Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the vissE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/vissE.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 2009/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vissE 1.0.0 (landing page) Dharmesh D. Bhuva
| 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: vissE |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vissE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vissE_1.0.0.tar.gz |
StartedAt: 2021-10-15 01:10:33 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:12:49 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 135.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vissE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vissE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vissE_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/vissE.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘vissE/DESCRIPTION’ ... OK * this is package ‘vissE’ version ‘1.0.0’ * 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 ‘vissE’ 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 ... 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotGeneStats: no visible binding for global variable ‘Count’ plotGeneStats: no visible binding for global variable ‘GeneStat’ plotGeneStats: no visible binding for global variable ‘Gene’ plotMsigNetwork: no visible binding for global variable ‘x_begin’ plotMsigNetwork: no visible binding for global variable ‘y_begin’ plotMsigNetwork: no visible binding for global variable ‘x_end’ plotMsigNetwork: no visible binding for global variable ‘y_end’ plotMsigNetwork: no visible binding for global variable ‘x’ plotMsigNetwork: no visible binding for global variable ‘y’ plotMsigNetwork: no visible binding for global variable ‘Size’ plotMsigNetwork: no visible binding for global variable ‘Category’ plotMsigNetwork: no visible binding for global variable ‘NodeGroup’ plotMsigWordcloud: no visible binding for global variable ‘word’ plotMsigWordcloud: no visible binding for global variable ‘freq’ plotMsigWordcloud: no visible binding for global variable ‘angle’ Undefined global functions or variables: Category Count Gene GeneStat NodeGroup Size angle freq word x x_begin x_end y y_begin y_end * 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 LazyData ... NOTE 'LazyDataCompression' is specified without 'LazyData' * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed computeMsigNetwork 9.586 0.346 10.749 characteriseGeneset 5.898 0.230 6.133 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/vissE.Rcheck/00check.log’ for details.
vissE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL vissE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘vissE’ ... ** 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 (vissE)
vissE.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > library(testthat) > library(vissE) > > test_check("vissE") [ FAIL 0 | WARN 133 | SKIP 0 | PASS 67 ] > > proc.time() user system elapsed 25.940 0.874 27.623
vissE.Rcheck/vissE-Ex.timings
name | user | system | elapsed | |
bhuvad_theme | 0.096 | 0.006 | 0.103 | |
characteriseGeneset | 5.898 | 0.230 | 6.133 | |
computeMsigNetwork | 9.586 | 0.346 | 10.749 | |
computeMsigOverlap | 0.588 | 0.007 | 0.597 | |
computeMsigWordFreq | 2.086 | 0.048 | 2.140 | |
getMsigBlacklist | 0.000 | 0.001 | 0.001 | |
plotGeneStats | 0.914 | 0.050 | 0.969 | |
plotMsigNetwork | 1.576 | 0.036 | 1.616 | |
plotMsigWordcloud | 1.635 | 0.071 | 1.722 | |