Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1507/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pcaExplorer 3.1.1 (landing page) Federico Marini
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 3.1.1 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pcaExplorer_3.1.1.tar.gz |
StartedAt: 2024-12-23 00:51:16 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 01:01:29 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 613.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pcaExplorer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pcaExplorer_3.1.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pcaExplorer.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘pcaExplorer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pcaExplorer’ version ‘3.1.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 31 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... 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 loading without being on the library search path ... 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 ‘pcaexplorer_env’ Undefined global functions or variables: 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 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/pcaExplorer.Rcheck/00check.log’ for details.
pcaExplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL pcaExplorer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 v3.1.1 If you use pcaExplorer in your work, please cite: pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components Federico Marini, Harald Binder BMC Bioinformatics, 2019 - https://doi.org/10.1186/s12859-019-2879-1 > > test_check("pcaExplorer") estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns [ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 32 ] > > proc.time() user system elapsed 143.461 8.388 152.140
pcaExplorer.Rcheck/pcaExplorer-Ex.timings
name | user | system | elapsed | |
correlatePCs | 1.962 | 0.137 | 2.099 | |
deprecated | 0 | 0 | 0 | |
distro_expr | 1.678 | 0.025 | 1.704 | |
geneprofiler | 1.276 | 0.000 | 1.276 | |
genespca | 2.037 | 0.017 | 2.053 | |
get_annotation | 4.085 | 0.063 | 4.148 | |
get_annotation_orgdb | 4.645 | 0.082 | 4.730 | |
hi_loadings | 1.231 | 0.004 | 1.235 | |
limmaquickpca2go | 1.946 | 0.038 | 1.984 | |
makeExampleDESeqDataSet_multifac | 0.300 | 0.041 | 0.342 | |
pair_corr | 2.082 | 0.037 | 2.118 | |
pca2go | 1.897 | 0.041 | 1.937 | |
pcaExplorer | 2.018 | 0.038 | 2.055 | |
pcaplot | 3.374 | 0.006 | 3.380 | |
pcaplot3d | 1.217 | 0.006 | 1.227 | |
pcascree | 1.559 | 0.000 | 1.559 | |
plotPCcorrs | 1.488 | 0.007 | 1.496 | |
topGOtable | 1.973 | 0.052 | 2.025 | |