Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 723/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
fenr 1.6.2 (landing page) Marek Gierlinski
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the fenr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fenr.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: fenr |
Version: 1.6.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fenr_1.6.2.tar.gz |
StartedAt: 2025-10-14 09:08:58 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 09:14:39 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 341.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: fenr.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fenr_1.6.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/fenr.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fenr/DESCRIPTION’ ... OK * this is package ‘fenr’ version ‘1.6.2’ * 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 ‘fenr’ 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 ‘fenr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fetch_reactome > ### Title: Get functional term data from Reactome > ### Aliases: fetch_reactome > > ### ** Examples > > reactome_data <- fetch_reactome("Saccharomyces cerevisiae", on_error = "warn") Warning: download failed web resource path: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’ local file path: ‘/home/biocbuild/.cache/R/fenr/d5c0b246e1ee_Ensembl2Reactome_PE_Pathway.txt’ reason: Failure when receiving data from the peer [reactome.org]: OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0 Warning: bfcadd() failed; resource removed rid: BFC8 fpath: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’ reason: download failed Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : bfcadd() failed; see warnings() Calls: fetch_reactome ... cache_path -> <Anonymous> -> <Anonymous> -> .util_download Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed fetch_go 32.323 1.542 45.659 fetch_kegg 1.282 0.218 22.499 * 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: 2. │ └─fenr:::fetch_reactome_ensembl_genes(...) 3. │ ├─dplyr::distinct(...) 4. │ ├─dplyr::filter(...) 5. │ ├─dplyr::select(...) 6. │ ├─dplyr::mutate(...) 7. │ ├─dplyr::filter(...) 8. │ └─readr::read_tsv(lpath, col_names = colms, show_col_types = FALSE) 9. │ └─vroom::vroom(...) 10. │ └─vroom:::vroom_(...) 11. ├─base (local) `<fn>`(`<curl>`, `<raw>`, 131071L) 12. └─curl:::raise_libcurl_error(...) [ FAIL 1 | WARN 0 | SKIP 1 | PASS 312 ] 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/fenr.Rcheck/00check.log’ for details.
fenr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL fenr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘fenr’ ... ** this is package ‘fenr’ version ‘1.6.2’ ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** 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 (fenr)
fenr.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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) > library(fenr) > > test_check("fenr") [ FAIL 1 | WARN 0 | SKIP 1 | PASS 312 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_bp.R:9:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_reactome.R:62:3'): Correct Reactome Ensembl from yeast ───────── <curl_error_recv_error/curl_error/error/condition> Error in `(function (con, what, n = 1L, size = NA_integer_, signed = TRUE, endian = .Platform$endian) { if (!endian %in% c("big", "little", "swap")) stop("invalid 'endian' argument") if (is.character(con)) { con <- file(con, "rb") on.exit(close(con)) } swap <- endian != .Platform$endian if (!is.character(what) || is.na(what) || length(what) != 1L || !any(what == c("numeric", "double", "integer", "int", "logical", "complex", "character", "raw"))) what <- typeof(what) .Internal(readBin(con, what, n, size, signed, swap)) })(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x27074630>), raw(0), 131071L)`: Failure when receiving data from the peer [reactome.org]: OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0 Backtrace: ▆ 1. ├─fenr::fetch_reactome(...) at test_reactome.R:62:3 2. │ └─fenr:::fetch_reactome_ensembl_genes(...) 3. │ ├─dplyr::distinct(...) 4. │ ├─dplyr::filter(...) 5. │ ├─dplyr::select(...) 6. │ ├─dplyr::mutate(...) 7. │ ├─dplyr::filter(...) 8. │ └─readr::read_tsv(lpath, col_names = colms, show_col_types = FALSE) 9. │ └─vroom::vroom(...) 10. │ └─vroom:::vroom_(...) 11. ├─base (local) `<fn>`(`<curl>`, `<raw>`, 131071L) 12. └─curl:::raise_libcurl_error(...) [ FAIL 1 | WARN 0 | SKIP 1 | PASS 312 ] Error: Test failures Execution halted
fenr.Rcheck/fenr-Ex.timings
name | user | system | elapsed | |
enrichment_interactive | 0 | 0 | 0 | |
fetch_bp | 0.387 | 0.000 | 1.673 | |
fetch_go | 32.323 | 1.542 | 45.659 | |
fetch_go_species | 0.035 | 0.020 | 0.504 | |
fetch_kegg | 1.282 | 0.218 | 22.499 | |
fetch_kegg_species | 0.104 | 0.034 | 2.398 | |