Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-17 11:40 -0400 (Sat, 17 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 162/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BgeeDB 2.31.1 (landing page) Julien Wollbrett
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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. |
Package: BgeeDB |
Version: 2.31.1 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeDB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BgeeDB_2.31.1.tar.gz |
StartedAt: 2024-08-16 22:35:36 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 22:52:47 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 1031.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: BgeeDB.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BgeeDB.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BgeeDB_2.31.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'BgeeDB/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BgeeDB' version '2.31.1' * 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 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 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: getCellRawData > ### Title: Retrieve Bgee processed expression values at cell level for > ### single cell data in Bgee. > ### Aliases: getCellRawData > > ### ** Examples > > { + bgee <- Bgee$new(species = "Drosophila_melanogaster", dataType = "sc_droplet_based") + flyCellAtlasH5AD <- getCellRawData(bgee, experimentId = "ERP129698") + + } Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/Drosophila_melanogaster_Bgee_15_2 folder. * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: ▆ 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_loadTopAnatData.R:6:3 2. └─BgeeDB:::bgee_download_file(...) 3. └─curl::curl_download(url = url, destfile = destfile, quiet = quiet) ── Error ('test_topAnat.R:6:3'): Creating the topAnat object is working ──────── Error in `curl_download(url = url, destfile = destfile, quiet = quiet)`: HTTP error 500. Backtrace: ▆ 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_topAnat.R:6:3 2. └─BgeeDB:::bgee_download_file(...) 3. └─curl::curl_download(url = url, destfile = destfile, quiet = quiet) [ FAIL 3 | WARN 3 | SKIP 0 | PASS 14 ] Error: Test failures Execution halted * 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: 2 ERRORs See 'F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/00check.log' for details.
BgeeDB.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BgeeDB ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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.fail
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(BgeeDB) Loading required package: topGO Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: SparseM groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:S4Vectors': expand The following object is masked from 'package:testthat': matches > > Sys.setenv("R_TESTS" = "") > test_check("BgeeDB") Querying Bgee to get release information... Building URL to query species in Bgee release 15_2... downloading Bgee species info... (https://www.bgee.org/ftp/bgee_v15_2/rPackageSpeciesInfo.tsv) Download of species information successful! API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_2 folder. Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_15_2 folder. Querying Bgee to get release information... Building URL to query species in Bgee release 13_2... downloading Bgee species info... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.31.1) Download of species information successful! API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/ Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder. Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 13_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 IMPORTANT INFORMATION: Be careful! You are not using the last release of the Bgee database! If it is not intentional you should update to the last version of Bioconductor and of the BgeeDB package. To update Bioconductor, see https://www.bioconductor.org/install/ Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Mus_musculus_Bgee_13_2 folder. Querying Bgee to get release information... Building URL to query species in Bgee release 14_2... downloading Bgee species info... (https://r.bgee.org/bgee14_2/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.31.1) Download of species information successful! Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 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=9913&attr_list=SOURCE_ID&attr_list=TARGET_ID&api_key=43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898&source=BgeeDB_R_package&source_version=2.31.1) Submitting URL to Bgee webservice (can be long) Got results from Bgee webservice. Files are written in "F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_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=9913&attr_list=ID&attr_list=NAME&api_key=43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898&source=BgeeDB_R_package&source_version=2.31.1) Submitting URL to Bgee webservice (can be long) Got results from Bgee webservice. Files are written in "F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_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=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898&source=BgeeDB_R_package&source_version=2.31.1&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092) Submitting URL to Bgee webservice (can be long) Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Saved annotation files in F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Drosophila_simulans_Bgee_15_2 folder. Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 Querying Bgee to get release information... NOTE: the file describing Bgee species information for release 15_2 was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat. Data will not be redownloaded. API key built: 43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898 NOTE: an organ relationships file was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded. NOTE: an organ names file was found in the download directory F:/biocbuild/bbs-3.20-bioc/meat/BgeeDB.Rcheck/tests/testthat/Bos_taurus_Bgee_15_2. Data will not be redownloaded. 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=9913&attr_list=GENE_ID&attr_list=ANAT_ENTITY_ID&api_key=43c24377150f9698c2e40461d64243d322bfdabf34f7e22cab753013bcdc6b393e6a75eee84da2f9bc47dd34df5d9d5c87996b500b0540aaec7876f9932da898&source=BgeeDB_R_package&source_version=2.31.1&data_type=RNA_SEQ&data_qual=SILVER&stage_id=UBERON:0000092) Submitting URL to Bgee webservice (can be long) [ FAIL 3 | WARN 3 | SKIP 0 | PASS 14 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_format_data.R:7:3'): Formatting gene expression files ────────── Error in `formatData(bgee, data_bgee_mouse_exp, callType = "present", stats = "fpkm")`: Choose whether data formatting should create a matrix of TPMs or read counts, with stats option set as "tpm" or "counts" Backtrace: ▆ 1. └─BgeeDB::formatData(...) at test_format_data.R:7:3 ── Error ('test_loadTopAnatData.R:6:3'): Loading of topAnatData files is working ── Error in `curl_download(url = url, destfile = destfile, quiet = quiet)`: HTTP error 500. Backtrace: ▆ 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_loadTopAnatData.R:6:3 2. └─BgeeDB:::bgee_download_file(...) 3. └─curl::curl_download(url = url, destfile = destfile, quiet = quiet) ── Error ('test_topAnat.R:6:3'): Creating the topAnat object is working ──────── Error in `curl_download(url = url, destfile = destfile, quiet = quiet)`: HTTP error 500. Backtrace: ▆ 1. └─BgeeDB::loadTopAnatData(bgee, stage = "UBERON:0000092") at test_topAnat.R:6:3 2. └─BgeeDB:::bgee_download_file(...) 3. └─curl::curl_download(url = url, destfile = destfile, quiet = quiet) [ FAIL 3 | WARN 3 | SKIP 0 | PASS 14 ] Error: Test failures Execution halted
BgeeDB.Rcheck/BgeeDB-Ex.timings
name | user | system | elapsed | |
Bgee-class | 0.03 | 0.07 | 0.90 | |
deleteLocalData | 3.39 | 0.36 | 5.74 | |
deleteOldData | 0.01 | 0.00 | 0.16 | |
formatData | 3.08 | 0.32 | 4.50 | |
geneList | 12.37 | 0.83 | 51.20 | |
getAnnotation | 0.07 | 0.00 | 0.44 | |