Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1767/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ROntoTools 2.33.0 (landing page) Sorin Draghici
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the ROntoTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ROntoTools.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: ROntoTools |
Version: 2.33.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ROntoTools_2.33.0.tar.gz |
StartedAt: 2024-08-26 22:59:37 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 23:02:37 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 180.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ROntoTools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ROntoTools_2.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ROntoTools.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ROntoTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ROntoTools’ version ‘2.33.0’ * 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 ‘ROntoTools’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: action between the genes (as edgeWeights) and the relevance of each gene (as Cannot process chunk/lines: weights to be used as nodeWeights * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘ROntoTools’ for: ‘Summary’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rgraphviz’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE KEGGpathway2Graph: no visible global function definition for ‘is’ KEGGpathway2Graph: no visible global function definition for ‘new’ compute.B: no visible global function definition for ‘as’ compute.B_pDis: no visible global function definition for ‘as’ compute.normalInv: no visible global function definition for ‘pnorm’ compute.normalInv: no visible binding for global variable ‘qnorm’ compute.pORA: no visible global function definition for ‘phyper’ get.totalAccNorm: no visible global function definition for ‘sd’ get.totalPertNorm: no visible global function definition for ‘sd’ get.totalpDisNorm: no visible global function definition for ‘sd’ graph2ftM: no visible global function definition for ‘as’ keggPathwayGraphs: no visible global function definition for ‘txtProgressBar’ keggPathwayGraphs : <anonymous>: no visible global function definition for ‘new’ keggPathwayGraphs : <anonymous>: no visible global function definition for ‘setTxtProgressBar’ keggPathwayGraphs : <anonymous>: no visible global function definition for ‘getTxtProgressBar’ loadKEGGpathwayDataREST: no visible global function definition for ‘txtProgressBar’ loadKEGGpathwayDataREST : <anonymous>: no visible global function definition for ‘setTxtProgressBar’ loadKEGGpathwayDataREST : <anonymous>: no visible global function definition for ‘getTxtProgressBar’ pDis.boot: no visible global function definition for ‘new’ pDis.helper: no visible global function definition for ‘txtProgressBar’ pDis.helper : <anonymous>: no visible global function definition for ‘setTxtProgressBar’ pDis.helper : <anonymous>: no visible global function definition for ‘getTxtProgressBar’ pDis.helper: no visible global function definition for ‘new’ pe.boot: no visible global function definition for ‘new’ peEdgeRenderInfo: no visible global function definition for ‘removedEdges’ peNodeRenderInfo: no visible global function definition for ‘slot’ peNodeRenderInfo: no visible global function definition for ‘colorRampPalette’ pf.helper: no visible global function definition for ‘txtProgressBar’ pf.helper : <anonymous>: no visible global function definition for ‘setTxtProgressBar’ pf.helper : <anonymous>: no visible global function definition for ‘getTxtProgressBar’ pf.helper: no visible global function definition for ‘new’ subGraphByNodeType: no visible global function definition for ‘new’ summary.pDisRes : <anonymous>: no visible global function definition for ‘p.adjust’ summary.peRes : <anonymous>: no visible global function definition for ‘p.adjust’ plot,pePathway-character: no visible global function definition for ‘slot’ plot,pePathway-character: no visible global function definition for ‘abline’ plot,pePathway-character: no visible global function definition for ‘points’ plot,pePathway-character: no visible global function definition for ‘sd’ plot,pePathway-character: no visible global function definition for ‘density’ plot,peRes-character: no visible global function definition for ‘Summary’ plot,peRes-character: no visible global function definition for ‘chull’ plot,peRes-character: no visible global function definition for ‘polygon’ plot,peRes-character: no visible global function definition for ‘points’ plot,peRes-character: no visible global function definition for ‘text’ plot,peRes-character: no visible global function definition for ‘abline’ Undefined global functions or variables: Summary abline as chull colorRampPalette density getTxtProgressBar is new p.adjust phyper pnorm points polygon qnorm removedEdges sd setTxtProgressBar slot text txtProgressBar Consider adding importFrom("grDevices", "chull", "colorRampPalette") importFrom("graphics", "abline", "points", "polygon", "text") importFrom("methods", "Summary", "as", "is", "new", "slot") importFrom("stats", "density", "p.adjust", "phyper", "pnorm", "qnorm", "sd") importFrom("utils", "getTxtProgressBar", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'compute.fisher.Rd': compute.fisher Code: function(p, eps = 1e-24) Docs: function(p, eps = 1e-06) Mismatches in argument default values: Name: 'eps' Code: 1e-24 Docs: 1e-06 * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'summary.pDisRes.Rd': ‘summary.pDisRes’ S3 methods shown with full name in Rd file 'summary.peRes.Rd': ‘summary.peRes’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.peRes-methods 9.539 0.128 9.735 peNodeRenderInfo 7.869 0.120 8.038 peEdgeRenderInfo 7.792 0.117 7.953 summary.peRes 7.630 0.110 7.798 plot.pePathway-methods 7.227 0.103 7.364 pe 6.954 0.126 7.121 pDis 6.780 0.160 6.983 summary.pDisRes 6.471 0.103 6.621 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ROntoTools.Rcheck/00check.log’ for details.
ROntoTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ROntoTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ROntoTools’ ... ** using staged installation ** R ** 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 (ROntoTools)
ROntoTools.Rcheck/tests/runTests.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-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. > BiocGenerics:::testPackage("ROntoTools") 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, 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: 'KEGGgraph' The following object is masked from 'package:graphics': plot The following object is masked from 'package:base': plot Using cached pathway data. Database info: pathway KEGG Pathway Database path Release 73.0+/01-03, Jan 15 Kanehisa Laboratories 343,170 entries Default parameters detected. Using pre-parsed data. Using cached pathway data. Database info: pathway KEGG Pathway Database path Release 73.0+/01-03, Jan 15 Kanehisa Laboratories 343,170 entries Default parameters detected. Using pre-parsed data. Using cached pathway data. Database info: pathway KEGG Pathway Database path Release 73.0+/01-03, Jan 15 Kanehisa Laboratories 343,170 entries Default parameters detected. Using pre-parsed data. 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RUNIT TEST PROTOCOL -- Mon Aug 26 23:02:27 2024 *********************************************** Number of test functions: 6 Number of errors: 0 Number of failures: 0 1 Test Suite : ROntoTools RUnit Tests - 6 test functions, 0 errors, 0 failures Number of test functions: 6 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 14.564 0.535 15.169
ROntoTools.Rcheck/ROntoTools-Ex.timings
name | user | system | elapsed | |
alpha1MR | 0.016 | 0.002 | 0.019 | |
alphaMLG | 0.014 | 0.001 | 0.015 | |
compute.fisher | 0.000 | 0.000 | 0.001 | |
compute.normalInv | 0.001 | 0.000 | 0.001 | |
keggPathwayGraphs | 0.514 | 0.014 | 0.534 | |
keggPathwayNames | 0.299 | 0.009 | 0.309 | |
nodeWeights | 0.006 | 0.000 | 0.006 | |
pDis | 6.780 | 0.160 | 6.983 | |
pe | 6.954 | 0.126 | 7.121 | |
peEdgeRenderInfo | 7.792 | 0.117 | 7.953 | |
peNodeRenderInfo | 7.869 | 0.120 | 8.038 | |
plot.pePathway-methods | 7.227 | 0.103 | 7.364 | |
plot.peRes-methods | 9.539 | 0.128 | 9.735 | |
setEdgeWeights | 2.308 | 0.035 | 2.359 | |
setNodeWeights | 0.472 | 0.006 | 0.479 | |
summary.pDisRes | 6.471 | 0.103 | 6.621 | |
summary.peRes | 7.630 | 0.110 | 7.798 | |