Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:26:17 -0400 (Wed, 17 Oct 2018).
Package 363/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DEGreport 1.16.0 Lorena Pantano
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: DEGreport |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEGreport_1.16.0.tar.gz |
StartedAt: 2018-10-15 23:43:54 -0400 (Mon, 15 Oct 2018) |
EndedAt: 2018-10-15 23:47:50 -0400 (Mon, 15 Oct 2018) |
EllapsedTime: 236.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEGreport.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DEGreport_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/DEGreport.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.16.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml 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 ‘DEGreport’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘knitr’ A package should be listed in only one of these fields. * 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 .convertIDs: no visible global function definition for ‘keys’ .generate_scatter_plot: no visible binding for global variable ‘compare’ .generate_scatter_plot: no visible binding for global variable ‘covar’ .get_counts: no visible global function definition for ‘counts’ .plotMA: no visible binding for global variable ‘base_mean’ .plotMA: no visible binding for global variable ‘log2fc’ .plot_raw: no visible binding for global variable ‘.x’ .plot_shrunken: no visible binding for global variable ‘.x’ .run_cluster_profiler: no visible global function definition for ‘enrichGO’ .run_cluster_profiler: no visible global function definition for ‘simplify’ .table_w_fc: no visible binding for global variable ‘comp’ .table_w_fc: no visible binding for global variable ‘log2FoldChange’ degCheckFactors: no visible binding for global variable ‘ratios’ degCorCov: no visible binding for global variable ‘compare’ degMV: no visible binding for global variable ‘min_median’ degMV: no visible binding for global variable ‘max_sd’ degPatterns: no visible global function definition for ‘rowMedians’ degPatterns: no visible binding for global variable ‘genes’ degPlotWide : <anonymous>: no visible binding for global variable ‘count’ significants,TopTags: no visible binding for global variable ‘FDR’ significants,TopTags: no visible binding for global variable ‘logFC’ significants,list : <anonymous>: no visible binding for global variable ‘gene’ Undefined global functions or variables: .x FDR base_mean comp compare count counts covar enrichGO gene genes keys log2FoldChange log2fc logFC max_sd min_median ratios rowMedians simplify * 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 Examples with CPU or elapsed time > 5s user system elapsed degResults 6.084 0.016 6.106 degPlot 5.272 0.004 5.279 * 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 ‘/home/biocbuild/bbs-3.7-bioc/meat/DEGreport.Rcheck/00check.log’ for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘DEGreport’ ... ** R ** data ** 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 * DONE (DEGreport)
DEGreport.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-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(edgeR) Loading required package: limma > library(DESeq2) Loading required package: S4Vectors 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 object is masked from 'package:limma': plotMA 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 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment 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 > library(DEGreport) Loading required package: quantreg Loading required package: SparseM Attaching package: 'SparseM' The following object is masked from 'package:base': backsolve > > test_check("DEGreport") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 56 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 21.284 0.376 21.674
DEGreport.Rcheck/DEGreport-Ex.timings
name | user | system | elapsed | |
DEGSet | 3.688 | 0.068 | 3.759 | |
degCheckFactors | 1.392 | 0.004 | 1.528 | |
degComps | 4.904 | 0.012 | 4.921 | |
degCorCov | 0.956 | 0.012 | 0.971 | |
degCovariates | 2.204 | 0.008 | 2.213 | |
degFilter | 0.304 | 0.000 | 0.306 | |
degMB | 2.928 | 0.000 | 2.928 | |
degMDS | 0.6 | 0.0 | 0.6 | |
degMV | 2.960 | 0.004 | 2.969 | |
degMean | 3.692 | 0.004 | 3.698 | |
degObj | 0.304 | 0.012 | 0.316 | |
degPCA | 0.648 | 0.000 | 0.650 | |
degPatterns | 1.016 | 0.000 | 1.017 | |
degPlot | 5.272 | 0.004 | 5.279 | |
degPlotWide | 2.748 | 0.000 | 2.749 | |
degQC | 4.360 | 0.008 | 4.371 | |
degResults | 6.084 | 0.016 | 6.106 | |
degSignature | 0.664 | 0.000 | 0.672 | |
degSummary | 2.444 | 0.024 | 2.472 | |
degVB | 3.104 | 0.012 | 3.119 | |
degVar | 3.124 | 0.000 | 3.127 | |
degVolcano | 1.876 | 0.000 | 1.876 | |
geom_cor | 0.508 | 0.000 | 0.507 | |
plotMA | 2.268 | 0.000 | 2.270 | |
significants | 4.360 | 0.000 | 4.365 | |