Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:34:36 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 768/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gemma.R 3.1.5 (landing page) Ogan Mancarci
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 3.1.5 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gemma.R_3.1.5.tar.gz |
StartedAt: 2024-05-29 20:11:46 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 20:22:06 -0400 (Wed, 29 May 2024) |
EllapsedTime: 620.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gemma.R.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gemma.R_3.1.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gemma.R.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘gemma.R/DESCRIPTION’ ... OK * this is package ‘gemma.R’ version ‘3.1.5’ * 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 ‘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 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 ... NOTE processSamples: no visible binding for global variable ‘sample.ID’ Undefined global functions or variables: sample.ID * 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 7.653 0.589 12.148 get_dataset_processed_expression 1.269 0.077 6.118 get_dataset_raw_expression 1.049 0.073 5.235 get_dataset_expression 0.885 0.163 7.376 get_dataset_differential_expression_analyses 0.489 0.026 5.087 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/gemma.R.Rcheck/00check.log’ for details.
gemma.R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gemma.R ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 183 ] ══ 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 183 ] > > > > proc.time() user system elapsed 66.729 4.089 282.502
gemma.R.Rcheck/gemma.R-Ex.timings
name | user | system | elapsed | |
dot-getResultSets | 0.000 | 0.000 | 0.001 | |
filter_properties | 0.065 | 0.003 | 0.069 | |
forget_gemma_memoised | 0.013 | 0.007 | 0.038 | |
gemma_call | 0.231 | 0.005 | 2.053 | |
get_child_terms | 0.305 | 0.085 | 0.509 | |
get_dataset_annotations | 0.009 | 0.000 | 0.088 | |
get_dataset_design | 0.233 | 0.004 | 0.362 | |
get_dataset_differential_expression_analyses | 0.489 | 0.026 | 5.087 | |
get_dataset_expression | 0.885 | 0.163 | 7.376 | |
get_dataset_expression_for_genes | 0.340 | 0.039 | 0.710 | |
get_dataset_object | 7.653 | 0.589 | 12.148 | |
get_dataset_platforms | 0.112 | 0.004 | 0.344 | |
get_dataset_processed_expression | 1.269 | 0.077 | 6.118 | |
get_dataset_quantitation_types | 0.010 | 0.000 | 0.212 | |
get_dataset_raw_expression | 1.049 | 0.073 | 5.235 | |
get_dataset_samples | 0.165 | 0.008 | 0.409 | |
get_datasets | 0.154 | 0.033 | 4.638 | |
get_datasets_by_ids | 0.062 | 0.011 | 0.241 | |
get_differential_expression_values | 0.332 | 0.024 | 2.620 | |
get_gene_go_terms | 0.055 | 0.001 | 0.224 | |
get_gene_locations | 0.029 | 0.003 | 0.239 | |
get_gene_probes | 0.028 | 0.005 | 0.216 | |
get_genes | 0.029 | 0.000 | 0.179 | |
get_platform_annotations | 0.867 | 0.043 | 2.999 | |
get_platform_datasets | 0.037 | 0.004 | 0.316 | |
get_platform_element_genes | 0.009 | 0.005 | 0.094 | |
get_platforms_by_ids | 0.032 | 0.000 | 0.221 | |
get_result_sets | 0.055 | 0.000 | 0.229 | |
get_taxa | 0.013 | 0.000 | 0.088 | |
get_taxa_by_ids | 0.013 | 0.000 | 0.086 | |
get_taxon_datasets | 0.069 | 0.000 | 0.366 | |
make_design | 0.621 | 0.004 | 0.891 | |
search_annotations | 0.011 | 0.000 | 0.090 | |
search_datasets | 0.038 | 0.000 | 0.439 | |
search_gemma | 0.109 | 0.004 | 0.544 | |
update_result | 0.776 | 0.044 | 3.981 | |