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This page was generated on 2021-12-06 13:05:06 -0500 (Mon, 06 Dec 2021).

CHECK results for PDATK on nebbiolo2

To the developers/maintainers of the PDATK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PDATK.git to
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raw results

Package 1388/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.2.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: RELEASE_3_14
git_last_commit: ecf1881
git_last_commit_date: 2021-10-26 13:07:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PDATK
Version: 1.2.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PDATK_1.2.0.tar.gz
StartedAt: 2021-12-05 09:04:51 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 09:10:13 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 321.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PDATK.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PDATK_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.2.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck/00check.log’
for details.



Installation output

PDATK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PDATK
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘PDATK’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PDATK)

Tests output

PDATK.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

> 
> test_check("PDATK")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 30.801   6.360  32.976 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0040.0000.005
ClinicalModel-class0.0890.0120.101
ClinicalModel0.1280.0160.144
CohortList0.0230.0000.023
ConsensusMetaclusteringModel0.0130.0000.012
CoxModel0.4440.0680.513
GeneFuModel0.1190.0160.135
ModelComparison2.9950.0333.061
PCOSP0.0790.0150.095
RandomGeneAssignmentModel0.0900.0090.098
RandomLabelShufflingModel0.0940.0030.098
SurvivalExperiment0.1810.0200.201
SurvivalModel-class0.0460.0000.046
SurvivalModel0.0470.0000.047
assignColDataColumn0.0420.0000.042
assignSubtypes-CohortList-list-method0.4160.0120.428
assignSubtypes-SurvivalExperiment-data.frame-method0.0440.0000.044
assignSubtypes0.0360.0070.044
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method0.8770.0090.887
barPlotModelComparison0.8070.0160.823
birnbaum0.0020.0000.002
chen0.0020.0000.003
cohortSubtypeDFs0.0020.0000.002
compareModels-ModelComparison-SurvivalModel-method0.7550.0080.763
compareModels-SurvivalModel-SurvivalModel-method0.7110.0240.734
compareModels0.7180.0000.718
dropNotCensored-CohortList-method0.7760.0110.787
dropNotCensored-SurvivalExperiment-method0.0820.0010.082
dropNotCensored0.0610.0000.060
existingClassifierData0.0020.0000.003
findCommonGenes-CohortList-method0.0530.0000.053
findCommonGenes0.0530.0000.052
findCommonSamples-CohortList-method0.0570.0000.057
findCommonSamples0.0560.0000.056
forestPlot-ModelComparison-method0.7940.0160.810
forestPlot-PCOSP_or_ClinicalModel-method0.0430.0000.043
forestPlot0.1060.0000.106
getModelSeed-SurvivalModel-method0.0070.0000.007
getModelSeed0.0060.0000.007
getTopFeatures-PCOSP-method0.0070.0000.008
getTopFeatures-SummarizedExperiment-method0.2060.0040.211
getTopFeatures0.0070.0000.007
haiderSigScores0.0030.0000.002
hasColDataColumns0.0220.0000.021
merge-SurvivalExperiment-SurvivalExperiment-method0.1800.0030.184
modelParams-set0.0080.0010.009
modelParams0.0110.0000.011
models-SurvivalModel-method0.0070.0000.007
models-set-SurvivalModel-SimpleList-method0.0070.0000.007
models-set0.0070.0000.007
models0.0070.0000.006
normalsMAE0.0020.0000.001
plotROC-PCOSP-method0.1250.0040.130
predictClasses-CohortList-ClinicalModel-method0.3710.0160.388
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.4480.0080.457
predictClasses-SurvivalExperiment-ClinicalModel-method0.1800.0030.184
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.1550.0050.159
predictClasses0.1720.0000.171
rankFeatures-SummarizedExperiment-method0.1990.0000.199
rankFeatures0.1670.0120.179
removeColDataFactorColumns0.0410.0000.041
removeFactorColumns0.0030.0000.003
renameColDataColumns0.0410.0000.041
renameColumns0.0020.0000.002
sampleClinicalModel0.0060.0000.005
sampleCohortList0.0220.0000.021
sampleICGCmicro0.0060.0000.006
samplePCOSPmodel0.0020.0030.006
samplePCOSPpredList0.0270.0000.027
samplePCSIsurvExp0.0050.0010.005
sampleRGAmodel0.0060.0000.006
sampleRLSmodel0.0070.0000.006
sampleTrainedPCOSPmodel0.0070.0000.006
sampleValPCOSPmodel0.0290.0000.028
show-S4Model-method0.0660.0040.069
subset-CohortList-method0.2690.0000.270
trainData-set0.0070.0000.008
trainData0.0060.0000.006
trainModel-ClinicalModel-method0.0500.0000.049
trainModel-PCOSP-method1.0510.0161.067
trainModel-RGAModel-method0.9460.0120.957
trainModel-RLSModel-method0.7990.0000.799
trainModel0.9150.0120.926
validateModel-ClinicalModel-CohortList-method0.3180.0000.319
validateModel-ClinicalModel-SurvivalExperiment-method0.6850.0040.689
validateModel-GeneFuModel-CohortList-method0.4920.0160.508
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method0.4370.0040.441
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method0.4600.0190.480
validateModel0.0680.0010.069
validationData-SurvivalModel-method0.0070.0000.008
validationData-set-SurvivalModel-CohortList-method0.0060.0000.006
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
validationStats0.0060.0000.006