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 163/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BgeeDB 2.33.0 (landing page) Julien Wollbrett
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the BgeeDB package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BgeeDB.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: BgeeDB |
Version: 2.33.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BgeeDB_2.33.0.tar.gz |
StartedAt: 2024-12-24 03:57:23 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 04:38:06 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 2443.3 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: BgeeDB.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BgeeDB.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BgeeDB_2.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.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 ‘BgeeDB/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BgeeDB’ version ‘2.33.0’ * 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 ‘BgeeDB’ 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 ... 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’ ... OK * checking examples ... ERROR Running examples in ‘BgeeDB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: geneList > ### Title: Example of gene list object used to run a topAnat enrichment > ### test, created on June 2018. The format of the gene list is the same > ### as the gene list required to build a 'topGOdata' object in the > ### 'topGO' package: a vector with background genes as names, and 0 or 1 > ### values depending if a gene is in the foreground or not. In this > ### example the foreground genes are zebrafish genes with an annotated > ### phenotype related to "pectoral fin", and the background is composed > ### of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. > ### The gene list was built using the biomaRt package, and the code used > ### can be found in the vignette of the package. > ### Aliases: geneList > ### Keywords: datasets > > ### ** Examples > > bgee <- Bgee$new(species = "Danio_rerio") NOTE: You did not specify any data type. The argument dataType will be set to c("rna_seq","affymetrix","est","in_situ","sc_full_length", "sc_droplet_based") for the next steps. Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory /home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded. API key built: cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3 > myTopAnatData <- loadTopAnatData(bgee) Building URLs to retrieve organ relationships from Bgee......... URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_anat_entity_relations&display_type=tsv&species_list=7955&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0) Submitting URL to Bgee webservice (can be long) Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_2" Building URLs to retrieve organ names from Bgee................. URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_anat_entities&display_type=tsv&species_list=7955&attr_list=ID&attr_list=NAME&api_key=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0) Submitting URL to Bgee webservice (can be long) Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_2" Building URLs to retrieve mapping of gene to organs from Bgee... URL successfully built (https://www.bgee.org/bgee15_2/api/?page=r_package&action=get_expression_calls&display_type=tsv&species_list=7955&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=cac8d6c96ccacca3f7357eb0673f3007860d20c17a0246ab1f7bf997a9185706c1bc9a49d42a8c7f9b6f1af5f378de4cc50980d71c16800a2e631b2fc78ea9e3&source=BgeeDB_R_package&source_version=2.33.0&data_qual=SILVER) Submitting URL to Bgee webservice (can be long) Got results from Bgee webservice. Files are written in "/home/biocbuild/bbs-3.21-bioc/meat/BgeeDB.Rcheck/Danio_rerio_Bgee_15_2" Parsing the results............................................. Examples with CPU (user + system) or elapsed time > 5s user system elapsed deleteLocalData 3.826 0.194 17.598 formatData 2.502 0.159 14.165 Bgee-class 0.151 0.031 9.528 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
BgeeDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BgeeDB ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘BgeeDB’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (BgeeDB)
BgeeDB.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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)
BgeeDB.Rcheck/BgeeDB-Ex.timings
name | user | system | elapsed | |
Bgee-class | 0.151 | 0.031 | 9.528 | |
deleteLocalData | 3.826 | 0.194 | 17.598 | |
deleteOldData | 0.053 | 0.004 | 1.388 | |
formatData | 2.502 | 0.159 | 14.165 | |