Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:05 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 67/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
animalcules 1.22.0 (landing page) Jessica McClintock
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the animalcules package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.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: animalcules |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.22.0.tar.gz |
StartedAt: 2024-11-19 19:26:37 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 19:33:45 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 428.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: animalcules.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/animalcules.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘animalcules/DESCRIPTION’ ... OK * this is package ‘animalcules’ version ‘1.22.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘animalcules’ 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 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘animalcules-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: find_taxonomy_300 > ### Title: Find the taxonomy for maximum 300 tids > ### Aliases: find_taxonomy_300 > > ### ** Examples > > taxonLevels <- find_taxonomy_300(tids = 1200) Error in entrez_check(response) : HTTP failure: 429, too many requests. Functions that contact the NCBI should not be called in parallel. If you are using a shared IP, consider registerring for an API key as described in the rate-limiting section of rentrez tutorial. NCBI message: {"error":"API rate limit exceeded","api-key":"155.52.47.207","count":"4","limit":"3"} Calls: find_taxonomy_300 ... entrez_fetch -> do.call -> <Anonymous> -> entrez_check Execution halted * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/Users/biocbuild/bbs-3.20-bioc/meat/animalcules.Rcheck/00check.log’ for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘animalcules’ ... ** 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 (animalcules)
animalcules.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(animalcules) > > test_check("animalcules") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 20.607 0.859 22.345
animalcules.Rcheck/animalcules-Ex.timings
name | user | system | elapsed | |
alpha_div_boxplot | 0.870 | 0.042 | 0.928 | |
alpha_div_test | 0.002 | 0.001 | 0.003 | |
counts_to_logcpm | 0.001 | 0.001 | 0.001 | |
counts_to_relabu | 0.002 | 0.000 | 0.002 | |
df_char_to_factor | 0.001 | 0.001 | 0.001 | |
differential_abundance | 2.968 | 0.071 | 3.045 | |
dimred_pca | 0.143 | 0.028 | 0.171 | |
dimred_pcoa | 0.092 | 0.025 | 0.117 | |
dimred_tsne | 3.954 | 0.145 | 4.114 | |
dimred_umap | 0.295 | 0.025 | 0.321 | |
diversities | 0.001 | 0.000 | 0.000 | |
diversities_help | 0 | 0 | 0 | |
diversity_beta_boxplot | 0.162 | 0.024 | 0.188 | |
diversity_beta_heatmap | 0.152 | 0.032 | 0.185 | |
diversity_beta_test | 0.137 | 0.003 | 0.139 | |
do_alpha_div_test | 0.040 | 0.001 | 0.041 | |
filter_categorize | 0.216 | 0.055 | 0.275 | |
filter_summary_bar_density | 0.789 | 0.032 | 0.824 | |
filter_summary_pie_box | 0.158 | 0.026 | 0.185 | |
find_biomarker | 3.212 | 0.124 | 3.366 | |
find_taxon_mat | 0.114 | 0.007 | 0.860 | |
find_taxonomy | 0.016 | 0.001 | 0.651 | |