Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:39 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 |
Package 534/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEGreport 1.40.1 (landing page) Lorena Pantano
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the DEGreport package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEGreport.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: DEGreport |
Version: 1.40.1 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEGreport_1.40.1.tar.gz |
StartedAt: 2024-07-07 22:23:53 -0400 (Sun, 07 Jul 2024) |
EndedAt: 2024-07-07 22:29:24 -0400 (Sun, 07 Jul 2024) |
EllapsedTime: 330.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEGreport.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DEGreport_1.40.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DEGreport.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.40.1’ * 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 License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... NOTE ':::' call which should be '::': ‘dendextend:::cutree’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .benckmark_cutoff: no visible binding for global variable ‘cutoff’ .benckmark_cutoff: no visible binding for global variable ‘cluster’ .convertIDs: no visible global function definition for ‘keys’ .correct_fdr: no visible global function definition for ‘fdrtool’ .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’ .model: no visible global function definition for ‘lm’ .plot_raw: no visible binding for global variable ‘.x’ .plot_shrunken: no visible binding for global variable ‘.x’ .process: no visible binding for global variable ‘genes’ .process: no visible binding for global variable ‘cluster’ .reduce : <anonymous> : <anonymous>: no visible global function definition for ‘boxplot’ .reduce_covariates : <anonymous>: no visible binding for global variable ‘fdr’ .reduce_covariates : <anonymous>: no visible binding for global variable ‘compare’ .reduce_covariates : <anonymous>: no visible binding for global variable ‘r’ .reduce_covariates : <anonymous>: no visible binding for global variable ‘p.value’ .run_cluster_profiler: no visible global function definition for ‘enrichGO’ .run_cluster_profiler: no visible global function definition for ‘simplify’ .select_concensus_genes: no visible global function definition for ‘desc’ .select_concensus_genes: no visible binding for global variable ‘score’ .select_concensus_genes: no visible binding for global variable ‘k’ .select_concensus_genes: no visible binding for global variable ‘itemConsensus’ .summarise_res: no visible global function definition for ‘matches’ .summarise_res: no visible binding for global variable ‘comparison’ .summarise_res: no visible binding for global variable ‘gene’ .summarise_res: no visible binding for global variable ‘value_fdr’ .summarise_res: no visible binding for global variable ‘value_fc’ .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’ degCovariates: no visible binding for global variable ‘x’ degCovariates: no visible binding for global variable ‘y’ degCovariates: no visible binding for global variable ‘xend’ degCovariates: no visible binding for global variable ‘yend’ degCovariates: no visible binding for global variable ‘pvalue’ degMA: no visible binding for global variable ‘base_mean’ degMA: no visible binding for global variable ‘log2fc’ 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’ degPlotCluster: no visible binding for global variable ‘genes’ degPlotCluster: no visible binding for global variable ‘cluster’ 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 global function definition for ‘matches’ Undefined global functions or variables: .x FDR base_mean boxplot cluster comp compare comparison count counts covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k keys lm log2FoldChange log2fc logFC matches max_sd min_median p.value pvalue r ratios rowMedians score simplify value_fc value_fdr x xend y yend Consider adding importFrom("graphics", "boxplot") importFrom("stats", "lm") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed degColors 6.485 0.120 6.606 degResults 6.436 0.071 6.509 degPlot 5.790 0.012 5.801 degComps 5.041 0.048 5.089 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/DEGreport.Rcheck/00check.log’ for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘DEGreport’ ... ** using staged installation ** 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 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 (DEGreport)
DEGreport.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 Attaching package: 'BiocGenerics' 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, 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, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb 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: 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 > library(DEGreport) > > # test_check("DEGreport") > > proc.time() user system elapsed 9.079 0.441 9.508
DEGreport.Rcheck/DEGreport-Ex.timings
name | user | system | elapsed | |
DEGSet | 4.311 | 0.164 | 4.474 | |
degCheckFactors | 0.865 | 0.020 | 0.885 | |
degColors | 6.485 | 0.120 | 6.606 | |
degComps | 5.041 | 0.048 | 5.089 | |
degCorCov | 0.623 | 0.024 | 0.646 | |
degCovariates | 1.785 | 0.028 | 1.814 | |
degDefault | 2.541 | 0.016 | 2.557 | |
degFilter | 0.286 | 0.016 | 0.302 | |
degMA | 2.582 | 0.060 | 2.641 | |
degMB | 4.015 | 0.036 | 4.052 | |
degMDS | 0.733 | 0.002 | 0.735 | |
degMV | 3.904 | 0.032 | 3.936 | |
degMean | 3.868 | 0.036 | 3.904 | |
degObj | 0.298 | 0.000 | 0.298 | |
degPCA | 0.638 | 0.004 | 0.642 | |
degPatterns | 1.588 | 0.064 | 1.652 | |
degPlot | 5.790 | 0.012 | 5.801 | |
degPlotCluster | 2.013 | 0.004 | 2.018 | |
degPlotWide | 3.852 | 0.020 | 3.872 | |
degQC | 4.856 | 0.040 | 4.897 | |
degResults | 6.436 | 0.071 | 6.509 | |
degSignature | 0.656 | 0.000 | 0.656 | |
degSummary | 4.249 | 0.048 | 4.298 | |
degVB | 4.071 | 0.024 | 4.095 | |
degVar | 4.258 | 0.020 | 4.278 | |
degVolcano | 1.994 | 0.008 | 2.001 | |
geom_cor | 0.514 | 0.016 | 0.530 | |
significants | 4.625 | 0.036 | 4.660 | |