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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1511/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.15.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: devel
git_last_commit: 6c52f5f
git_last_commit_date: 2024-10-29 10:56:10 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for PDATK on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PDATK
Version: 1.15.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PDATK_1.15.0.tar.gz
StartedAt: 2024-12-24 09:42:43 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:49:41 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 418.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: PDATK.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PDATK_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PDATK.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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-3.21-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(s) 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 5.008  0.183   5.232
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/PDATK.Rcheck/00check.log’
for details.


Installation output

PDATK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PDATK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 14 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 37.487   8.575  43.091 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0050.0000.005
ClinicalModel-class0.1070.0040.111
ClinicalModel0.1090.0160.126
CohortList0.0320.0000.033
ConsensusMetaclusteringModel0.0150.0000.015
CoxModel0.3500.0440.395
GeneFuModel0.1230.0040.127
ModelComparison5.0080.1835.232
PCOSP0.1200.0120.132
RandomGeneAssignmentModel0.0920.0000.092
RandomLabelShufflingModel0.0910.0000.091
SurvivalExperiment0.0950.0120.107
SurvivalModel-class0.0460.0000.046
SurvivalModel0.0420.0040.046
assignColDataColumn0.0360.0000.036
assignSubtypes-CohortList-list-method0.5750.0120.589
assignSubtypes-SurvivalExperiment-data.frame-method0.0420.0000.043
assignSubtypes0.0570.0080.065
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method0.9610.0561.020
barPlotModelComparison0.9580.0240.990
birnbaum0.0030.0000.003
chen0.0030.0000.003
cohortSubtypeDFs0.0040.0000.004
compareModels-ModelComparison-SurvivalModel-method0.9260.0160.946
compareModels-SurvivalModel-SurvivalModel-method0.8470.0160.866
compareModels0.8720.0200.896
dropNotCensored-CohortList-method0.5920.0150.610
dropNotCensored-SurvivalExperiment-method0.0480.0030.052
dropNotCensored0.0510.0000.051
existingClassifierData0.0030.0000.003
findCommonGenes-CohortList-method0.0230.0000.023
findCommonGenes0.0180.0040.022
findCommonSamples-CohortList-method0.0280.0040.033
findCommonSamples0.0270.0040.031
forestPlot-ModelComparison-method0.9730.0120.993
forestPlot-PCOSP_or_ClinicalModel-method0.0570.0030.060
forestPlot0.1610.0000.162
getModelSeed-SurvivalModel-method0.0080.0000.008
getModelSeed0.0070.0000.007
getTopFeatures-PCOSP-method0.0080.0000.008
getTopFeatures-SummarizedExperiment-method0.1560.0080.164
getTopFeatures0.0080.0000.007
haiderSigScores0.0030.0000.003
hasColDataColumns0.0160.0000.016
merge-SurvivalExperiment-SurvivalExperiment-method0.1820.0040.186
modelParams-set0.0170.0000.017
modelParams0.0150.0000.015
models-SurvivalModel-method0.0070.0000.007
models-set-SurvivalModel-SimpleList-method0.0080.0000.008
models-set0.0170.0000.017
models0.0010.0070.009
normalsMAE0.0010.0000.002
plotROC-PCOSP-method0.3420.0080.351
predictClasses-CohortList-ClinicalModel-method0.3180.0040.323
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.4010.0320.434
predictClasses-SurvivalExperiment-ClinicalModel-method0.1490.0040.154
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.150.000.15
predictClasses0.1450.0040.149
rankFeatures-SummarizedExperiment-method0.1780.0040.182
rankFeatures0.1160.0070.125
removeColDataFactorColumns0.0200.0000.021
removeFactorColumns0.0030.0000.003
renameColDataColumns0.0180.0040.021
renameColumns0.0020.0000.002
sampleClinicalModel0.0050.0000.006
sampleCohortList0.0210.0000.021
sampleICGCmicro0.0070.0000.006
samplePCOSPmodel0.0070.0000.007
samplePCOSPpredList0.0240.0040.029
samplePCSIsurvExp0.0060.0000.005
sampleRGAmodel0.0070.0000.007
sampleRLSmodel0.0060.0000.006
sampleTrainedPCOSPmodel0.0070.0000.007
sampleValPCOSPmodel0.0310.0000.031
show-S4Model-method0.0690.0000.069
subset-CohortList-method0.2150.0040.220
trainData-set0.0170.0000.016
trainData0.0080.0000.008
trainModel-ClinicalModel-method0.0580.0000.058
trainModel-PCOSP-method1.1990.0761.284
trainModel-RGAModel-method1.2010.0081.306
trainModel-RLSModel-method1.1190.0321.165
trainModel1.2490.0281.280
validateModel-ClinicalModel-CohortList-method0.2870.0000.288
validateModel-ClinicalModel-SurvivalExperiment-method0.7790.0190.925
validateModel-GeneFuModel-CohortList-method1.5160.1161.645
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method1.4970.0911.595
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method1.4400.0241.468
validateModel0.0960.0040.100
validationData-SurvivalModel-method0.0080.0000.008
validationData-set-SurvivalModel-CohortList-method0.0060.0000.007
validationData-set0.0090.0000.009
validationData0.0090.0000.008
validationStats-SurvivalModel-method0.0030.0040.006
validationStats-set-SurvivalModel-data.frame-method0.0070.0000.008
validationStats-set0.0090.0000.008
validationStats0.0080.0000.008