Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:44 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 MetaboSignal package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaboSignal.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 1133/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetaboSignal 1.29.0 (landing page) Andrea Rodriguez-Martinez
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: MetaboSignal |
Version: 1.29.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MetaboSignal_1.29.0.tar.gz |
StartedAt: 2023-02-28 07:35:28 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 07:44:29 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 540.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetaboSignal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MetaboSignal.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MetaboSignal_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MetaboSignal.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MetaboSignal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaboSignal’ version ‘1.29.0’ * package encoding: UTF-8 * 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 ‘MetaboSignal’ 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 get_molecule_type: no visible binding for global variable 'regulatory_interactions' Undefined global functions or variables: regulatory_interactions * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘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 ... ‘MetaboSignal.Rmd’ using ‘UTF-8’... OK ‘MetaboSignal2.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/MetaboSignal.Rcheck/00check.log’ for details.
MetaboSignal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MetaboSignal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘MetaboSignal’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading snapshotDate(): 2023-02-14 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location snapshotDate(): 2023-02-14 ** testing if installed package can be loaded from final location snapshotDate(): 2023-02-14 ** testing if installed package keeps a record of temporary installation path * DONE (MetaboSignal)
MetaboSignal.Rcheck/tests/runTests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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("MetaboSignal") snapshotDate(): 2023-02-14 Note: some source_nodes or target_nodes were not mapped onto the network Calculating distances Building shortest path network Note that all source_nodes and target_nodes were successfully mapped onto the network Calculating distances Building shortest path network Note that all source_nodes and target_nodes were successfully mapped onto the network Calculating distances Building shortest path network Note that all source_nodes and target_nodes were successfully mapped onto the network Network features: Number of nodes:59 Number of edges:100 Network features: Number of nodes:59 Number of edges:100 RUNIT TEST PROTOCOL -- Tue Feb 28 07:43:06 2023 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : MetaboSignal RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 Warning messages: 1: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 2: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 3: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 4: In betweenness(networkBW_i, gene, directed = TRUE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 5: In betweenness(network_i, all_nodes, directed = FALSE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 6: In betweenness(network_i, nodes, directed = FALSE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 7: In betweenness(network_i, nodes, directed = FALSE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 8: In betweenness(network_i, all_nodes, directed = FALSE, weights = NULL, : 'nobigint' is deprecated since igraph 1.3 and will be removed in igraph 1.4 > > proc.time() user system elapsed 22.553 1.382 26.824
MetaboSignal.Rcheck/MetaboSignal-Ex.timings
name | user | system | elapsed | |
MS2_mergeNetworks | 0.216 | 0.004 | 0.221 | |
MS2_ppiNetwork | 1.756 | 0.100 | 1.856 | |
MS_changeNames | 0.001 | 0.000 | 0.000 | |
MS_convertGene | 0.073 | 0.012 | 1.015 | |
MS_distances | 0.094 | 0.003 | 0.098 | |
MS_exportCytoscape | 0 | 0 | 0 | |
MS_findMappedNodes | 0.003 | 0.000 | 0.003 | |
MS_getPathIds | 0 | 0 | 0 | |
MS_keggFinder | 0.165 | 0.004 | 1.972 | |
MS_keggNetwork | 0 | 0 | 0 | |
MS_nodeBW | 0.025 | 0.007 | 0.033 | |
MS_reactionNetwork | 0 | 0 | 0 | |
MS_removeDrugs | 0.003 | 0.000 | 0.004 | |
MS_removeNode | 0.013 | 0.000 | 0.013 | |
MS_replaceNode | 0.008 | 0.003 | 0.012 | |
MS_shortestPaths | 0.018 | 0.005 | 0.022 | |
MS_shortestPathsNetwork | 0 | 0 | 0 | |
MS_tissueFilter | 0 | 0 | 0 | |
MS_topologyFilter | 0.221 | 0.004 | 0.225 | |