Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-09-12 11:49 -0400 (Thu, 12 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 469/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CTDquerier 2.13.0 (landing page) Xavier Escribà-Montagut
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the CTDquerier package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CTDquerier.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: CTDquerier |
Version: 2.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CTDquerier_2.13.0.tar.gz |
StartedAt: 2024-09-12 04:03:23 -0000 (Thu, 12 Sep 2024) |
EndedAt: 2024-09-12 04:05:28 -0000 (Thu, 12 Sep 2024) |
EllapsedTime: 125.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CTDquerier.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CTDquerier.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CTDquerier_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CTDquerier.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CTDquerier/DESCRIPTION’ ... OK * this is package ‘CTDquerier’ version ‘2.13.0’ * 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 ‘CTDquerier’ can be installed ... OK * checking installed package size ... OK * checking package 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 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 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 176 marked UTF-8 strings * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘batch_query.Rmd’ ‘biomed-central.csl’ ‘case_study.Rmd’ ‘case_study.bib’ ‘img/01_CTDbase.png’ ‘img/02_XKR4_keyword.png’ ‘img/03_BatchQuery.png’ ‘vignette.Rmd’ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed load_ctd_gene 14.508 0.360 14.902 query_ctd_gene 12.301 0.619 20.162 enrich-methods 7.828 0.383 9.758 query_ctd_chem 5.642 0.051 8.985 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/CTDquerier.Rcheck/00check.log’ for details.
CTDquerier.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CTDquerier ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘CTDquerier’ ... ** using staged installation ** R ** data ** 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 (CTDquerier)
CTDquerier.Rcheck/CTDquerier-Ex.timings
name | user | system | elapsed | |
download_ctd_chem | 1.380 | 0.028 | 1.415 | |
download_ctd_dise | 0.171 | 0.004 | 0.175 | |
download_ctd_genes | 0.173 | 0.004 | 0.178 | |
enrich-methods | 7.828 | 0.383 | 9.758 | |
gala | 2.090 | 0.331 | 2.431 | |
get_table-methods | 1.057 | 0.018 | 1.077 | |
get_terms-methods | 1.035 | 0.020 | 1.057 | |
leaf_plot | 0.767 | 0.099 | 0.868 | |
load_ctd_chem | 3.056 | 0.083 | 3.147 | |
load_ctd_dise | 1.182 | 0.028 | 1.215 | |
load_ctd_gene | 14.508 | 0.360 | 14.902 | |
query_ctd_chem | 5.642 | 0.051 | 8.985 | |
query_ctd_dise | 0.830 | 0.112 | 2.390 | |
query_ctd_gene | 12.301 | 0.619 | 20.162 | |