Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:40 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1498/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pcaExplorer 2.29.0 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the pcaExplorer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pcaExplorer.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: pcaExplorer |
Version: 2.29.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pcaExplorer_2.29.0.tar.gz |
StartedAt: 2024-03-02 08:16:57 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 08:31:37 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 879.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pcaExplorer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pcaExplorer_2.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/pcaExplorer.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pcaExplorer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pcaExplorer’ version ‘2.29.0’ * 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 ‘pcaExplorer’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... NOTE pcaExplorer: no visible binding for '<<-' assignment to ‘pcaexplorer_env’ pcaExplorer : <anonymous>: no visible binding for global variable ‘airway’ pcaExplorer : <anonymous>: no visible binding for global variable ‘pcaexplorer_env’ Undefined global functions or variables: airway pcaexplorer_env * 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 get_annotation_orgdb 6.400 0.155 7.995 get_annotation 5.100 0.174 6.496 pcaplot 4.866 0.085 6.276 genespca 4.531 0.054 5.434 correlatePCs 4.071 0.233 5.860 * 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-3.19-bioc/meat/pcaExplorer.Rcheck/00check.log’ for details.
pcaExplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pcaExplorer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘pcaExplorer’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (pcaExplorer)
pcaExplorer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 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(pcaExplorer) Welcome to pcaExplorer v2.29.0 If you use pcaExplorer in your work, please cite: Federico Marini, Harald Binder pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components BMC Bioinformatics, 2019 - https://doi.org/10.1186/s12859-019-2879-1 > > test_check("pcaExplorer") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 17 ] > > proc.time() user system elapsed 113.355 3.759 146.227
pcaExplorer.Rcheck/pcaExplorer-Ex.timings
name | user | system | elapsed | |
correlatePCs | 4.071 | 0.233 | 5.860 | |
distro_expr | 3.844 | 0.060 | 4.600 | |
geneprofiler | 2.874 | 0.024 | 3.518 | |
genespca | 4.531 | 0.054 | 5.434 | |
get_annotation | 5.100 | 0.174 | 6.496 | |
get_annotation_orgdb | 6.400 | 0.155 | 7.995 | |
hi_loadings | 2.901 | 0.129 | 3.917 | |
limmaquickpca2go | 3.456 | 0.095 | 4.468 | |
makeExampleDESeqDataSet_multifac | 0.707 | 0.007 | 0.847 | |
pair_corr | 3.612 | 0.090 | 4.455 | |
pca2go | 3.401 | 0.084 | 4.318 | |
pcaExplorer | 3.455 | 0.077 | 4.340 | |
pcaplot | 4.866 | 0.085 | 6.276 | |
pcaplot3d | 2.878 | 0.127 | 3.725 | |
pcascree | 3.494 | 0.089 | 4.294 | |
plotPCcorrs | 3.195 | 0.049 | 3.849 | |
topGOtable | 3.381 | 0.084 | 4.275 | |