Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the DEGreport package: - Please 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 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 467/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DEGreport 1.28.0 (landing page) Lorena Pantano
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DEGreport |
Version: 1.28.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEGreport_1.28.0.tar.gz |
StartedAt: 2021-10-14 22:03:02 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:14:38 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 696.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DEGreport.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DEGreport_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEGreport.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'DEGreport/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'DEGreport' version '1.28.0' * 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 whether package 'DEGreport' can be installed ... OK * checking installed package size ... OK * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 binding for global variable 'gene' Undefined global functions or variables: .x FDR base_mean boxplot cluster comp compare count counts covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k keys lm log2FoldChange log2fc logFC 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed degResults 11.04 0.02 11.07 degComps 10.05 0.11 10.16 significants 9.48 0.00 9.48 degQC 9.16 0.03 9.18 degPlot 8.83 0.05 8.88 degPlotWide 8.31 0.03 8.35 degMV 7.87 0.06 7.94 DEGSet 7.25 0.51 7.77 degVar 7.75 0.00 7.75 degVB 7.69 0.01 7.70 degSummary 7.60 0.06 7.66 degMB 7.27 0.05 7.31 degMean 7.05 0.05 7.10 degDefault 5.67 0.00 5.67 degMA 5.36 0.00 5.36 degColors 5.03 0.10 5.14 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed degComps 12.91 0.00 12.91 degResults 12.06 0.03 12.09 degPlot 11.52 0.05 11.69 degMV 10.85 0.10 11.01 significants 9.77 0.06 9.83 degMean 9.48 0.12 10.21 degMB 8.99 0.05 9.08 degPlotWide 8.89 0.06 8.95 DEGSet 8.78 0.13 8.91 degQC 8.73 0.02 8.75 degVar 8.45 0.02 8.47 degVB 8.01 0.00 8.01 degSummary 7.72 0.06 7.78 degMA 6.75 0.06 7.00 degDefault 6.72 0.01 6.76 degColors 6.06 0.04 6.11 degVolcano 5.81 0.03 5.94 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DEGreport.Rcheck/00check.log' for details.
DEGreport.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DEGreport_1.28.0.tar.gz && rm -rf DEGreport.buildbin-libdir && mkdir DEGreport.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEGreport.buildbin-libdir DEGreport_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DEGreport_1.28.0.zip && rm DEGreport_1.28.0.tar.gz DEGreport_1.28.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 18.1M 0 152k 0 0 520k 0 0:00:35 --:--:-- 0:00:35 520k 8 18.1M 8 1597k 0 0 1232k 0 0:00:15 0:00:01 0:00:14 1231k 19 18.1M 19 3691k 0 0 1617k 0 0:00:11 0:00:02 0:00:09 1616k 35 18.1M 35 6602k 0 0 2018k 0 0:00:09 0:00:03 0:00:06 2019k 55 18.1M 55 10.0M 0 0 2413k 0 0:00:07 0:00:04 0:00:03 2413k 80 18.1M 80 14.5M 0 0 2821k 0 0:00:06 0:00:05 0:00:01 2956k 100 18.1M 100 18.1M 0 0 3120k 0 0:00:05 0:00:05 --:--:-- 3648k install for i386 * installing *source* package 'DEGreport' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'DEGreport' finding HTML links ... done DEGSet html DEGreport-deprecated html createReport html deg html degCheckFactors html degColors html degComps html degCorCov html degCovariates html degDefault html degFilter html degMA html finding level-2 HTML links ... done degMB html degMDS html degMV html degMean html degMerge html degObj html degPCA html degPatterns html degPlot html degPlotCluster html degPlotWide html degQC html degResults html degSignature html degSummary html degVB html degVar html degVolcano html geneInfo html geom_cor html humanGender html significants html ** 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 install for x64 * installing *source* package 'DEGreport' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'DEGreport' as DEGreport_1.28.0.zip * DONE (DEGreport) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'DEGreport' successfully unpacked and MD5 sums checked
DEGreport.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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, 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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") [ FAIL 0 | WARN 20 | SKIP 0 | PASS 64 ] > > proc.time() user system elapsed 47.21 2.14 51.68 |
DEGreport.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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, 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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") [ FAIL 0 | WARN 22 | SKIP 0 | PASS 64 ] > > proc.time() user system elapsed 49.98 0.84 50.81 |
DEGreport.Rcheck/examples_i386/DEGreport-Ex.timings
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DEGreport.Rcheck/examples_x64/DEGreport-Ex.timings
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