Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:57 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 1424/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NetSAM 1.44.0 (landing page) Zhiao Shi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the NetSAM package: - 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 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: NetSAM |
Version: 1.44.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NetSAM.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings NetSAM_1.44.0.tar.gz |
StartedAt: 2024-05-22 04:32:56 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 04:56:32 -0400 (Wed, 22 May 2024) |
EllapsedTime: 1416.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: NetSAM.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NetSAM.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings NetSAM_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/NetSAM.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'NetSAM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'NetSAM' version '1.44.0' * 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 '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 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 whether startup messages can be suppressed ... 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 sizes of PDF files under 'inst/doc' ... 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") Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site. 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See 'F:/biocbuild/bbs-3.19-bioc/meat/NetSAM.Rcheck/00check.log' for details.
NetSAM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL NetSAM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-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 version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 multi-threading with up to 3 threads. 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 -- Wed May 22 04:56:22 2024 *********************************************** 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 147.00 1.25 149.25
NetSAM.Rcheck/NetSAM-Ex.timings
name | user | system | elapsed | |
GOAssociation | 69.94 | 3.61 | 73.72 | |
MatNet | 14.25 | 1.19 | 17.26 | |
MatSAM | 727.72 | 6.36 | 735.39 | |
NetAnalyzer | 0.39 | 0.00 | 0.41 | |
NetSAM | 133.05 | 0.05 | 133.17 | |
consensusNet | 0.52 | 0.08 | 93.89 | |
featureAssociation | 21.06 | 2.41 | 29.87 | |