Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:57:57 -0400 (Wed, 17 Oct 2018).
Package 344/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DaMiRseq 1.4.2 Mattia Chiesa
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: DaMiRseq |
Version: 1.4.2 |
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_1.4.2.tar.gz |
StartedAt: 2018-10-16 20:47:40 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 20:54:38 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 418.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DaMiRseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.4.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DaMiRseq.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.2’ * 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 ‘DaMiRseq’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 5.5Mb * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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.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 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’ Undefined global functions or variables: Accuracy Classifiers MCC Sensitivity Specificity X1 X2 colSds * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.7-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/3.5/Resources/library’ * installing *source* package ‘DaMiRseq’ ... ** 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 ‘DaMiRseq.Rnw’ using ‘UTF-8’ ** testing if installed package can be loaded * DONE (DaMiRseq)
DaMiRseq.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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: 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, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid 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")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply 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. 15 Genes have been discarded for classification 985 Genes remained. All the genes have been discarded!!! th.VIP argument is too high. Please choose a lower level of th.VIPPlease wait. This operation will take about 21 seconds (i.e. about 0 minutes).Your dataset has: 100 Features; 11 Samples, divided in: 5 A 6 B 3 variables: a b class ; 'class' included. Your dataset has: 100 Features; 11 Samples, divided in: 5 A 6 B 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══ testthat results ═══════════════════════════════════════════════════════════ OK: 294 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 37.336 1.687 37.873
DaMiRseq.Rcheck/DaMiRseq-Ex.timings
name | user | system | elapsed | |
DaMiR.Allplot | 2.734 | 0.075 | 2.824 | |
DaMiR.Clustplot | 0.388 | 0.009 | 0.399 | |
DaMiR.EnsembleLearning | 0.007 | 0.004 | 0.011 | |
DaMiR.EnsembleLearning2cl | 0.006 | 0.003 | 0.010 | |
DaMiR.EnsembleLearningNcl | 0.006 | 0.003 | 0.010 | |
DaMiR.FBest | 0.019 | 0.004 | 0.024 | |
DaMiR.FReduct | 0.021 | 0.003 | 0.024 | |
DaMiR.FSelect | 0.661 | 0.025 | 0.688 | |
DaMiR.FSort | 0.641 | 0.021 | 0.671 | |
DaMiR.MDSplot | 0.346 | 0.005 | 0.350 | |
DaMiR.SV | 0.839 | 0.038 | 0.883 | |
DaMiR.SVadjust | 0.176 | 0.012 | 0.188 | |
DaMiR.corrplot | 0.025 | 0.003 | 0.028 | |
DaMiR.goldenDice | 0.003 | 0.000 | 0.004 | |
DaMiR.makeSE | 0.090 | 0.001 | 0.091 | |
DaMiR.normalization | 1.456 | 0.038 | 1.503 | |
DaMiR.sampleFilt | 0.991 | 0.017 | 1.012 | |
DaMiR.transpose | 0.076 | 0.014 | 0.091 | |