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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1489/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.13.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 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
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for PDATK on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PDATK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PDATK_1.13.0.tar.gz
StartedAt: 2024-06-10 07:48:17 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:00:33 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 735.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PDATK.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PDATK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PDATK_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.13.0’
* 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 ‘/Users/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 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
ModelComparison 5.739  0.077   6.791
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck/00check.log’
for details.


Installation output

PDATK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PDATK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 2 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 58.374  12.047  76.285 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0070.0040.011
ClinicalModel-class0.1760.0070.213
ClinicalModel0.2060.0060.248
CohortList0.0550.0050.069
ConsensusMetaclusteringModel0.0240.0030.032
CoxModel0.6040.0160.710
GeneFuModel0.2150.0040.254
ModelComparison5.7390.0776.791
PCOSP0.1900.0140.244
RandomGeneAssignmentModel0.1540.0080.190
RandomLabelShufflingModel0.1540.0070.192
SurvivalExperiment0.1680.0060.205
SurvivalModel-class0.0750.0040.097
SurvivalModel0.0760.0050.098
assignColDataColumn0.0620.0010.069
assignSubtypes-CohortList-list-method1.0780.0191.297
assignSubtypes-SurvivalExperiment-data.frame-method0.0900.0080.108
assignSubtypes0.0750.0080.092
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method1.6450.0331.978
barPlotModelComparison1.6080.0341.911
birnbaum0.0040.0040.009
chen0.0040.0040.009
cohortSubtypeDFs0.0050.0030.009
compareModels-ModelComparison-SurvivalModel-method1.5700.0351.869
compareModels-SurvivalModel-SurvivalModel-method1.4690.0331.736
compareModels1.4780.0331.770
dropNotCensored-CohortList-method1.0120.0091.146
dropNotCensored-SurvivalExperiment-method0.0900.0040.106
dropNotCensored0.0910.0040.107
existingClassifierData0.0030.0030.008
findCommonGenes-CohortList-method0.0380.0050.051
findCommonGenes0.0370.0040.044
findCommonSamples-CohortList-method0.0540.0050.065
findCommonSamples0.0530.0050.062
forestPlot-ModelComparison-method1.5450.0311.769
forestPlot-PCOSP_or_ClinicalModel-method0.0940.0050.113
forestPlot0.2820.0060.321
getModelSeed-SurvivalModel-method0.0120.0030.018
getModelSeed0.0100.0040.018
getTopFeatures-PCOSP-method0.0130.0040.020
getTopFeatures-SummarizedExperiment-method0.2740.0060.317
getTopFeatures0.0110.0040.019
haiderSigScores0.0040.0040.009
hasColDataColumns0.0280.0010.032
merge-SurvivalExperiment-SurvivalExperiment-method0.2970.0050.341
modelParams-set0.0250.0050.033
modelParams0.0250.0040.032
models-SurvivalModel-method0.0110.0040.016
models-set-SurvivalModel-SimpleList-method0.0130.0030.018
models-set0.0270.0050.037
models0.0140.0040.024
normalsMAE0.0020.0040.007
plotROC-PCOSP-method0.5790.0110.660
predictClasses-CohortList-ClinicalModel-method0.5780.0140.664
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.7280.0200.875
predictClasses-SurvivalExperiment-ClinicalModel-method0.2680.0120.318
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.2670.0100.317
predictClasses0.2670.0100.309
rankFeatures-SummarizedExperiment-method0.3080.0060.367
rankFeatures0.2270.0060.271
removeColDataFactorColumns0.0350.0040.047
removeFactorColumns0.0060.0010.006
renameColDataColumns0.0360.0040.048
renameColumns0.0030.0010.004
sampleClinicalModel0.0090.0040.015
sampleCohortList0.0350.0040.047
sampleICGCmicro0.0100.0030.018
samplePCOSPmodel0.0110.0040.018
samplePCOSPpredList0.0490.0050.064
samplePCSIsurvExp0.0080.0040.015
sampleRGAmodel0.0100.0040.016
sampleRLSmodel0.0110.0040.016
sampleTrainedPCOSPmodel0.0110.0040.017
sampleValPCOSPmodel0.0530.0040.064
show-S4Model-method0.1350.0050.159
subset-CohortList-method0.2870.0060.343
trainData-set0.0270.0040.040
trainData0.0130.0040.018
trainModel-ClinicalModel-method0.1030.0050.129
trainModel-PCOSP-method1.3280.0161.517
trainModel-RGAModel-method1.3140.0091.483
trainModel-RLSModel-method1.2500.0101.486
trainModel1.3330.0121.570
validateModel-ClinicalModel-CohortList-method0.5040.0110.586
validateModel-ClinicalModel-SurvivalExperiment-method1.4110.0841.747
validateModel-GeneFuModel-CohortList-method2.6230.2363.443
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method2.4850.0912.950
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method2.4320.0852.872
validateModel0.1800.0110.229
validationData-SurvivalModel-method0.0130.0040.020
validationData-set-SurvivalModel-CohortList-method0.0110.0050.019
validationData-set0.0140.0040.021
validationData0.0140.0050.022
validationStats-SurvivalModel-method0.0100.0040.015
validationStats-set-SurvivalModel-data.frame-method0.0110.0040.018
validationStats-set0.0160.0050.024
validationStats0.0140.0040.022