Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:17 -0000 (Wed, 08 Feb 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" | 4164 |
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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 1337/2164 | 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: 2023-02-07 09:49:22 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 10:16:35 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 1632.4 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: consensusNet > ### Title: Construction of a consensus coexpression network > ### Aliases: consensusNet > ### Keywords: methods > > ### ** Examples > > inputMatDir <- system.file("extdata","exampleExpressionData.cct",package="NetSAM") > data <- read.table(inputMatDir, header=TRUE, row.names=1, stringsAsFactors=FALSE) > net <- consensusNet(data, organism="hsapiens",bootstrapNum=10, naPer=0.5, meanPer=0.8,varPer=0.8,method="rank_unsig",value=3/1000,pth=1e-6, nMatNet=2, nThreads=4) starting worker pid=3693495 on localhost:11443 at 10:12:57.026 starting worker pid=3693496 on localhost:11443 at 10:12:57.074 Creating random networks..... Loading required package: NetSAM Loading required package: seriation Loading required package: NetSAM Loading required package: seriation Loading required package: igraph Loading required package: igraph 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 Loading required package: tools Loading required package: WGCNA Loading required package: dynamicTreeCut Loading required package: fastcluster Attaching package: ‘igraph’ Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust 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 Loading required package: tools Loading required package: WGCNA Loading required package: dynamicTreeCut Loading required package: fastcluster Attaching package: ‘fastcluster’ The following object is masked from ‘package:stats’: hclust Attaching package: ‘WGCNA’ Attaching package: ‘WGCNA’ The following object is masked from ‘package:stats’: cor The following object is masked from ‘package:stats’: cor Loading required package: biomaRt Loading required package: biomaRt ****************************************** * Welcome to NetSAM ! * ****************************************** loaded NetSAM and set parent environment ****************************************** * Welcome to NetSAM ! * ****************************************** loaded NetSAM and set parent environment The input data contain 3899 ids and 90 samples. No missing values in the data. The input data contain 3899 ids and 90 samples. No missing values in the data. After removing ids based on parameters 'naPer', 'meanPer' and 'varPer', 2495 ids are remained! After removing ids based on parameters 'naPer', 'meanPer' and 'varPer', 2495 ids are remained! Allowing parallel execution with up to 7 working processes. Allowing parallel execution with up to 7 working processes. Calculating spearman correlation for each pair of ids... Calculating spearman correlation for each pair of ids... Base on rank-based method, an undirected network with 2265 nodes and 3731 edges was identified when selecting most similar 7 nodes. Base on rank-based method, an undirected network with 2262 nodes and 3857 edges was identified when selecting most similar 7 nodes. The input data contain 3899 ids and 90 samples. No missing values in the data. After removing ids based on parameters 'naPer', 'meanPer' and 'varPer', 2495 ids are remained! The input data contain 3899 ids and 90 samples. No missing values in the data. After removing ids based on parameters 'naPer', 'meanPer' and 'varPer', 2495 ids are remained! Allowing parallel execution with up to 7 working processes. Calculating spearman correlation for each pair of ids... Allowing parallel execution with up to 7 working processes. Calculating spearman correlation for each pair of ids... Killed * 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 7 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 7 10:16:25 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 124.380 0.600 129.027
NetSAM.Rcheck/NetSAM-Ex.timings
name | user | system | elapsed | |
GOAssociation | 95.911 | 1.205 | 118.677 | |
MatNet | 47.690 | 0.571 | 51.012 | |
MatSAM | 826.323 | 2.440 | 894.661 | |
NetAnalyzer | 0.180 | 0.004 | 0.256 | |
NetSAM | 121.768 | 0.292 | 127.046 | |