Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BioNetStat package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNetStat.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 187/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioNetStat 1.12.0 (landing page) Vinicius Jardim
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BioNetStat |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioNetStat_1.12.0.tar.gz |
StartedAt: 2021-10-14 09:03:13 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:06:12 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 178.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioNetStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioNetStat_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BioNetStat.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioNetStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioNetStat’ version ‘1.12.0’ * package encoding: UTF-8 * 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 ‘BioNetStat’ 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION Most likely ‘inst/CITATION’ should be used instead. * 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 ... NOTE Namespaces in Imports field not imported from: ‘BiocParallel’ ‘RColorBrewer’ ‘RJSONIO’ ‘ggplot2’ ‘knitr’ ‘markdown’ ‘pheatmap’ ‘plyr’ ‘rmarkdown’ ‘stats’ ‘utils’ ‘whisker’ ‘yaml’ All declared Imports should be used. Packages in Depends field not imported from: ‘DT’ ‘shiny’ ‘shinyBS’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE adjacencyMatrix : <anonymous>: no visible global function definition for ‘cor’ adjacencyMatrix : <anonymous>: no visible global function definition for ‘p.adjust’ betweennessCentralityTest: no visible global function definition for ‘bplapply’ betweennessCentralityVertexTest: no visible global function definition for ‘bplapply’ closenessCentralityTest: no visible global function definition for ‘bplapply’ closenessCentralityVertexTest: no visible global function definition for ‘bplapply’ clusteringCoefficientTest : <anonymous>: no visible global function definition for ‘dist’ clusteringCoefficientTest : <anonymous> : <anonymous>: no visible global function definition for ‘dist’ clusteringCoefficientTest: no visible global function definition for ‘bplapply’ clusteringCoefficientVertexTest: no visible global function definition for ‘bplapply’ degreeCentralityTest: no visible global function definition for ‘bplapply’ degreeCentralityVertexTest: no visible global function definition for ‘bplapply’ degreeDistributionTest: no visible global function definition for ‘bplapply’ diffNetAnalysis: no visible binding for global variable ‘expr’ diffNetAnalysis: no visible global function definition for ‘p.adjust’ doLabels: no visible global function definition for ‘read.csv’ edgeBetweennessEdgeTest: no visible global function definition for ‘bplapply’ edgeBetweennessTest: no visible global function definition for ‘bplapply’ edgesResInt : <anonymous>: no visible global function definition for ‘dist’ eigenvectorCentralityTest: no visible global function definition for ‘bplapply’ eigenvectorCentralityVertexTest: no visible global function definition for ‘bplapply’ gaussianDensity: no visible global function definition for ‘bw.nrd0’ gaussianDensity: no visible global function definition for ‘density’ pathPlot: no visible binding for global variable ‘median’ readVarFile: no visible global function definition for ‘read.table’ resInt : <anonymous>: no visible global function definition for ‘dist’ retEdgesTable: no visible global function definition for ‘p.adjust’ retTable: no visible global function definition for ‘p.adjust’ spectralDistributionTest: no visible global function definition for ‘bplapply’ spectralEntropyTest: no visible global function definition for ‘bplapply’ var.list: no visible global function definition for ‘aggregate’ Undefined global functions or variables: aggregate bplapply bw.nrd0 cor density dist expr median p.adjust read.csv read.table Consider adding importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist", "median", "p.adjust") importFrom("utils", "read.csv", "read.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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed networkTest 10.187 0.088 10.275 centralityPathPlot 8.754 0.721 13.684 pathPlot 6.080 0.944 7.025 * 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 ‘/home/biocbuild/bbs-3.13-bioc/meat/BioNetStat.Rcheck/00check.log’ for details.
BioNetStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BioNetStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘BioNetStat’ ... ** 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 (BioNetStat)
BioNetStat.Rcheck/BioNetStat-Ex.timings
name | user | system | elapsed | |
KLdegree | 0.005 | 0.008 | 0.012 | |
KLspectrum | 0.016 | 0.004 | 0.021 | |
adjacencyMatrix | 0.002 | 0.000 | 0.001 | |
centralityPathPlot | 8.754 | 0.721 | 13.684 | |
diffNetAnalysis | 1.265 | 0.024 | 1.292 | |
doLabels | 0.079 | 0.000 | 0.079 | |
edgeTest | 0.052 | 0.008 | 0.060 | |
labels | 0.001 | 0.000 | 0.002 | |
nDegreeDensities | 0.053 | 0.004 | 0.057 | |
nSpectralDensities | 0.098 | 0.004 | 0.102 | |
networkFeature | 0.061 | 0.007 | 0.069 | |
networkTest | 10.187 | 0.088 | 10.275 | |
nodeScores | 0.061 | 0.008 | 0.069 | |
nodeTest | 0.081 | 0.012 | 0.094 | |
pathPlot | 6.080 | 0.944 | 7.025 | |
readSetFile | 0.080 | 0.000 | 0.083 | |
readVarFile | 0.101 | 0.000 | 0.101 | |
runBioNetStat | 0 | 0 | 0 | |
varFile | 0.007 | 0.000 | 0.007 | |