Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:40 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the NetSAM package: - 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetSAM_1.44.0.tar.gz |
StartedAt: 2024-05-06 23:24:56 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 23:32:48 -0400 (Mon, 06 May 2024) |
EllapsedTime: 472.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NetSAM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetSAM_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/NetSAM.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * 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 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MatSAM 248.871 1.571 250.489 NetSAM 46.626 0.038 46.665 GOAssociation 23.007 1.021 24.050 mapToSymbol 1.837 0.121 12.132 consensusNet 0.165 0.009 23.541 * 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: OK
NetSAM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetSAM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 -- Mon May 6 23:32:45 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 49.207 0.161 49.383
NetSAM.Rcheck/NetSAM-Ex.timings
name | user | system | elapsed | |
GOAssociation | 23.007 | 1.021 | 24.050 | |
MatNet | 4.101 | 0.220 | 4.322 | |
MatSAM | 248.871 | 1.571 | 250.489 | |
NetAnalyzer | 0.054 | 0.003 | 0.057 | |
NetSAM | 46.626 | 0.038 | 46.665 | |
consensusNet | 0.165 | 0.009 | 23.541 | |
featureAssociation | 3.279 | 0.314 | 3.595 | |
mapToSymbol | 1.837 | 0.121 | 12.132 | |
mergeDuplicate | 0.032 | 0.001 | 0.033 | |
testFileFormat | 0.284 | 0.003 | 0.286 | |