| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1474/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PDATK 1.7.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: PDATK |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PDATK_1.7.0.tar.gz |
| StartedAt: 2023-04-11 22:20:22 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 22:32:33 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 730.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PDATK.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings PDATK_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PDATK.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.7.0’
* 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 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 documentation object '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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ModelComparison 8.38 0.672 9.609
* 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 ...
‘PCOSP_model_analysis.Rmd’ using ‘UTF-8’... OK
‘PDATK_introduction.rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/PDATK.Rcheck/00check.log’
for details.
PDATK.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PDATK ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)
PDATK.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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, 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, 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 12 | SKIP 0 | PASS 77 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 77 ]
>
> proc.time()
user system elapsed
46.788 12.382 53.572
PDATK.Rcheck/PDATK-Ex.timings
| name | user | system | elapsed | |
| CSPC_MAE | 0.002 | 0.004 | 0.006 | |
| ClinicalModel-class | 0.091 | 0.000 | 0.091 | |
| ClinicalModel | 0.102 | 0.008 | 0.110 | |
| CohortList | 0.029 | 0.004 | 0.033 | |
| ConsensusMetaclusteringModel | 0.016 | 0.000 | 0.015 | |
| CoxModel | 0.405 | 0.015 | 0.421 | |
| GeneFuModel | 0.103 | 0.000 | 0.102 | |
| ModelComparison | 8.380 | 0.672 | 9.609 | |
| PCOSP | 0.169 | 0.003 | 0.172 | |
| RandomGeneAssignmentModel | 0.153 | 0.017 | 0.172 | |
| RandomLabelShufflingModel | 0.164 | 0.027 | 0.191 | |
| SurvivalExperiment | 0.167 | 0.004 | 0.202 | |
| SurvivalModel-class | 0.078 | 0.005 | 0.161 | |
| SurvivalModel | 0.078 | 0.003 | 0.113 | |
| assignColDataColumn | 0.072 | 0.000 | 0.073 | |
| assignSubtypes-CohortList-list-method | 0.858 | 0.012 | 0.870 | |
| assignSubtypes-SurvivalExperiment-data.frame-method | 0.072 | 0.008 | 0.079 | |
| assignSubtypes | 0.083 | 0.000 | 0.084 | |
| barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method | 1.595 | 0.078 | 1.723 | |
| barPlotModelComparison | 1.308 | 0.052 | 1.361 | |
| birnbaum | 0.000 | 0.003 | 0.003 | |
| chen | 0.003 | 0.000 | 0.003 | |
| cohortSubtypeDFs | 0.000 | 0.003 | 0.003 | |
| compareModels-ModelComparison-SurvivalModel-method | 0.959 | 0.039 | 0.999 | |
| compareModels-SurvivalModel-SurvivalModel-method | 0.859 | 0.040 | 0.898 | |
| compareModels | 0.844 | 0.028 | 0.872 | |
| dropNotCensored-CohortList-method | 0.593 | 0.024 | 0.617 | |
| dropNotCensored-SurvivalExperiment-method | 0.056 | 0.004 | 0.060 | |
| dropNotCensored | 0.054 | 0.000 | 0.054 | |
| existingClassifierData | 0.000 | 0.003 | 0.003 | |
| findCommonGenes-CohortList-method | 0.025 | 0.000 | 0.024 | |
| findCommonGenes | 0.016 | 0.007 | 0.023 | |
| findCommonSamples-CohortList-method | 0.032 | 0.000 | 0.032 | |
| findCommonSamples | 0.030 | 0.000 | 0.031 | |
| forestPlot-ModelComparison-method | 1.033 | 0.020 | 1.053 | |
| forestPlot-PCOSP_or_ClinicalModel-method | 0.06 | 0.00 | 0.06 | |
| forestPlot | 0.126 | 0.003 | 0.130 | |
| getModelSeed-SurvivalModel-method | 0.008 | 0.000 | 0.008 | |
| getModelSeed | 0.007 | 0.000 | 0.007 | |
| getTopFeatures-PCOSP-method | 0.008 | 0.000 | 0.008 | |
| getTopFeatures-SummarizedExperiment-method | 0.172 | 0.008 | 0.179 | |
| getTopFeatures | 0.007 | 0.000 | 0.008 | |
| haiderSigScores | 0.003 | 0.000 | 0.003 | |
| hasColDataColumns | 0.014 | 0.000 | 0.014 | |
| merge-SurvivalExperiment-SurvivalExperiment-method | 0.111 | 0.000 | 0.111 | |
| modelParams-set | 0.010 | 0.004 | 0.013 | |
| modelParams | 0.014 | 0.000 | 0.014 | |
| models-SurvivalModel-method | 0.008 | 0.000 | 0.007 | |
| models-set-SurvivalModel-SimpleList-method | 0.008 | 0.000 | 0.008 | |
| models-set | 0.013 | 0.000 | 0.013 | |
| models | 0.008 | 0.000 | 0.008 | |
| normalsMAE | 0.000 | 0.002 | 0.002 | |
| plotROC-PCOSP-method | 0.245 | 0.009 | 0.253 | |
| predictClasses-CohortList-ClinicalModel-method | 0.26 | 0.00 | 0.26 | |
| predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method | 0.339 | 0.016 | 0.355 | |
| predictClasses-SurvivalExperiment-ClinicalModel-method | 0.123 | 0.000 | 0.123 | |
| predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method | 0.122 | 0.000 | 0.122 | |
| predictClasses | 0.117 | 0.011 | 0.128 | |
| rankFeatures-SummarizedExperiment-method | 0.137 | 0.000 | 0.137 | |
| rankFeatures | 0.123 | 0.004 | 0.127 | |
| removeColDataFactorColumns | 0.017 | 0.000 | 0.017 | |
| removeFactorColumns | 0.000 | 0.004 | 0.004 | |
| renameColDataColumns | 0.018 | 0.000 | 0.019 | |
| renameColumns | 0.001 | 0.000 | 0.001 | |
| sampleClinicalModel | 0.005 | 0.000 | 0.005 | |
| sampleCohortList | 0.018 | 0.004 | 0.022 | |
| sampleICGCmicro | 0.007 | 0.000 | 0.006 | |
| samplePCOSPmodel | 0.007 | 0.000 | 0.007 | |
| samplePCOSPpredList | 0.027 | 0.000 | 0.027 | |
| samplePCSIsurvExp | 0.006 | 0.000 | 0.006 | |
| sampleRGAmodel | 0.006 | 0.000 | 0.007 | |
| sampleRLSmodel | 0.007 | 0.000 | 0.007 | |
| sampleTrainedPCOSPmodel | 0.006 | 0.000 | 0.006 | |
| sampleValPCOSPmodel | 0.029 | 0.000 | 0.029 | |
| show-S4Model-method | 0.037 | 0.011 | 0.047 | |
| subset-CohortList-method | 0.149 | 0.004 | 0.153 | |
| trainData-set | 0.015 | 0.000 | 0.015 | |
| trainData | 0.007 | 0.000 | 0.008 | |
| trainModel-ClinicalModel-method | 0.048 | 0.000 | 0.048 | |
| trainModel-PCOSP-method | 0.949 | 0.124 | 1.073 | |
| trainModel-RGAModel-method | 1.073 | 0.003 | 1.076 | |
| trainModel-RLSModel-method | 1.101 | 0.032 | 1.133 | |
| trainModel | 1.084 | 0.008 | 1.092 | |
| validateModel-ClinicalModel-CohortList-method | 0.239 | 0.000 | 0.239 | |
| validateModel-ClinicalModel-SurvivalExperiment-method | 0.667 | 0.012 | 0.679 | |
| validateModel-GeneFuModel-CohortList-method | 1.187 | 0.032 | 1.218 | |
| validateModel-PCOSP_or_RLS_or_RGA-CohortList-method | 1.900 | 0.060 | 2.247 | |
| validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method | 2.239 | 0.068 | 3.100 | |
| validateModel | 0.151 | 0.016 | 0.168 | |
| validationData-SurvivalModel-method | 0.010 | 0.004 | 0.014 | |
| validationData-set-SurvivalModel-CohortList-method | 0.01 | 0.00 | 0.01 | |
| validationData-set | 0.011 | 0.004 | 0.030 | |
| validationData | 0.014 | 0.000 | 0.038 | |
| validationStats-SurvivalModel-method | 0.011 | 0.000 | 0.011 | |
| validationStats-set-SurvivalModel-data.frame-method | 0.009 | 0.004 | 0.029 | |
| validationStats-set | 0.015 | 0.000 | 0.031 | |
| validationStats | 0.013 | 0.000 | 0.029 | |