Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1004/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ideal 2.0.0 (landing page) Federico Marini
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ideal package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ideal.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: ideal |
Version: 2.0.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ideal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ideal_2.0.0.tar.gz |
StartedAt: 2024-12-20 04:47:27 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:02:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 882.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ideal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ideal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ideal_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ideal.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ideal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ideal’ version ‘2.0.0’ * 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 ‘ideal’ 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 whether startup messages can be suppressed ... NOTE groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 ideal: no visible binding for '<<-' assignment to ‘ideal_env’ ideal : <anonymous>: no visible binding for global variable ‘pvalue’ ideal : <anonymous>: no visible binding for global variable ‘baseMean’ ideal : <anonymous>: no visible binding for global variable ‘ideal_env’ Undefined global functions or variables: baseMean ideal_env pvalue * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed goseqTable 43.456 0.485 49.531 wrapup_for_iSEE 13.859 0.110 15.012 plot_ma 11.160 0.130 13.154 plot_volcano 9.778 0.093 10.930 ggplotCounts 7.254 0.208 8.101 deseqresult2DEgenes 4.661 0.317 5.433 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/ideal.Rcheck/00check.log’ for details.
ideal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ideal ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ideal’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (ideal)
ideal.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(ideal) Loading required package: topGO Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: SparseM groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members Welcome to ideal v2.0.0 If you use ideal in your work, please cite: ideal: an R/Bioconductor package for Interactive Differential Expression Analysis Federico Marini, Jan Linke, Harald Binder BMC Bioinformatics, 2020 - https://doi.org/10.1186/s12859-020-03819-5 > > test_check("ideal") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 36.907 2.069 43.164
ideal.Rcheck/ideal-Ex.timings
name | user | system | elapsed | |
deprecated | 0.000 | 0.001 | 0.001 | |
deseqresult2DEgenes | 4.661 | 0.317 | 5.433 | |
deseqresult2tbl | 3.840 | 0.112 | 4.258 | |
ggplotCounts | 7.254 | 0.208 | 8.101 | |
goseqTable | 43.456 | 0.485 | 49.531 | |
ideal | 3.646 | 0.048 | 4.328 | |
plot_ma | 11.160 | 0.130 | 13.154 | |
plot_volcano | 9.778 | 0.093 | 10.930 | |
read_gmt | 0.000 | 0.001 | 0.001 | |
sepguesser | 0.013 | 0.004 | 0.023 | |
sig_heatmap | 3.465 | 0.054 | 3.803 | |
wrapup_for_iSEE | 13.859 | 0.110 | 15.012 | |