Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -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 NetSAM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NetSAM.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 1339/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NetSAM 1.39.0 (landing page) Zhiao Shi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: NetSAM |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NetSAM_1.39.0.tar.gz |
StartedAt: 2023-02-28 09:49:40 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 10:19:16 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1775.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: NetSAM.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NetSAM_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NetSAM.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 ‘NetSAM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NetSAM’ version ‘1.39.0’ * 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 ‘NetSAM’ 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 ... OK * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘NetSAM-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: mapToSymbol > ### Title: Map other ids to gene symbols > ### Aliases: mapToSymbol > ### Keywords: methods > > ### ** Examples > > > ###transform ids from a gene list to gene symbols### > geneListDir <- system.file("extdata","exampleGeneList.txt",package="NetSAM") > geneList <- read.table(geneListDir,header=FALSE,sep="\t",stringsAsFactors=FALSE) > geneList <- as.vector(as.matrix(geneList)) > geneList_symbol <- mapToSymbol(inputData=geneList, organism="hsapiens", inputType="genelist",idType="affy_hg_u133_plus_2") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" > > ###transform ids in the input network to gene symbols### > inputNetwork <- system.file("extdata","exampleNetwork_nonsymbol.net",package="NetSAM") > network_symbol <- mapToSymbol(inputData=inputNetwork,organism="hsapiens",inputType="network",idType="entrezgene_id",edgeType="unweighted") Transforming the ids in the input network to gene symbols... Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" > > ###transform ids in the input matrix to gene symbols### > inputMatDir <- system.file("extdata","exampleExpressionData_nonsymbol.cct",package="NetSAM") > matrix_symbol <- mapToSymbol(inputData=inputMatDir,organism="hsapiens",inputType="matrix",idType="affy_hg_u133_plus_2",collapse_mode="maxSD") Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Error in .GeneToSymbol(inputId, organism, idType, verbose) : The function can not connect to Biomart. Please try again! Calls: mapToSymbol -> .MatToSymbol -> .GeneToSymbol Execution halted * 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 ... ‘NetSAM.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/NetSAM.Rcheck/00check.log’ for details.
NetSAM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NetSAM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘NetSAM’ ... ** using staged installation ** R ** data ** 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 (NetSAM)
NetSAM.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("NetSAM") Attaching package: 'igraph' The following object is masked from 'package:seriation': permute The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'fastcluster' The following object is masked from 'package:stats': hclust Attaching package: 'WGCNA' The following object is masked from 'package:stats': cor ****************************************** * Welcome to NetSAM ! * ****************************************** Allowing parallel execution with up to 31 working processes. Identifying the hierarchical modules of the network... Starting to analysis connected component 1! Evaluating networks in Level 1 ... Network modularity: 0.5512183 Evaluating networks in Level 2 ... Modularity of network 1: 0.2083333 Modularity of network 2: 0.2915519 Modularity of network 3: 0.377551 Modularity of network 4: 0.4114896 Modularity of network 5: 0.3669114 Modularity of network 6: 0.4228597 Modularity of network 7: 0.25 Modularity of network 8: 0.1985731 Modularity of network 9: 0.21875 Modularity of network 10: 0.07986111 Modularity of network 11: 0 Evaluating networks in Level 3 ... Modularity of network 1: 0 Modularity of network 2: 0.2040816 Modularity of network 3: 0.1417769 Modularity of network 4: 0.3047337 Modularity of network 5: 0.3584807 Modularity of network 6: 0.1725207 Modularity of network 7: 0.1982249 Modularity of network 8: 0 Modularity of network 9: 0 Modularity of network 10: 0.1942149 Modularity of network 11: 0.2904 Modularity of network 12: 0.2366864 Modularity of network 13: 0.3010204 Modularity of network 14: 0.02664399 Modularity of network 15: 0.1938776 Modularity of network 16: 0.1064815 Modularity of network 17: 0.21875 Evaluating networks in Level 4 ... Modularity of network 1: 0.03061224 Modularity of network 2: 0.1577778 Modularity of network 3: 0.1342593 Modularity of network 4: 0.08 Modularity of network 5: 0.2167969 Modularity of network 6: 0.21875 Modularity of network 7: 2.379049e-17 Modularity of network 8: 0 Modularity of network 9: 0.08 Evaluating networks in Level 5 ... Modularity of network 1: 0 Reordering the genes in the one dimentional layout... NetSAM identified 39 modules in 5 levels! Processing completed! RUNIT TEST PROTOCOL -- Tue Feb 28 10:19:04 2023 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : NetSAM RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 133.658 1.036 137.725
NetSAM.Rcheck/NetSAM-Ex.timings
name | user | system | elapsed | |
GOAssociation | 96.748 | 2.268 | 99.022 | |
MatNet | 47.155 | 0.841 | 47.999 | |
MatSAM | 833.603 | 5.336 | 849.856 | |
NetAnalyzer | 0.184 | 0.008 | 0.198 | |
NetSAM | 127.163 | 0.550 | 130.899 | |
consensusNet | 0.577 | 0.016 | 254.259 | |
featureAssociation | 17.526 | 0.316 | 18.116 | |