Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:14 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the netbiov package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netbiov.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 1260/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netbiov 1.26.0 (landing page) Shailesh tripathi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: netbiov |
Version: 1.26.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings netbiov_1.26.0.tar.gz |
StartedAt: 2021-10-15 02:41:43 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 02:47:09 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 325.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: netbiov.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:netbiov.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings netbiov_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/netbiov.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'netbiov/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'netbiov' version '1.26.0' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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' .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.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 rnorm Consider adding importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette", "pdf") importFrom("graphics", "hist", "par") 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 ... WARNING Documented arguments not in \usage in documentation object 'level.plot': '...' Documented arguments not in \usage in documentation object 'mst.plot': '...' Documented arguments not in \usage in documentation object 'mst.plot.mod': '...' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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' ... NOTE The following files are already in R: 'Sweave.sty' Please remove them from your package. * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed level.plot 49.32 0.30 49.64 plot.abstract.module 30.08 0.16 30.23 plot.modules 23.91 0.07 24.00 mst.plot 14.23 0.14 14.38 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed level.plot 49.39 0.27 49.66 plot.abstract.module 28.47 0.21 28.67 plot.modules 21.45 0.12 21.58 mst.plot 12.27 0.11 12.38 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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 WARNING, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/netbiov.Rcheck/00check.log' for details.
netbiov.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/netbiov_1.26.0.tar.gz && rm -rf netbiov.buildbin-libdir && mkdir netbiov.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=netbiov.buildbin-libdir netbiov_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL netbiov_1.26.0.zip && rm netbiov_1.26.0.tar.gz netbiov_1.26.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 524k 100 524k 0 0 1723k 0 --:--:-- --:--:-- --:--:-- 1730k install for i386 * installing *source* package 'netbiov' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'netbiov' finding HTML links ... done PPI_Athalina html color_list html gnet_bcell html level.plot html modules_PPI_Athalina html modules_bcell html mst.plot html mst.plot.mod html plot.NetworkSperical html plot.NetworkSperical.startSet html plot.abstract.module html plot.abstract.nodes html plot.modules html plot.netbiov html plot.spiral.graph html split.mst html ** 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 install for x64 * installing *source* package 'netbiov' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'netbiov' as netbiov_1.26.0.zip * DONE (netbiov) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'netbiov' successfully unpacked and MD5 sums checked
netbiov.Rcheck/tests_i386/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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$" > runitDirs <- c(".") > TEST_DATA_DIR <- "data" > BiocGenerics:::testPackage("netbiov") RUNIT TEST PROTOCOL -- Fri Oct 15 02:46:47 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : netbiov RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > suite <- defineTestSuite(name="NetBioV Suite", + dirs=runitDirs, + testFileRegexp=pattern, + rngKind="default", + rngNormalKind="default") > result <- runTestSuite(suite) > printTextProtocol(result) RUNIT TEST PROTOCOL -- Fri Oct 15 02:46:47 2021 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : NetBioV Suite - 0 test functions, 0 errors, 0 failures Details *************************** Test Suite: NetBioV Suite Test function regexp: ^test.+ Test file regexp: ^test_.*\.R$ Involved directory: . no test files > > proc.time() user system elapsed 9.31 0.39 9.68 |
netbiov.Rcheck/tests_x64/runTests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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$" > runitDirs <- c(".") > TEST_DATA_DIR <- "data" > BiocGenerics:::testPackage("netbiov") RUNIT TEST PROTOCOL -- Fri Oct 15 02:46:58 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : netbiov RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > suite <- defineTestSuite(name="NetBioV Suite", + dirs=runitDirs, + testFileRegexp=pattern, + rngKind="default", + rngNormalKind="default") > result <- runTestSuite(suite) > printTextProtocol(result) RUNIT TEST PROTOCOL -- Fri Oct 15 02:46:58 2021 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : NetBioV Suite - 0 test functions, 0 errors, 0 failures Details *************************** Test Suite: NetBioV Suite Test function regexp: ^test.+ Test file regexp: ^test_.*\.R$ Involved directory: . no test files > > proc.time() user system elapsed 10.17 0.20 10.36 |
netbiov.Rcheck/examples_i386/netbiov-Ex.timings
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netbiov.Rcheck/examples_x64/netbiov-Ex.timings
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