Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-26 11:35:00 -0400 (Sun, 26 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" | 4665 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
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 1659/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ReactomeGSA 1.19.0 (landing page) Johannes Griss
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the ReactomeGSA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReactomeGSA.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: ReactomeGSA |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReactomeGSA_1.19.0.tar.gz |
StartedAt: 2024-05-25 01:44:36 -0400 (Sat, 25 May 2024) |
EndedAt: 2024-05-25 02:01:14 -0400 (Sat, 25 May 2024) |
EllapsedTime: 997.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ReactomeGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ReactomeGSA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ReactomeGSA_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ReactomeGSA.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 ‘ReactomeGSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ReactomeGSA’ version ‘1.19.0’ * 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 ‘ReactomeGSA’ 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 whether startup messages can be suppressed ... 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 plot_correlations,ReactomeAnalysisResult: no visible binding for global variable ‘combined_sig’ plot_correlations,ReactomeAnalysisResult: no visible binding for global variable ‘alpha’ plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global variable ‘cluster_id’ plot_gsva_pathway,ReactomeAnalysisResult: no visible binding for global variable ‘expr’ plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global variable ‘gsva_result’ plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global variable ‘PC1’ plot_gsva_pca,ReactomeAnalysisResult: no visible binding for global variable ‘PC2’ plot_heatmap,ReactomeAnalysisResult: no visible global function definition for ‘desc’ plot_heatmap,ReactomeAnalysisResult: no visible binding for global variable ‘n_sig’ plot_heatmap,ReactomeAnalysisResult: no visible binding for global variable ‘dataset’ plot_heatmap,ReactomeAnalysisResult: no visible binding for global variable ‘Name’ plot_volcano,ReactomeAnalysisResult: no visible binding for global variable ‘av_foldchange’ plot_volcano,ReactomeAnalysisResult: no visible binding for global variable ‘FDR’ Undefined global functions or variables: FDR Name PC1 PC2 alpha av_foldchange cluster_id combined_sig dataset desc expr gsva_result n_sig * 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 analyse_sc_clusters-Seurat-method 32.641 1.385 76.955 analyse_sc_clusters-SingleCellExperiment-method 31.839 1.163 75.443 plot_gsva_heatmap 32.212 0.444 72.638 plot_gsva_heatmap-ReactomeAnalysisResult-method 32.145 0.280 74.390 plot_gsva_pathway 31.987 0.292 73.570 plot_gsva_pathway-ReactomeAnalysisResult-method 31.775 0.356 72.124 plot_gsva_pca-ReactomeAnalysisResult-method 31.178 0.312 71.025 analyse_sc_clusters 30.911 0.497 73.294 plot_gsva_pca 30.755 0.321 71.157 ReactomeAnalysisRequest 4.827 0.344 5.172 load_public_dataset 4.046 0.032 35.358 perform_reactome_analysis 3.465 0.112 16.086 * 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/ReactomeGSA.Rcheck/00check.log’ for details.
ReactomeGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ReactomeGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘ReactomeGSA’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘analyse_sc_clusters’ with signature ‘object="Seurat"’: no definition for class “Seurat” in method for ‘analyse_sc_clusters’ with signature ‘object="SingleCellExperiment"’: no definition for class “SingleCellExperiment” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="EList"’: no definition for class “EList” in method for ‘add_dataset’ with signature ‘request="ReactomeAnalysisRequest",expression_values="DGEList"’: no definition for class “DGEList” ** 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 (ReactomeGSA)
ReactomeGSA.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(ReactomeGSA) > > test_check("ReactomeGSA") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ] > > proc.time() user system elapsed 1.438 0.071 1.498
ReactomeGSA.Rcheck/ReactomeGSA-Ex.timings
name | user | system | elapsed | |
ReactomeAnalysisRequest | 4.827 | 0.344 | 5.172 | |
ReactomeAnalysisResult-class | 1.252 | 0.052 | 1.304 | |
add_dataset-ReactomeAnalysisRequest-DGEList-method | 0.772 | 0.052 | 0.824 | |
add_dataset-ReactomeAnalysisRequest-EList-method | 0.651 | 0.003 | 0.653 | |
add_dataset-ReactomeAnalysisRequest-ExpressionSet-method | 0.649 | 0.019 | 0.669 | |
add_dataset-ReactomeAnalysisRequest-data.frame-method | 0.992 | 0.100 | 1.092 | |
add_dataset-ReactomeAnalysisRequest-matrix-method | 0.621 | 0.028 | 0.648 | |
add_dataset | 0.623 | 0.004 | 0.627 | |
analyse_sc_clusters-Seurat-method | 32.641 | 1.385 | 76.955 | |
analyse_sc_clusters-SingleCellExperiment-method | 31.839 | 1.163 | 75.443 | |
analyse_sc_clusters | 30.911 | 0.497 | 73.294 | |
find_public_datasets | 0.470 | 0.004 | 3.287 | |
get_public_species | 0.121 | 0.000 | 0.589 | |
get_reactome_data_types | 0.237 | 0.008 | 1.198 | |
get_reactome_methods | 0.506 | 0.004 | 2.581 | |
get_result-ReactomeAnalysisResult-method | 0.197 | 0.012 | 0.209 | |
get_result | 0.170 | 0.008 | 0.177 | |
load_public_dataset | 4.046 | 0.032 | 35.358 | |
names-ReactomeAnalysisResult-method | 0.174 | 0.008 | 0.182 | |
open_reactome-ReactomeAnalysisResult-method | 0.196 | 0.004 | 0.200 | |
open_reactome | 0.234 | 0.000 | 0.234 | |
pathways-ReactomeAnalysisResult-method | 1.252 | 0.000 | 1.252 | |
pathways | 1.272 | 0.000 | 1.272 | |
perform_reactome_analysis | 3.465 | 0.112 | 16.086 | |
plot_correlations-ReactomeAnalysisResult-method | 1.229 | 0.008 | 1.238 | |
plot_correlations | 1.278 | 0.016 | 1.293 | |
plot_gsva_heatmap-ReactomeAnalysisResult-method | 32.145 | 0.280 | 74.390 | |
plot_gsva_heatmap | 32.212 | 0.444 | 72.638 | |
plot_gsva_pathway-ReactomeAnalysisResult-method | 31.775 | 0.356 | 72.124 | |
plot_gsva_pathway | 31.987 | 0.292 | 73.570 | |
plot_gsva_pca-ReactomeAnalysisResult-method | 31.178 | 0.312 | 71.025 | |
plot_gsva_pca | 30.755 | 0.321 | 71.157 | |
plot_heatmap-ReactomeAnalysisResult-method | 1.457 | 0.012 | 1.468 | |
plot_heatmap | 1.571 | 0.004 | 1.575 | |
plot_volcano-ReactomeAnalysisResult-method | 0.176 | 0.016 | 0.192 | |
plot_volcano | 0.192 | 0.003 | 0.196 | |
print-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
print-ReactomeAnalysisResult-method | 0.170 | 0.004 | 0.174 | |
reactome_links-ReactomeAnalysisResult-method | 0.179 | 0.000 | 0.178 | |
reactome_links | 0.174 | 0.000 | 0.175 | |
result_types-ReactomeAnalysisResult-method | 0.156 | 0.012 | 0.168 | |
result_types | 0.169 | 0.000 | 0.169 | |
set_method-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_method | 0.001 | 0.000 | 0.002 | |
set_parameters-ReactomeAnalysisRequest-method | 0.002 | 0.000 | 0.002 | |
set_parameters | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisRequest-method | 0.001 | 0.000 | 0.001 | |
show-ReactomeAnalysisResult-method | 0.17 | 0.00 | 0.17 | |