Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GraphPAC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphPAC.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 809/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GraphPAC 1.34.0 (landing page) Gregory Ryslik
| 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: GraphPAC |
Version: 1.34.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GraphPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GraphPAC_1.34.0.tar.gz |
StartedAt: 2021-10-15 00:05:20 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:08:04 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 164.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GraphPAC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GraphPAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GraphPAC_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GraphPAC.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 'GraphPAC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GraphPAC' version '1.34.0' * 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 whether package 'GraphPAC' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE Packages in Depends field not imported from: 'RMallow' 'TSP' 'iPAC' 'igraph' 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 Find.TSP.Path: no visible global function definition for 'dist' Find.TSP.Path: no visible global function definition for 'ATSP' Find.TSP.Path: no visible global function definition for 'insert_dummy' Find.TSP.Path: no visible global function definition for 'solve_TSP' Find.TSP.Path: no visible global function definition for 'cut_tour' GraphClust: no visible global function definition for 'graph.empty' GraphClust: no visible global function definition for 'V' GraphClust: no visible global function definition for 'V<-' GraphClust: no visible global function definition for 'add.edges' GraphClust: no visible global function definition for 'nmc' Plot.Protein: no visible global function definition for 'heat.colors' Plot.Protein: no visible global function definition for 'vcount' Plot.Protein: no visible global function definition for 'gray' Plot.Protein: no visible global function definition for 'topo.colors' Plot.Protein: no visible global function definition for 'cm.colors' Plot.Protein: no visible global function definition for 'V' Plot.Protein: no visible global function definition for 'tkplot' Plot.Protein: no visible binding for global variable 'layout.circle' Undefined global functions or variables: ATSP V V<- add.edges cm.colors cut_tour dist graph.empty gray heat.colors insert_dummy layout.circle nmc solve_TSP tkplot topo.colors vcount Consider adding importFrom("grDevices", "cm.colors", "gray", "heat.colors", "topo.colors") importFrom("stats", "dist") 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Find.TSP.Path 4.45 0.77 5.83 * 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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GraphPAC.Rcheck/00check.log' for details.
GraphPAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GraphPAC_1.34.0.tar.gz && rm -rf GraphPAC.buildbin-libdir && mkdir GraphPAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GraphPAC.buildbin-libdir GraphPAC_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GraphPAC_1.34.0.zip && rm GraphPAC_1.34.0.tar.gz GraphPAC_1.34.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 223k 100 223k 0 0 840k 0 --:--:-- --:--:-- --:--:-- 845k install for i386 * installing *source* package 'GraphPAC' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GraphPAC' finding HTML links ... done Find.TSP.Path html GraphClust html Plot.Protein html graphPAC-package 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 'GraphPAC' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GraphPAC' as GraphPAC_1.34.0.zip * DONE (GraphPAC) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'GraphPAC' successfully unpacked and MD5 sums checked
GraphPAC.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("GraphPAC") gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith 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:gdata': combine 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:gdata': first, first<- The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:gdata': trim The following object is masked from 'package:grDevices': windows Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'igraph' The following object is masked from 'package:Biostrings': union The following object is masked from 'package:XVector': path The following object is masked from 'package:IRanges': union The following object is masked from 'package:S4Vectors': union The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'combinat' The following object is masked from 'package:utils': combn Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters. RUNIT TEST PROTOCOL -- Fri Oct 15 00:07:47 2021 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : GraphPAC RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 4.76 0.37 6.23 |
GraphPAC.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("GraphPAC") gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith 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:gdata': combine 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:gdata': first, first<- The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:gdata': trim The following object is masked from 'package:grDevices': windows Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'igraph' The following object is masked from 'package:Biostrings': union The following object is masked from 'package:XVector': path The following object is masked from 'package:IRanges': union The following object is masked from 'package:S4Vectors': union The following objects are masked from 'package:BiocGenerics': normalize, path, union The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'combinat' The following object is masked from 'package:utils': combn Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters. RUNIT TEST PROTOCOL -- Fri Oct 15 00:07:55 2021 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : GraphPAC RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 5.62 0.25 6.96 |
GraphPAC.Rcheck/examples_i386/GraphPAC-Ex.timings
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GraphPAC.Rcheck/examples_x64/GraphPAC-Ex.timings
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