Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ROntoTools package: - Please 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 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 1620/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ROntoTools 2.20.0 (landing page) Calin Voichita
| 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: ROntoTools |
Version: 2.20.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ROntoTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ROntoTools_2.20.0.tar.gz |
StartedAt: 2021-10-15 04:47:19 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 04:51:38 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 259.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ROntoTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ROntoTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ROntoTools_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ROntoTools.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 'ROntoTools/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ROntoTools' version '2.20.0' * 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 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 ... 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 ... 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 * 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 ... 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 ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in documentation object 'summary.pDisRes': 'summary.pDisRes' S3 methods shown with full name in documentation object 'summary.peRes': '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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.peRes-methods 7.69 0.05 7.73 peNodeRenderInfo 6.83 0.03 6.86 peEdgeRenderInfo 6.05 0.07 6.11 summary.peRes 5.93 0.05 5.99 plot.pePathway-methods 5.67 0.04 5.72 pe 5.40 0.01 5.42 pDis 5.14 0.13 5.27 summary.pDisRes 5.18 0.01 5.19 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.peRes-methods 8.83 0.01 8.85 pDis 7.64 0.08 7.74 peNodeRenderInfo 7.17 0.00 7.17 peEdgeRenderInfo 6.66 0.03 6.69 pe 6.54 0.00 6.54 summary.peRes 6.44 0.06 6.50 plot.pePathway-methods 6.25 0.03 6.28 summary.pDisRes 6.22 0.02 6.24 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ROntoTools.Rcheck/00check.log' for details.
ROntoTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ROntoTools_2.20.0.tar.gz && rm -rf ROntoTools.buildbin-libdir && mkdir ROntoTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ROntoTools.buildbin-libdir ROntoTools_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ROntoTools_2.20.0.zip && rm ROntoTools_2.20.0.tar.gz ROntoTools_2.20.0.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 35 1149k 35 403k 0 0 1202k 0 --:--:-- --:--:-- --:--:-- 1203k 100 1149k 100 1149k 0 0 1870k 0 --:--:-- --:--:-- --:--:-- 1868k install for i386 * installing *source* package 'ROntoTools' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ROntoTools' finding HTML links ... done KEGGpathway2Graph html Summary-pDisRes-method html Summary-peRes-method html alpha1MR html alphaMLG html compute.fisher html compute.normalInv html keggPathwayGraphs html finding level-2 HTML links ... done keggPathwayNames html nodeWeights html pDis html pDisPathway-class html pDisRes-class html pe html peEdgeRenderInfo html peNodeRenderInfo html pePathway-class html peRes-class html plot.pePathway-methods html plot.peRes-methods html setEdgeWeights html setNodeWeights html subGraphByNodeType html summary.pDisRes html summary.peRes 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 'ROntoTools' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ROntoTools' as ROntoTools_2.20.0.zip * DONE (ROntoTools) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'ROntoTools' successfully unpacked and MD5 sums checked
ROntoTools.Rcheck/tests_i386/runTests.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. > BiocGenerics:::testPackage("ROntoTools") 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 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: '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 -- Fri Oct 15 04:51:12 2021 *********************************************** 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 12.75 0.29 13.07 |
ROntoTools.Rcheck/tests_x64/runTests.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. > BiocGenerics:::testPackage("ROntoTools") 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 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: '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. Performing pathway analysis... | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 19% | |============== | 20% | |=============== | 21% | |================ | 22% | |================ | 23% | |================= | 24% | |================= | 25% | |================== | 26% | |=================== | 27% | |=================== | 28% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 32% | |======================= | 33% | |======================= | 34% | |======================== | 34% | |======================== | 35% | 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94% | |================================================================== | 95% | |=================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100%Analysis completed in 4.609369 secs. RUNIT TEST PROTOCOL -- Fri Oct 15 04:51:28 2021 *********************************************** 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 15.09 0.32 15.48 |
ROntoTools.Rcheck/examples_i386/ROntoTools-Ex.timings
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ROntoTools.Rcheck/examples_x64/ROntoTools-Ex.timings
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