Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 904/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GraphPAC 1.48.0 (landing page) Gregory Ryslik
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the GraphPAC package: - 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 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: GraphPAC |
Version: 1.48.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GraphPAC_1.48.0.tar.gz |
StartedAt: 2024-11-20 04:02:14 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 04:04:22 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 127.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GraphPAC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GraphPAC_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphPAC.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GraphPAC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GraphPAC’ version ‘1.48.0’ * 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 ‘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 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... NOTE checkRd: (-1) Plot.Protein.Rd:33: Lost braces 33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help. | ^ checkRd: (-1) Plot.Protein.Rd:33: Lost braces 33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help. | ^ * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Find.TSP.Path 3.456 0.15 5.827 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GraphPAC.Rcheck/00check.log’ for details.
GraphPAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GraphPAC ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘GraphPAC’ ... ** 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 (GraphPAC)
GraphPAC.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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") 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'pwalign' The following objects are masked from 'package:Biostrings': PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned, alignedPattern, alignedSubject, compareStrings, deletion, errorSubstitutionMatrices, indel, insertion, mismatchSummary, mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix, pairwiseAlignment, pid, qualitySubstitutionMatrices, stringDist, unaligned, writePairwiseAlignments 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 -- Wed Nov 20 04:03:13 2024 *********************************************** 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 3.541 0.685 4.659
GraphPAC.Rcheck/GraphPAC-Ex.timings
name | user | system | elapsed | |
Find.TSP.Path | 3.456 | 0.150 | 5.827 | |
GraphClust | 0 | 0 | 0 | |
Plot.Protein | 0 | 0 | 0 | |
graphPAC-package | 0 | 0 | 0 | |