Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:30:03 -0400 (Tue, 09 Apr 2019).
Package 1074/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
netbiov 1.17.0 Shailesh tripathi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: netbiov |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netbiov_1.17.0.tar.gz |
StartedAt: 2019-04-09 02:30:33 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:35:03 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 269.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: netbiov.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netbiov_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/netbiov.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘netbiov/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netbiov’ version ‘1.17.0’ * 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 ‘netbiov’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: plot.NetworkSperical plot.NetworkSperical.startSet plot.abstract.module plot.abstract.nodes plot.modules plot.netbiov plot.spiral.graph See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .edgeCol: no visible global function definition for ‘colors’ .get.coord.abstract : dst: no visible global function definition for ‘dist’ .get.coord.mod : dst: no visible global function definition for ‘dist’ .get.coord.mod_abs : dst: no visible global function definition for ‘dist’ .getalllevels: no visible global function definition for ‘pdf’ .getalllevels: no visible global function definition for ‘dev.off’ .getcrd.mod : dst: no visible global function definition for ‘dist’ .getcrd.mod: no visible global function definition for ‘rnorm’ .getcrd.mod.nodes : dst: no visible global function definition for ‘dist’ .getcrd.mod_abs : dst: no visible global function definition for ‘dist’ .getcrd.mod_abs: no visible global function definition for ‘rnorm’ .getcrd.mod_mst : dst: no visible global function definition for ‘dist’ .getcrd.mod_mst: no visible global function definition for ‘rnorm’ .ploteachstep: no visible global function definition for ‘plot’ .set.mst.node.col: no visible global function definition for ‘heat.colors’ .set.mst.node.col_mod: no visible global function definition for ‘heat.colors’ .set.rank.abstract: no visible global function definition for ‘colors’ .set.rank.abstract: no visible global function definition for ‘hist’ .set.rank.abstract: no visible global function definition for ‘heat.colors’ .set.rank.mod: no visible global function definition for ‘hist’ .set.rank.mod: no visible global function definition for ‘colors’ .set.rank.mod: no visible global function definition for ‘heat.colors’ .set.rank.mod_abs: no visible global function definition for ‘hist’ .set.rank.mod_abs: no visible global function definition for ‘colors’ .set.rank.mod_abs: no visible global function definition for ‘heat.colors’ .set.rank.nodes: no visible global function definition for ‘hist’ .set.rank.nodes: no visible global function definition for ‘colors’ .set.rank.nodes: no visible global function definition for ‘heat.colors’ .set.rank.spiral: no visible global function definition for ‘hist’ .set.rank.spiral: no visible global function definition for ‘colors’ .set.rank.spiral: no visible global function definition for ‘heat.colors’ .set.split.vertex.color: no visible global function definition for ‘colors’ level.plot: no visible global function definition for ‘colors’ plot.NetworkSperical: no visible global function definition for ‘colors’ plot.NetworkSperical: no visible global function definition for ‘palette’ plot.NetworkSperical.startSet: no visible global function definition for ‘colors’ plot.NetworkSperical.startSet: no visible global function definition for ‘palette’ plot.netbiov: no visible global function definition for ‘par’ plot.netbiov: no visible global function definition for ‘plot’ plot.spiral.graph : dst: no visible global function definition for ‘dist’ tkplot.netbiov: no visible global function definition for ‘par’ Undefined global functions or variables: colors dev.off dist heat.colors hist palette par pdf plot rnorm Consider adding importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette", "pdf") importFrom("graphics", "hist", "par", "plot") importFrom("stats", "dist", "rnorm") 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 files in ‘vignettes’ ... NOTE The following files are already in R: ‘Sweave.sty’ Please remove them from your package. * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed level.plot 82.418 1.709 85.434 plot.abstract.module 51.406 1.291 54.520 plot.modules 38.003 1.214 39.590 mst.plot 17.037 0.202 17.471 mst.plot.mod 5.958 0.184 6.194 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/netbiov.Rcheck/00check.log’ for details.
netbiov.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL netbiov ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘netbiov’ ... ** 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 * DONE (netbiov)
netbiov.Rcheck/tests/runTests.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" 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. > require("RUnit") Loading required package: RUnit > require("netbiov") Loading required package: netbiov Loading required package: igraph Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > > pattern="^test_.*\\.R$" > runitDirs <- c(".") > TEST_DATA_DIR <- "data" > BiocGenerics:::testPackage("netbiov") RUNIT TEST PROTOCOL -- Tue Apr 9 02:34:48 2019 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : netbiov RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > suite <- defineTestSuite(name="NetBioV Suite", + dirs=runitDirs, + testFileRegexp=pattern, + rngKind="default", + rngNormalKind="default") > result <- runTestSuite(suite) > printTextProtocol(result) RUNIT TEST PROTOCOL -- Tue Apr 9 02:34:48 2019 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : NetBioV Suite - 0 test functions, 0 errors, 0 failures Details *************************** Test Suite: NetBioV Suite Test function regexp: ^test.+ Test file regexp: ^test_.*\.R$ Involved directory: . no test files > > proc.time() user system elapsed 10.872 0.595 11.517
netbiov.Rcheck/netbiov-Ex.timings
name | user | system | elapsed | |
PPI_Athalina | 0.022 | 0.004 | 0.027 | |
level.plot | 82.418 | 1.709 | 85.434 | |
mst.plot | 17.037 | 0.202 | 17.471 | |
mst.plot.mod | 5.958 | 0.184 | 6.194 | |
plot.NetworkSperical | 0.760 | 0.003 | 0.769 | |
plot.NetworkSperical.startSet | 0.327 | 0.041 | 0.370 | |
plot.abstract.module | 51.406 | 1.291 | 54.520 | |
plot.abstract.nodes | 0.286 | 0.006 | 0.293 | |
plot.modules | 38.003 | 1.214 | 39.590 | |
plot.netbiov | 0.691 | 0.005 | 0.701 | |
plot.spiral.graph | 0.372 | 0.006 | 0.383 | |
split.mst | 0.709 | 0.015 | 0.765 | |