Back to Multiple platform build/check report for BioC 3.6 |
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This page was generated on 2018-04-12 13:36:59 -0400 (Thu, 12 Apr 2018).
Package 941/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
NetSAM 1.18.0 Bing Zhang
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | ![]() |
Package: NetSAM |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetSAM_1.18.0.tar.gz |
StartedAt: 2018-04-12 07:05:07 -0400 (Thu, 12 Apr 2018) |
EndedAt: 2018-04-12 07:06:25 -0400 (Thu, 12 Apr 2018) |
EllapsedTime: 77.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NetSAM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetSAM_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/NetSAM.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NetSAM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NetSAM’ version ‘1.18.0’ * 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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: ‘graph’ ‘igraph’ ‘seriation’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘igraph:::degree’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘NetSAM/R/zzz.R’: .onLoad calls: cat("******************************************\n") cat("* *\n") cat("* Welcome to use NetSAM ! *\n") cat("* *\n") cat("******************************************\n") require(methods) Package startup functions should not change the search path. Package startup functions should use ‘packageStartupMessage’ to generate messages. See section ‘Good practice’ in '?.onAttach'. ****************************************** * * * Welcome to use NetSAM ! * * * ****************************************** NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function definition for ‘V’ NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function definition for ‘add.edges’ NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function definition for ‘get.adjacency’ NetSAM : transformFromWalktrapToHclust: no visible global function definition for ‘as.dendrogram’ NetSAM : transformFromWalktrapToHclust: no visible global function definition for ‘order.dendrogram’ NetSAM : evaluateWalktrapStep: no visible global function definition for ‘walktrap.community’ NetSAM : evaluateWalktrapStep: no visible global function definition for ‘as.dist’ NetSAM : evaluateWalktrapStep: no visible global function definition for ‘seriate’ NetSAM : evaluateWalktrapStep: no visible global function definition for ‘get_order’ NetSAM : identifySig: no visible global function definition for ‘degree.sequence.game’ NetSAM : identifySig: no visible global function definition for ‘walktrap.community’ NetSAM : identifySig: no visible global function definition for ‘sd’ NetSAM : identifySig: no visible global function definition for ‘pnorm’ NetSAM : identifyHierOr: no visible global function definition for ‘induced.subgraph’ NetSAM : createHMIFile: no visible global function definition for ‘V’ NetSAM: no visible global function definition for ‘read.graph’ NetSAM: no visible global function definition for ‘graph.edgelist’ NetSAM: no visible global function definition for ‘igraph.from.graphNEL’ NetSAM: no visible global function definition for ‘V’ NetSAM: no visible global function definition for ‘vcount’ NetSAM: no visible global function definition for ‘ecount’ NetSAM: no visible global function definition for ‘simplify’ NetSAM: no visible global function definition for ‘clusters’ NetSAM: no visible global function definition for ‘induced.subgraph’ NetSAM: no visible global function definition for ‘get.edgelist’ NetSAM: no visible global function definition for ‘write.table’ Undefined global functions or variables: V add.edges as.dendrogram as.dist clusters degree.sequence.game ecount get.adjacency get.edgelist get_order graph.edgelist igraph.from.graphNEL induced.subgraph order.dendrogram pnorm read.graph sd seriate simplify vcount walktrap.community write.table Consider adding importFrom("stats", "as.dendrogram", "as.dist", "order.dendrogram", "pnorm", "sd") importFrom("utils", "write.table") to your NAMESPACE file. * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed NetSAM 7.754 0.078 7.947 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.6-bioc/meat/NetSAM.Rcheck/00check.log’ for details.
NetSAM.Rcheck/00install.out
* installing *source* package ‘NetSAM’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded ****************************************** * * * Welcome to use NetSAM ! * * * ****************************************** * DONE (NetSAM)
NetSAM.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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 objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union Attaching package: 'seriation' The following object is masked from 'package:igraph': permute Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:igraph': normalize, union The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Attaching package: 'graph' The following objects are masked from 'package:igraph': degree, edges, intersection ****************************************** * * * Welcome to use NetSAM ! * * * ****************************************** Network has 320 nodes and 769 edges Identifying the hierarchical modules of the network... Start to analysis subnetwork 1 ! Evaluate Leve 1 network... Evaluate Level 2 networks... Evaluate Level 3 networks... Evaluate Level 4 networks... Reorder the genes in the one dimentional layout... Processing completed! RUNIT TEST PROTOCOL -- Thu Apr 12 07:06:21 2018 *********************************************** 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 10.058 0.207 10.411
NetSAM.Rcheck/NetSAM-Ex.timings
name | user | system | elapsed | |
NetSAM | 7.754 | 0.078 | 7.947 | |