Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 |
Package 2208/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
vissE 1.13.0 (landing page) Dharmesh D. Bhuva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the vissE package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: vissE |
Version: 1.13.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:vissE.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings vissE_1.13.0.tar.gz |
StartedAt: 2024-07-16 05:23:38 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 05:26:39 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 180.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: vissE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:vissE.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings vissE_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/vissE.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'vissE/DESCRIPTION' ... OK * this is package 'vissE' version '1.13.0' * 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 '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 code 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 checkGroups: no visible global function definition for 'na.omit' 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 'Size' plotMsigNetwork: no visible binding for global variable 'Category' plotMsigNetwork: no visible binding for global variable 'x' plotMsigNetwork: no visible binding for global variable 'y' plotMsigNetwork: no visible binding for global variable 'NodeGroup' plotMsigPPI: no visible binding for global variable 'weight' plotMsigPPI: no visible binding for global variable 'Degree' plotMsigPPI: no visible binding for global variable 'label' plotMsigPPI: no visible binding for global variable 'Label' 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 Degree Gene GeneStat Label NodeGroup Size angle freq label na.omit weight word x y Consider adding importFrom("stats", "na.omit") 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 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 computeMsigWordFreq 13.93 8.27 58.41 plotMsigWordcloud 9.03 0.78 11.59 plotMsigPPI 7.31 0.83 9.30 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 'C:/Users/biocbuild/bbs-3.20-bioc/meat/vissE.Rcheck/00check.log' for details.
vissE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL vissE ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 7 | SKIP 0 | PASS 63 ] [ FAIL 0 | WARN 7 | SKIP 0 | PASS 63 ] > > proc.time() user system elapsed 29.42 4.85 36.81
vissE.Rcheck/vissE-Ex.timings
name | user | system | elapsed | |
bhuvad_theme | 0.04 | 0.03 | 0.06 | |
characteriseGeneset | 3.28 | 0.25 | 3.56 | |
computeMsigNetwork | 0.11 | 0.07 | 0.17 | |
computeMsigOverlap | 0.00 | 0.04 | 0.05 | |
computeMsigWordFreq | 13.93 | 8.27 | 58.41 | |
findMsigClusters | 0.07 | 0.02 | 0.07 | |
getMsigExclusionList | 0 | 0 | 0 | |
plotGeneStats | 0.48 | 0.07 | 0.57 | |
plotMsigNetwork | 1.36 | 0.08 | 1.43 | |
plotMsigPPI | 7.31 | 0.83 | 9.30 | |
plotMsigWordcloud | 9.03 | 0.78 | 11.59 | |