Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:36 -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 BiocPkgTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocPkgTools.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 169/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocPkgTools 1.17.10 (landing page) Sean Davis
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
Package: BiocPkgTools |
Version: 1.17.10 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BiocPkgTools_1.17.10.tar.gz |
StartedAt: 2023-02-27 21:45:41 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 21:52:19 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 398.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BiocPkgTools.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BiocPkgTools_1.17.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocPkgTools.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 ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.17.10’ * 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 ‘BiocPkgTools’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘BiocManager:::.repositories’ ‘BiocManager:::.repositories_bioc’ ‘BiocManager:::.repository_container_version’ ‘BiocManager:::.version_bioc’ See the note in ?`:::` about the use of this operator. * 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 files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: 'biocLastBuildDate' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_bioc_data 12.907 0.610 21.145 biocBuildReport 7.965 4.932 9.904 firstInBioc 11.481 0.432 11.929 biocDownloadStats 9.028 0.348 9.995 pkgDepMetrics 8.755 0.369 18.737 pkgCombDependencyGain 8.641 0.481 20.432 class-dependencies 6.231 0.304 6.536 buildPkgDependencyDataFrame 2.964 0.131 8.380 githubDetails 1.839 0.087 11.724 biocRevDepEmail 1.779 0.085 8.558 getBiocVignette 1.577 0.088 10.776 githubURLParts 1.408 0.036 6.211 subgraphByDegree 1.364 0.078 8.719 * 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 ... ‘BiocPkgTools.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocPkgTools.Rcheck/00check.log’ for details.
BiocPkgTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocPkgTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘BiocPkgTools’ ... ** 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 (BiocPkgTools)
BiocPkgTools.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(BiocPkgTools) Loading required package: htmlwidgets > > test_check("BiocPkgTools") trying URL 'https://bioconductor.org/packages/3.17/bioc/vignettes/a4/inst/doc/a4vignette.pdf' Content type 'application/pdf' length 1304018 bytes (1.2 MB) ================================================== downloaded 1.2 MB [ FAIL 0 | WARN 6 | SKIP 0 | PASS 30 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 30 ] > > proc.time() user system elapsed 37.752 5.017 65.146
BiocPkgTools.Rcheck/BiocPkgTools-Ex.timings
name | user | system | elapsed | |
BiocPkgTools-deprecated | 0.352 | 0.024 | 1.373 | |
activitySince | 0.000 | 0.000 | 0.001 | |
anacondaDownloadStats | 1.819 | 0.045 | 3.356 | |
biocBuildReport | 7.965 | 4.932 | 9.904 | |
biocDownloadStats | 9.028 | 0.348 | 9.995 | |
biocMaintained | 1.717 | 0.064 | 3.804 | |
biocPkgList | 1.537 | 0.055 | 3.030 | |
biocPkgRanges | 0 | 0 | 0 | |
biocRevDepEmail | 1.779 | 0.085 | 8.558 | |
buildPkgDependencyDataFrame | 2.964 | 0.131 | 8.380 | |
buildPkgDependencyIgraph | 1.490 | 0.051 | 4.189 | |
class-dependencies | 6.231 | 0.304 | 6.536 | |
firstInBioc | 11.481 | 0.432 | 11.929 | |
generateBiocPkgDOI | 0 | 0 | 0 | |
getBiocVignette | 1.577 | 0.088 | 10.776 | |
get_bioc_data | 12.907 | 0.610 | 21.145 | |
get_cre_orcids | 0.008 | 0.000 | 0.008 | |
githubDetails | 1.839 | 0.087 | 11.724 | |
githubURLParts | 1.408 | 0.036 | 6.211 | |
inducedSubgraphByPkgs | 1.488 | 0.056 | 3.933 | |
latestPkgStats | 0 | 0 | 0 | |
orcid_table | 0 | 0 | 0 | |
pkgBiocDeps | 0.310 | 0.000 | 1.037 | |
pkgCombDependencyGain | 8.641 | 0.481 | 20.432 | |
pkgDepImports | 0.203 | 0.016 | 0.218 | |
pkgDepMetrics | 8.755 | 0.369 | 18.737 | |
pkgDownloadRank | 1.130 | 0.028 | 1.844 | |
pkgDownloadStats | 0.080 | 0.005 | 0.585 | |
problemPage | 0 | 0 | 0 | |
repositoryStats | 0.293 | 0.020 | 1.033 | |
subgraphByDegree | 1.364 | 0.078 | 8.719 | |