Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 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" | 4373 |
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 465/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CTDquerier 2.15.0 (landing page) Xavier Escribà-Montagut
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 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: 2.15.0 |
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_2.15.0.tar.gz |
StartedAt: 2024-12-24 05:46:38 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 05:48:46 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 128.1 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_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CTDquerier.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CTDquerier/DESCRIPTION’ ... OK * this is package ‘CTDquerier’ version ‘2.15.0’ * 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 ... OK * 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 14.248 0.244 14.524 query_ctd_gene 12.051 0.471 19.885 enrich-methods 8.499 0.479 10.573 query_ctd_chem 6.932 0.056 10.373 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-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-4.5.0-devel_2024-11-24/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 | 1.448 | 0.048 | 1.502 | |
download_ctd_dise | 0.173 | 0.000 | 0.173 | |
download_ctd_genes | 0.168 | 0.000 | 0.169 | |
enrich-methods | 8.499 | 0.479 | 10.573 | |
gala | 1.364 | 0.048 | 1.415 | |
get_table-methods | 1.129 | 0.016 | 1.148 | |
get_terms-methods | 1.187 | 0.056 | 1.247 | |
leaf_plot | 0.961 | 0.028 | 0.991 | |
load_ctd_chem | 3.849 | 0.108 | 3.965 | |
load_ctd_dise | 0.690 | 0.007 | 0.702 | |
load_ctd_gene | 14.248 | 0.244 | 14.524 | |
query_ctd_chem | 6.932 | 0.056 | 10.373 | |
query_ctd_dise | 0.789 | 0.012 | 2.358 | |
query_ctd_gene | 12.051 | 0.471 | 19.885 | |