Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:21 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the BioNetStat package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 196/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BioNetStat 1.19.0 (landing page) Vinicius Jardim
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: BioNetStat |
Version: 1.19.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNetStat.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BioNetStat_1.19.0.tar.gz |
StartedAt: 2022-12-28 22:01:30 -0500 (Wed, 28 Dec 2022) |
EndedAt: 2022-12-28 22:04:41 -0500 (Wed, 28 Dec 2022) |
EllapsedTime: 191.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BioNetStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BioNetStat.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings BioNetStat_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BioNetStat.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BioNetStat/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BioNetStat' version '1.19.0' * 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 whether package 'BioNetStat' can be installed ... OK * checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 1.9Mb shiny 1.9Mb * 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 ... NOTE checkRd: (-1) centralityPathPlot.Rd:47: Escaped LaTeX specials: \# * 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 9.75 0.38 10.13 centralityPathPlot 5.46 0.57 9.96 pathPlot 5.09 0.76 5.85 * 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: 5 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/BioNetStat.Rcheck/00check.log' for details.
BioNetStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL BioNetStat ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 | 0 | 0 | |
KLspectrum | 0.02 | 0.00 | 0.02 | |
adjacencyMatrix | 0 | 0 | 0 | |
centralityPathPlot | 5.46 | 0.57 | 9.96 | |
diffNetAnalysis | 1.32 | 0.05 | 1.38 | |
doLabels | 0.10 | 0.00 | 0.11 | |
edgeTest | 0.06 | 0.00 | 0.06 | |
labels | 0 | 0 | 0 | |
nDegreeDensities | 0.05 | 0.00 | 0.05 | |
nSpectralDensities | 0.09 | 0.00 | 0.09 | |
networkFeature | 0.06 | 0.00 | 0.06 | |
networkTest | 9.75 | 0.38 | 10.13 | |
nodeScores | 0.05 | 0.00 | 0.05 | |
nodeTest | 0.09 | 0.00 | 0.10 | |
pathPlot | 5.09 | 0.76 | 5.85 | |
readSetFile | 0.07 | 0.00 | 0.07 | |
readVarFile | 0.11 | 0.00 | 0.11 | |
runBioNetStat | 0 | 0 | 0 | |
varFile | 0 | 0 | 0 | |