModel-ClinicalModel-CohortList-method0.1950.0040.198
validateModel-ClinicalModel-SurvivalExperiment-method0.5370.0280.564
validateModel-GeneFuModel-CohortList-method0.9870.1161.103
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method0.9590.0280.987
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method0.9500.0440.993
validateModel0.0730.0080.081
validationData-SurvivalModel-method0.0030.0040.008
validationData-set-SurvivalModel-CohortList-method0.0030.0040.007
validationData-set0.0070.0000.007
validationData0.0060.0000.006
validationStats-SurvivalModel-method0.0060.0000.006
validationStats-set-SurvivalModel-data.frame-method0.0070.0000.007
validationStats-set0.0070.0000.007
validationStats0.0070.0000.007