Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the pcaExplorer package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1440/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pcaExplorer 2.25.0 (landing page) Federico Marini
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: pcaExplorer |
Version: 2.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pcaExplorer_2.25.0.tar.gz |
StartedAt: 2023-02-28 10:52:30 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 11:00:56 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 506.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pcaExplorer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pcaExplorer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pcaExplorer_2.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pcaExplorer.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘pcaExplorer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pcaExplorer’ version ‘2.25.0’ * 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 ... OK * 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 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘pcaExplorer.Rmd’ using ‘UTF-8’... OK ‘upandrunning.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/pcaExplorer.Rcheck/00check.log’ for details.
pcaExplorer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pcaExplorer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘pcaExplorer’ ... ** 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 (pcaExplorer)
pcaExplorer.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 v2.25.0 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 70.842 1.637 72.469
pcaExplorer.Rcheck/pcaExplorer-Ex.timings
name | user | system | elapsed | |
correlatePCs | 2.677 | 0.091 | 2.769 | |
distro_expr | 2.547 | 0.141 | 2.687 | |
geneprofiler | 1.826 | 0.016 | 1.842 | |
genespca | 2.683 | 0.067 | 2.751 | |
get_annotation | 3.838 | 0.168 | 4.007 | |
get_annotation_orgdb | 4.444 | 0.140 | 4.585 | |
hi_loadings | 1.904 | 0.032 | 1.936 | |
limmaquickpca2go | 2.064 | 0.044 | 2.108 | |
makeExampleDESeqDataSet_multifac | 0.435 | 0.000 | 0.436 | |
pair_corr | 2.278 | 0.040 | 2.318 | |
pca2go | 3.197 | 0.108 | 3.305 | |
pcaExplorer | 2.075 | 0.056 | 2.131 | |
pcaplot | 2.562 | 0.036 | 2.598 | |
pcaplot3d | 2.857 | 0.063 | 2.929 | |
pcascree | 2.196 | 0.004 | 2.200 | |
plotPCcorrs | 2.041 | 0.016 | 2.056 | |
topGOtable | 2.039 | 0.040 | 2.079 | |