############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:NetSAM.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings NetSAM_1.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NetSAM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NetSAM’ version ‘1.42.0’ * 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 loading without being on the library search path ... OK * checking 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 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: MatSAM > ### Title: Correlation network construction, seriation and modularization > ### from a matrix > ### Aliases: MatSAM > ### Keywords: methods > > ### ** Examples > > inputMatDir <- system.file("extdata","exampleExpressionData.cct",package="NetSAM") > cat(inputMatDir) /home/biocbuild/R/R-4.3.1/site-library/NetSAM/extdata/exampleExpressionData.cct> sampleAnnDir <- system.file("extdata","sampleAnnotation.tsi",package="NetSAM") > cat(sampleAnnDir) /home/biocbuild/R/R-4.3.1/site-library/NetSAM/extdata/sampleAnnotation.tsi> outputFileName <- paste(getwd(),"/MatSAM",sep="") > matModule <- MatSAM(inputMat=inputMatDir, sampleAnn=sampleAnnDir, outputFileName=outputFileName, outputFormat="msm", organism="hsapiens", map_to_symbol=FALSE, idType="auto", collapse_mode="maxSD", naPer=0.7, meanPer=0.8, varPer=0.8, corrType="spearman", matNetMethod="rank", valueThr=0.6, rankBest=0.003, networkType="signed", netFDRMethod="BH", netFDRThr=0.05, minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod="cutoff", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, idNumThr=(-1), nThreads=3) 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 multi-threading with up to 3 threads. Calculating spearman correlation for each pair of ids... Base on rank-based method, an undirected network with 1993 nodes and 3048 edges was identified when selecting most similar 7 nodes. 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: 0.8002244 Evaluating networks in Level 2 ... Modularity of network 1: 0.7213026 Modularity of network 2: 0.5231162 Modularity of network 3: 0.566358 Modularity of network 4: 0.6766937 Modularity of network 5: 0.505102 Modularity of network 6: 0.4201183 Modularity of network 7: 0.3163265 Modularity of network 8: 0.465374 Modularity of network 9: 0.5625 Modularity of network 10: 0.2956104 Modularity of network 11: 0.6538086 Modularity of network 12: 0.4965278 Modularity of network 13: 0.4756944 Modularity of network 14: 0.6963684 Modularity of network 15: 0.5321181 Modularity of network 16: 0.5478316 Modularity of network 17: 0.6276706 Modularity of network 18: 0.5371094 Modularity of network 19: 0.355 Modularity of network 20: 0.4669421 Modularity of network 21: 0.3417609 Modularity of network 22: 0.4002268 Modularity of network 23: 0.2205679 Modularity of network 24: 0.4244444 Modularity of network 25: 0.4387755 Modularity of network 26: 0.3571429 Modularity of network 27: 0.5117188 Modularity of network 28: 0.3671875 Modularity of network 29: 0.4584775 Modularity of network 30: 0.3571429 Modularity of network 31: 0.3571429 Modularity of network 32: 0.2578125 Modularity of network 33: 0.4012346 Modularity of network 34: 0.504017 Modularity of network 35: 0.4171598 Modularity of network 36: 0.4822485 Modularity of network 37: 0.06568878 Modularity of network 38: 0.26 Modularity of network 39: 0.3 Modularity of network 40: 0.500651 Modularity of network 41: 0.26 Modularity of network 42: 0.26 Modularity of network 43: 0.165 Modularity of network 44: 0.4380165 Modularity of network 45: 0.3571429 Modularity of network 46: 0.26 Modularity of network 47: 0.2109375 Modularity of network 48: 0.26 Modularity of network 49: 0.2083333 Modularity of network 50: 0.2916667 Modularity of network 51: 0.26 Modularity of network 52: 0.3671875 Modularity of network 53: 0.4467456 Modularity of network 54: 0.3571429 Modularity of network 55: 0.2916667 Modularity of network 56: 0.3571429 Modularity of network 57: 0.3264463 Modularity of network 58: 0.3671875 Modularity of network 59: 0.257716 Modularity of network 60: 0.3644444 Modularity of network 61: 0.3828125 Modularity of network 62: 0.4723183 Modularity of network 63: 0.2844444 Modularity of network 64: 0.26 Modularity of network 65: 0.3571429 Modularity of network 66: 0.2301587 Modularity of network 67: 0.3571429 Modularity of network 68: 0.2901235 Modularity of network 69: 0.1938776 Modularity of network 70: 0.3194444 Modularity of network 71: 0.2083333 Modularity of network 72: 0.2959184 Modularity of network 73: 0.3194444 Modularity of network 74: 0.3194444 Modularity of network 75: 0.3 Modularity of network 76: 0.1938776 Modularity of network 77: 0.3194444 Modularity of network 78: 0.1122449 Modularity of network 79: 0.15625 Modularity of network 80: 0.1694215 Modularity of network 81: 0.0672 Modularity of network 82: 0.1234568 Modularity of network 83: 0.2541091 Modularity of network 84: 0.09259259 Evaluating networks in Level 3 ... Modularity of network 1: 0.2916667 Modularity of network 2: 0.3222656 Modularity of network 3: 0.4157986 Modularity of network 4: 0.4158951 Modularity of network 5: 0.2142857 Modularity of network 6: 0.1631944 Modularity of network 7: 0.002835539 Modularity of network 8: 0 Modularity of network 9: 0 Modularity of network 10: 0.1770833 Modularity of network 11: 0.125 Modularity of network 12: 0.1626276 Modularity of network 13: 0.3298611 Modularity of network 14: 0.5918913 Modularity of network 15: 0.395 Modularity of network 16: 0.5145682 Modularity of network 17: 0.5367461 Modularity of network 18: 0.26 Modularity of network 19: 0.2530864 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.18-bioc/meat/NetSAM.Rcheck/00check.log’ for details.