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This page was generated on 2021-10-15 15:06:33 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the DaMiRseq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DaMiRseq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 441/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DaMiRseq 2.4.3 (landing page) Mattia Chiesa
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: DaMiRseq |
Version: 2.4.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DaMiRseq_2.4.3.tar.gz |
StartedAt: 2021-10-14 18:04:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:12:05 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 478.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DaMiRseq.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DaMiRseq_2.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DaMiRseq.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DaMiRseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DaMiRseq’ version ‘2.4.3’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DaMiRseq’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 6.0Mb * 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 DaMiR.Allplot: warning in pheatmap(sampleDistMatrix, clustering_distance_rows = mydist, clustering_distance_cols = mydist, col = colors, breaks = seque, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Clustplot: warning in pheatmap(count_data, clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale = "row", col = colors, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Allplot: no visible binding for global variable ‘X1’ DaMiR.Allplot: no visible binding for global variable ‘X2’ DaMiR.Allplot: no visible binding for global variable ‘value’ DaMiR.Allplot: no visible binding for global variable ‘variable’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘MCC’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Specificity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘Sensitivity’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘PPV’ DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘NPV’ DaMiR.EnsembleLearning2cl: no visible global function definition for ‘colSds’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Classifiers’ DaMiR.EnsembleLearningNcl: no visible binding for global variable ‘Accuracy’ DaMiR.EnsembleLearningNcl: no visible global function definition for ‘colSds’ DaMiR.MDSplot: no visible binding for global variable ‘X1’ DaMiR.MDSplot: no visible binding for global variable ‘X2’ DaMiR.ModelSelect: no visible binding for global variable ‘Accuracy’ DaMiR.ModelSelect: no visible binding for global variable ‘N.predictors’ DaMiR.ModelSelect: no visible binding for global variable ‘counts’ DaMiR.iTSadjust: no visible binding for global variable ‘value’ DaMiR.iTSadjust: no visible binding for global variable ‘variable’ DaMiR.iTSnorm: no visible binding for global variable ‘value’ DaMiR.iTSnorm: no visible binding for global variable ‘variable’ Undefined global functions or variables: Accuracy Classifiers MCC N.predictors NPV PPV Sensitivity Specificity X1 X2 colSds counts value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'DaMiR.normalization.Rd': ‘estimateDispersions’ 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 LazyData ... WARNING LazyData DB of 5.5 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed DaMiR.Allplot 6.26 0.267 6.528 * 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: 2 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/DaMiRseq.Rcheck/00check.log’ for details.
DaMiRseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DaMiRseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘DaMiRseq’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (DaMiRseq)
DaMiRseq.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(DaMiRseq) 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: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 Loading required package: ggplot2 > > test_check("DaMiRseq") 10 Predictors have been selected for classification 3 Predictors have been selected for classification 100 Highly correlated features have been discarded for classification. 0 Features remained. 100 Highly correlated features have been discarded for classification. 0 Features remained. Your dataset has: 100 Features; 11 Samples, divided in: 3 variables: a b class ; 'class' included. Your dataset has: 100 Features; 11 Samples, divided in: 3 variables: a b class ; 'class' included. 0 Features have been filtered out by espression. 100 Features remained. 0 'Hypervariant' Features have been filtered out. 100 Features remained. Performing Normalization by 'vst' with dispersion parameter: parametric 0 Samples have been excluded by averaged Sample-per-Sample correlation. 40 Samples remained. The number of SVs identified, which explain 95 % of Variance, is: 4 All the sv have been used to adjust the dataAll the sv have been used to adjust the data[ FAIL 0 | WARN 0 | SKIP 0 | PASS 106 ] > > proc.time() user system elapsed 30.052 1.381 30.349
DaMiRseq.Rcheck/DaMiRseq-Ex.timings
name | user | system | elapsed | |
DaMiR.Allplot | 6.260 | 0.267 | 6.528 | |
DaMiR.Clustplot | 0.276 | 0.011 | 0.288 | |
DaMiR.EnsL_Predict | 0.004 | 0.006 | 0.009 | |
DaMiR.EnsL_Test | 0.003 | 0.006 | 0.009 | |
DaMiR.EnsL_Train | 0.004 | 0.006 | 0.009 | |
DaMiR.EnsembleLearning | 0.003 | 0.006 | 0.009 | |
DaMiR.EnsembleLearning2cl | 0.004 | 0.006 | 0.009 | |
DaMiR.EnsembleLearningNcl | 0.002 | 0.003 | 0.005 | |
DaMiR.FBest | 0.015 | 0.006 | 0.021 | |
DaMiR.FReduct | 0.021 | 0.002 | 0.023 | |
DaMiR.FSelect | 0.675 | 0.029 | 0.704 | |
DaMiR.FSort | 0.817 | 0.031 | 0.849 | |
DaMiR.MDSplot | 0.280 | 0.006 | 0.286 | |
DaMiR.ModelSelect | 0 | 0 | 0 | |
DaMiR.SV | 0.673 | 0.024 | 0.696 | |
DaMiR.SVadjust | 1.022 | 0.019 | 1.041 | |
DaMiR.corrplot | 0.002 | 0.002 | 0.005 | |
DaMiR.goldenDice | 0.001 | 0.000 | 0.001 | |
DaMiR.iTSadjust | 0.002 | 0.001 | 0.003 | |
DaMiR.iTSnorm | 0.002 | 0.001 | 0.003 | |
DaMiR.makeSE | 0.068 | 0.002 | 0.070 | |
DaMiR.normalization | 3.361 | 0.067 | 3.428 | |
DaMiR.sampleFilt | 0.146 | 0.007 | 0.152 | |
DaMiR.transpose | 0.113 | 0.010 | 0.124 | |