| 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 |
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###
### 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
###
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* 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 | |