Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:38 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the ReportingTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReportingTools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1579/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReportingTools 2.34.0 (landing page) Jason A. Hackney
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: ReportingTools |
Version: 2.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReportingTools_2.34.0.tar.gz |
StartedAt: 2022-04-12 17:29:38 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 17:43:38 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 839.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReportingTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReportingTools_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReportingTools.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ReportingTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReportingTools’ version ‘2.34.0’ * 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 ‘ReportingTools’ 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 * 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 .GeneSetCollection.to.data.frame: no visible binding for global variable 'description' .GeneSetCollection.to.html: no visible binding for global variable 'description' .GeneSetCollection.to.html2: no visible binding for global variable 'description' .PFAMhyperG.to.html: no visible binding for global variable 'keytype' .PFAMhyperG.to.html: no visible binding for global variable 'columns' .make.gene.plots: no visible global function definition for 'exprs' .marrayLM.to.data.frame: no visible global function definition for 'featureNames' .marrayLM.to.data.frame: no visible global function definition for 'fData' .marrayLM.to.html: no visible global function definition for 'featureNames' .marrayLM.to.html: no visible global function definition for 'fData' check.ids: no visible binding for global variable 'org.Hs.eg.db' check.ids: no visible global function definition for 'keys' custHeaderPanel : <anonymous>: no visible binding for global variable 'tags' custHeaderPanel : <anonymous>: no visible global function definition for 'HTML' custHeaderPanel: no visible global function definition for 'tagList' custHeaderPanel: no visible global function definition for 'tag' custHeaderPanel: no visible global function definition for 'div' custHeaderPanel: no visible global function definition for 'h1' publish,trellis-HTMLReport: no visible binding for global variable 'htmlRep' toReportDF,DESeqDataSet: no visible global function definition for 'mcols' Undefined global functions or variables: HTML columns description div exprs fData featureNames h1 htmlRep keys keytype mcols org.Hs.eg.db tag tagList tags * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/ReportingTools.Rcheck/00check.log’ for details.
ReportingTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReportingTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ReportingTools’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio" ** 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 (ReportingTools)
ReportingTools.Rcheck/tests/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > require("ReportingTools") || stop("unable to load ReportingTools") Loading required package: ReportingTools Loading required package: knitr [1] TRUE > BiocGenerics:::testPackage("ReportingTools") Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: org.Hs.eg.db Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians 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 The following object is masked from 'package:Biobase': rowMedians estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Loading required package: annotate Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode Loading required package: Category Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns <script language="JavaScript" src="jslib/jquery-1.8.0.min.js"></script> <script language="JavaScript" src="jslib/jquery.dataTables-1.9.3.js"></script> <script language="JavaScript" src="jslib/jquery.dataTables.columnFilter.js"></script> <script language="JavaScript" src="jslib/jquery.dataTables.plugins.js"></script> <script language="JavaScript" src="jslib/jquery.dataTables.reprise.js"></script> <script language="JavaScript" src="jslib/bootstrap.js"></script> <link rel="stylesheet" type="text/css" href="csslib/bootstrap.css" /> <link rel="stylesheet" type="text/css" href="csslib/reprise.table.bootstrap.css" /> processing file: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/ReportingTools/examples/testRmd.Rmd ordinary text without R code label: unnamed-chunk-1 (with options) List of 2 $ message: logi FALSE $ output : chr "hide" ordinary text without R code label: unnamed-chunk-2 (with options) List of 1 $ results: chr "asis" ordinary text without R code label: unnamed-chunk-3 (with options) List of 1 $ results: chr "asis" ordinary text without R code label: unnamed-chunk-4 (with options) List of 1 $ results: chr "asis" output file: testRmd.md Created file named 'testDataPackage/testPkg/man/my.df2.Rd'. Edit the file and move it to the appropriate directory. RUNIT TEST PROTOCOL -- Tue Apr 12 17:43:29 2022 *********************************************** Number of test functions: 45 Number of errors: 0 Number of failures: 0 1 Test Suite : ReportingTools RUnit Tests - 45 test functions, 0 errors, 0 failures Number of test functions: 45 Number of errors: 0 Number of failures: 0 Warning messages: 1: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 2: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors > > proc.time() user system elapsed 319.878 26.650 348.701
ReportingTools.Rcheck/ReportingTools-Ex.timings
name | user | system | elapsed | |
BaseReportType-class | 0.001 | 0.001 | 0.002 | |
CSVFile-class | 0.000 | 0.000 | 0.001 | |
CSVFile | 0.008 | 0.002 | 0.009 | |
DataPackage-class | 0.011 | 0.004 | 0.015 | |
DataPackage | 0.005 | 0.003 | 0.009 | |
HTMLReport | 0.030 | 0.019 | 0.051 | |
HTMLReportRef-class | 0.001 | 0.001 | 0.001 | |
Link | 0.008 | 0.001 | 0.010 | |
ReportHandlers-class | 0.001 | 0.000 | 0.001 | |
finish-methods | 0 | 0 | 0 | |
mockRnaSeqData | 0.019 | 0.001 | 0.021 | |
publish-methods | 0.000 | 0.000 | 0.001 | |
reporting.theme | 0.018 | 0.001 | 0.019 | |
reporting.theme.alternate | 0.022 | 0.002 | 0.023 | |
validConnection | 0.096 | 0.028 | 0.124 | |