Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:04 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 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 1002/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HuBMAPR 1.3.1 (landing page) Christine Hou
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the HuBMAPR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HuBMAPR.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: HuBMAPR |
Version: 1.3.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HuBMAPR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HuBMAPR_1.3.1.tar.gz |
StartedAt: 2025-10-12 22:38:51 -0400 (Sun, 12 Oct 2025) |
EndedAt: 2025-10-12 22:40:45 -0400 (Sun, 12 Oct 2025) |
EllapsedTime: 113.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: HuBMAPR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HuBMAPR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HuBMAPR_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HuBMAPR.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HuBMAPR/DESCRIPTION’ ... OK * this is package ‘HuBMAPR’ version ‘1.3.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘HuBMAPR’ 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 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘HuBMAPR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: publications > ### Title: HuBMAP Samples > ### Aliases: publications publications_default_columns publication_data > ### publication_authors > > ### ** Examples > > publications() # A tibble: 14 × 7 uuid hubmap_id last_modified_timest…¹ publication_date publication_status <chr> <chr> <chr> <chr> <chr> 1 f53d60b… HBM536.H… 2025-10-06 2025-08-20 FALSE 2 213e89c… HBM545.W… 2025-09-22 2025-07-01 TRUE 3 a10041a… HBM923.V… 2025-06-10 2025-05-23 FALSE 4 64ca708… HBM827.D… 2025-05-21 2025-06-03 TRUE 5 fa99f1a… HBM326.T… 2025-03-12 2025-03-12 TRUE 6 2ced91f… HBM885.X… 2023-07-18 2024-09-27 TRUE 7 aea510e… HBM332.M… 2023-07-18 2022-10-24 TRUE 8 77ab358… HBM222.S… 2023-07-18 2023-07-20 TRUE 9 dd0e7ae… HBM599.D… 2023-07-18 2023-07-19 TRUE 10 3c72736… HBM629.D… 2023-07-18 2023-07-19 TRUE 11 e833896… HBM695.W… 2023-07-18 2023-07-19 TRUE 12 0de8528… HBM473.R… 2023-07-18 2023-07-19 TRUE 13 eb97581… HBM464.W… 2023-07-18 2023-07-19 TRUE 14 72cbeb8… HBM222.Z… 2023-07-18 2023-07-19 TRUE # ℹ abbreviated name: ¹last_modified_timestamp # ℹ 2 more variables: publication_venue <chr>, title <chr> > publications_default_columns() # A tibble: 7 × 1 columns <chr> 1 uuid 2 hubmap_id 3 title 4 publication_venue 5 last_modified_timestamp 6 publication_date 7 publication_status > > uuid <- "3c7273660cdf9ab91a7901533b2cd9a5" > publication_data(uuid) Error in `mutate()`: ℹ In argument: `dataset_type = ifelse(...)`. Caused by error in `map_chr()`: ℹ In index: 61. Caused by error: ! Result must be length 1, not 0. Backtrace: ▆ 1. ├─HuBMAPR::publication_data(uuid) 2. │ ├─dplyr::mutate(...) 3. │ └─dplyr:::mutate.data.frame(...) 4. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 5. │ ├─base::withCallingHandlers(...) 6. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 7. │ └─mask$eval_all_mutate(quo) 8. │ └─dplyr (local) eval() 9. ├─base::ifelse(...) 10. ├─purrr::map_chr(.data$uuid, ~.uuid_category(.x)) 11. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ └─purrr:::call_with_cleanup(...) 15. └─base::.handleSimpleError(...) 16. └─purrr (local) h(simpleError(msg, call)) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed donors 6.011 0.353 22.828 datasets 2.525 0.215 5.661 * 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: -"rui_location"), everything()), dataset_type = ifelse(is.na(.data$dataset_type), map_chr(.data$uuid, ~.uuid_category(.x)), .data$dataset_type))`: i In argument: `dataset_type = ifelse(...)`. Caused by error in `map_chr()`: i In index: 61. Caused by error: ! Result must be length 1, not 0. ── Failure ('test_utilities.R:51:3'): '.uuid_category()' works ───────────────── .uuid_category("2e7123dcf2e9092a42ac42e44c2d686b") (`actual`) not equal to "Dataset" (`expected`). `actual` is NULL `expected` is a character vector ('Dataset') [ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ] 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/HuBMAPR.Rcheck/00check.log’ for details.
HuBMAPR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HuBMAPR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘HuBMAPR’ ... ** this is package ‘HuBMAPR’ version ‘1.3.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (HuBMAPR)
HuBMAPR.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(HuBMAPR) > > test_check("HuBMAPR") [ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_datasets.R:45:3'): 'dataset_metadata()' works ──────────────── nrow(tbl) > 0L && all(c("Key", "Value") %in% names(tbl)) is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test_publications.R:30:3'): 'publication_authors()', 'publication_information()' and 'publication_data()' work with specific uuid ── <dplyr:::mutate_error/rlang_error/error/condition> Error in `mutate(unnest(select(.query_match(uuid, "hits.hits[]._source.ancestors[]"), -"rui_location"), everything()), dataset_type = ifelse(is.na(.data$dataset_type), map_chr(.data$uuid, ~.uuid_category(.x)), .data$dataset_type))`: i In argument: `dataset_type = ifelse(...)`. Caused by error in `map_chr()`: i In index: 61. Caused by error: ! Result must be length 1, not 0. ── Failure ('test_utilities.R:51:3'): '.uuid_category()' works ───────────────── .uuid_category("2e7123dcf2e9092a42ac42e44c2d686b") (`actual`) not equal to "Dataset" (`expected`). `actual` is NULL `expected` is a character vector ('Dataset') [ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ] Error: Test failures Execution halted
HuBMAPR.Rcheck/HuBMAPR-Ex.timings
name | user | system | elapsed | |
collection_information | 0.241 | 0.017 | 0.801 | |
collections | 0.336 | 0.032 | 0.830 | |
datasets | 2.525 | 0.215 | 5.661 | |
donors | 6.011 | 0.353 | 22.828 | |
files | 0.001 | 0.000 | 0.000 | |
organs | 0.030 | 0.000 | 0.099 | |
provenance | 0.235 | 0.017 | 0.727 | |
publication_information | 0.148 | 0.008 | 0.539 | |