Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:32 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 1.40.0 (landing page) Lorena Pantano
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the DEGreport package: - 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: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEGreport_1.40.0.tar.gz |
StartedAt: 2024-05-06 20:59:32 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 21:01:21 -0400 (Mon, 06 May 2024) |
EllapsedTime: 109.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEGreport.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEGreport_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/DEGreport.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.40.0’ * 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 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 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 .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’ degPatterns: no visible global function definition for ‘color_branches’ degPatterns: no visible global function definition for ‘set’ 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,list : <anonymous>: no visible global function definition for ‘matches’ significants,TopTags: no visible binding for global variable ‘FDR’ significants,TopTags: no visible binding for global variable ‘logFC’ Undefined global functions or variables: .x base_mean boxplot cluster color_branches comp compare comparison count counts covar cutoff desc enrichGO fdr FDR fdrtool gene genes itemConsensus k keys lm log2fc log2FoldChange logFC matches max_sd min_median p.value pvalue r ratios rowMedians score set 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 * 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 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-3.19-bioc-mac-arm64/meat/DEGreport.Rcheck/00check.log’ for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEGreport ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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': expand.grid, I, 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 3.416 0.149 3.562
DEGreport.Rcheck/DEGreport-Ex.timings
name | user | system | elapsed | |
DEGSet | 1.544 | 0.027 | 1.572 | |
degCheckFactors | 0.370 | 0.016 | 0.386 | |
degColors | 1.964 | 0.045 | 2.018 | |
degComps | 1.648 | 0.010 | 1.658 | |
degCorCov | 0.230 | 0.005 | 0.236 | |
degCovariates | 0.585 | 0.008 | 0.595 | |
degDefault | 1.176 | 0.010 | 1.187 | |
degFilter | 0.125 | 0.005 | 0.130 | |
degMA | 0.861 | 0.009 | 0.870 | |
degMB | 1.255 | 0.010 | 1.265 | |
degMDS | 0.233 | 0.006 | 0.239 | |
degMV | 1.308 | 0.033 | 1.342 | |
degMean | 1.305 | 0.011 | 1.317 | |
degObj | 0.121 | 0.005 | 0.126 | |
degPCA | 0.234 | 0.005 | 0.239 | |
degPatterns | 0.547 | 0.009 | 0.556 | |
degPlot | 1.879 | 0.012 | 1.891 | |
degPlotCluster | 0.613 | 0.009 | 0.623 | |
degPlotWide | 1.303 | 0.015 | 1.319 | |
degQC | 1.514 | 0.019 | 1.534 | |
degResults | 2.368 | 0.016 | 2.384 | |
degSignature | 0.203 | 0.003 | 0.206 | |
degSummary | 1.300 | 0.013 | 1.314 | |
degVB | 1.239 | 0.013 | 1.257 | |
degVar | 1.242 | 0.012 | 1.254 | |
degVolcano | 0.629 | 0.006 | 0.636 | |
geom_cor | 0.179 | 0.007 | 0.185 | |
significants | 1.381 | 0.008 | 1.391 | |