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 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 787/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemma.R 3.2.0 (landing page) Ogan Mancarci
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the gemma.R package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.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: gemma.R |
Version: 3.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.2.0.tar.gz |
StartedAt: 2024-11-19 22:19:15 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 22:29:30 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 614.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemma.R.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_3.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gemma.R.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 ‘gemma.R/DESCRIPTION’ ... OK * this is package ‘gemma.R’ version ‘3.2.0’ * 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 ‘gemma.R’ 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_dataset_object 6.104 0.289 10.471 get_dataset_processed_expression 0.806 0.072 5.682 get_dataset_raw_expression 0.778 0.064 6.304 get_dataset_expression 0.535 0.088 8.265 get_dataset_differential_expression_analyses 0.284 0.035 6.077 get_datasets 0.134 0.022 5.033 * 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: OK
gemma.R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gemma.R ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘gemma.R’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (gemma.R)
gemma.R.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(dplyr) Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > # Prevent certificate issues for GitHub actions > options(gemma.SSL = FALSE) > # get gemma api path if it's set in the environment > gemma.R:::setGemmaPath('prod') [1] "https://gemma.msl.ubc.ca/rest/v2/" > print(gemma.R:::gemmaPath()) [1] "https://gemma.msl.ubc.ca/rest/v2/" > test_check("gemma.R") Loading required package: gemma.R [ FAIL 0 | WARN 0 | SKIP 4 | PASS 193 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5', 'testConvenience.R:37:5', 'testDatasetEndpoints.R:86:5' [ FAIL 0 | WARN 0 | SKIP 4 | PASS 193 ] > > > > proc.time() user system elapsed 43.687 3.161 292.913
gemma.R.Rcheck/gemma.R-Ex.timings
name | user | system | elapsed | |
dot-getResultSets | 0 | 0 | 0 | |
filter_properties | 0.062 | 0.010 | 0.074 | |
forget_gemma_memoised | 0.013 | 0.041 | 0.199 | |
gemma_call | 0.108 | 0.019 | 0.670 | |
get_child_terms | 0.211 | 0.021 | 0.329 | |
get_dataset_annotations | 0.006 | 0.001 | 0.091 | |
get_dataset_design | 0.186 | 0.012 | 0.366 | |
get_dataset_differential_expression_analyses | 0.284 | 0.035 | 6.077 | |
get_dataset_expression | 0.535 | 0.088 | 8.265 | |
get_dataset_expression_for_genes | 0.185 | 0.016 | 0.464 | |
get_dataset_object | 6.104 | 0.289 | 10.471 | |
get_dataset_platforms | 0.010 | 0.001 | 0.248 | |
get_dataset_processed_expression | 0.806 | 0.072 | 5.682 | |
get_dataset_quantitation_types | 0.008 | 0.001 | 0.198 | |
get_dataset_raw_expression | 0.778 | 0.064 | 6.304 | |
get_dataset_samples | 0.138 | 0.012 | 0.325 | |
get_datasets | 0.134 | 0.022 | 5.033 | |
get_datasets_by_ids | 0.034 | 0.004 | 0.208 | |
get_differential_expression_values | 0.147 | 0.030 | 3.176 | |
get_gene_differential_expression_values | 0.659 | 0.058 | 3.722 | |
get_gene_go_terms | 0.027 | 0.001 | 0.345 | |
get_gene_locations | 0.016 | 0.001 | 0.240 | |
get_gene_probes | 0.022 | 0.003 | 0.257 | |
get_genes | 0.019 | 0.002 | 0.232 | |
get_platform_annotations | 0.422 | 0.037 | 2.724 | |
get_platform_datasets | 0.026 | 0.003 | 0.307 | |
get_platform_element_genes | 0.009 | 0.001 | 0.113 | |
get_platforms_by_ids | 0.020 | 0.002 | 0.206 | |
get_result_sets | 0.030 | 0.002 | 0.214 | |
get_taxa | 0.007 | 0.001 | 0.086 | |
get_taxa_by_ids | 0.007 | 0.000 | 0.083 | |
get_taxon_datasets | 0.029 | 0.003 | 0.277 | |
make_design | 0.415 | 0.015 | 0.632 | |
search_annotations | 0.008 | 0.001 | 0.087 | |
search_datasets | 0.026 | 0.002 | 0.350 | |
search_gemma | 0.085 | 0.017 | 0.448 | |
update_result | 0.357 | 0.022 | 3.469 | |