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 |
---|---|---|---|---|
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 847/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
geva 1.14.0 (landing page) Itamar José Guimarães Nunes
| 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 geva package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geva.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: geva |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geva.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geva_1.14.0.tar.gz |
StartedAt: 2024-12-20 04:03:15 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:11:09 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 474.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geva.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geva.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geva_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/geva.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 ‘geva/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geva’ version ‘1.14.0’ * 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 ‘geva’ 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 ... 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 ... OK * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed geva.quick 112.703 0.485 115.499 geva.finalize 52.543 0.248 54.771 top.genes 50.696 0.182 51.564 geva.hcluster 11.214 0.115 12.100 geva.cluster 10.725 0.476 11.341 geva.quantiles 5.392 0.160 5.684 geva.dcluster 5.221 0.172 5.464 * 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: OK
geva.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geva ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘geva’ ... ** using staged installation ** R ** 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 (geva)
geva.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(geva) > > test_check("geva") Merging scores... Searching for dependent factors... Searching for specific factors... Found 54 significant genes: similar: 33 factor-specific: 7 factor-dependent: 14 Input summarized Calculating hierarchical clustering... Found 6 clusters Merging scores... Searching for dependent factors... Searching for specific factors... Found 60 significant genes: factor-specific: 18 factor-dependent: 39 similar: 3 Testing plot with GEVAResults Testing with cluster.method = 'hierarchical' Calculating hierarchical clustering... Found 6 clusters Testing with cluster.method = 'density' Calculating density clustering... Found 3 clusters Testing quantiles grouping Testing with quantile.method = 'range.slice' Testing with quantile.method = 'proportional' Testing with quantile.method = 'density' Testing with quantile.method = 'k.max.sd' Testing with quantile.method = 'custom' Testing plot with GEVACluster and GEVAQuantiles Reading 'gevainput794b6795923b.txt' ... Reading 'gevainput794bcb3949e.txt' ... Reading 'gevainput794b61e21795.txt' ... Reading 'gevainput794b427a6967.txt' ... Reading 'gevainput794b729e0b49.txt' ... Reading 'gevainput794b65f72068.txt' ... Reading 'gevainput794b4370c024.txt' ... Reading 'gevainput794b1f569e13.txt' ... Reading 'gevainput794b6fa40177.txt' ... Read 9 columns with 10000 probes Testing with summary.method = 'mean' Testing with summary.method = 'median' Testing with variation.method = 'sd' Testing with variation.method = 'var' Testing with variation.method = 'mad' Testing plot with GEVASummary [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 125.866 1.612 138.316
geva.Rcheck/geva-Ex.timings
name | user | system | elapsed | |
SVTable-class | 0.007 | 0.001 | 0.009 | |
TypedList-class | 0.004 | 0.001 | 0.004 | |
generics | 0.688 | 0.018 | 0.866 | |
geva.cluster | 10.725 | 0.476 | 11.341 | |
geva.dcluster | 5.221 | 0.172 | 5.464 | |
geva.finalize | 52.543 | 0.248 | 54.771 | |
geva.hcluster | 11.214 | 0.115 | 12.100 | |
geva.ideal.example | 1.253 | 0.045 | 1.377 | |
geva.input.correct | 0.239 | 0.005 | 0.275 | |
geva.merge.input | 0.072 | 0.004 | 0.081 | |
geva.quantiles | 5.392 | 0.160 | 5.684 | |
geva.quick | 112.703 | 0.485 | 115.499 | |
geva.summarize | 1.203 | 0.033 | 1.256 | |
top.genes | 50.696 | 0.182 | 51.564 | |