Multiple platform build/check report for BioC 3.22 - CHECK results for GWENA on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4822
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4617
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4564
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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*

CHECK results for GWENA on lconway

To the developers/maintainers of the GWENA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GWENA.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.

raw results

Summary

Package: GWENA

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.19.0.tar.gz

StartedAt: 2025-09-03 21:19:34 -0400 (Wed, 03 Sep 2025)

EndedAt: 2025-09-03 21:27:43 -0400 (Wed, 03 Sep 2025)

EllapsedTime: 488.9 seconds

RetCode: 1

Status: ERROR

CheckDir: GWENA.Rcheck

Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.19.0’
* 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 ‘GWENA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
  Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
  Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
  Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
 OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... WARNING
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
 NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  build_net.Rd: adjacency.fromSimilarity
  get_fit.cor.Rd: pickSoftThreshold.fromSimilarity
  get_fit.expr.Rd: pickSoftThreshold.fromSimilarity
  plot_module.Rd: igraph.plotting
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GWENA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bio_enrich
> ### Title: Modules enrichment
> ### Aliases: bio_enrich
> 
> ### ** Examples
> 
> custom_path <- system.file("extdata", "h.all.v6.2.symbols.gmt",
+                            package = "GWENA", mustWork = TRUE)
> 
> single_module <- c("BIRC3", "PMAIP1", "CASP8", "JUN", "BCL2L11", "MCL1",
+                    "IL1B", "SPTAN1", "DIABLO", "BAX", "BIK", "IL1A", "BID",
+                    "CDKN1A", "GADD45A")
> single_module_enriched <- bio_enrich(single_module, custom_path)
Error in value[[3L]](cond) : 
  Something went wrong. You can validate your GMT file using our web helper: https://biit.cs.ut.ee/gmt-helper/ (tab Validate GMT file).
Calls: bio_enrich ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-biological_integration.R:16:1'): (code run outside of `test_that()`) ──
  Error in `value[[3L]](cond)`: Something went wrong. You can validate your GMT file using our web helper: https://biit.cs.ut.ee/gmt-helper/ (tab Validate GMT file).
  Backtrace:
      ▆
   1. └─gprofiler2::upload_GMT_file(gmt_entrez_path) at test-biological_integration.R:16:1
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]
  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, 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00check.log’
for details.

Installation output

GWENA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWENA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GWENA’ ...
** this is package ‘GWENA’ version ‘1.19.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
*** 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 (GWENA)

Tests output

GWENA.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "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.

> library(testthat)
> library(GWENA)

> 
> test_check("GWENA")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biological_integration.R:16:1'): (code run outside of `test_that()`) ──
Error in `value[[3L]](cond)`: Something went wrong. You can validate your GMT file using our web helper: https://biit.cs.ut.ee/gmt-helper/ (tab Validate GMT file).
Backtrace:
    ▆
 1. └─gprofiler2::upload_GMT_file(gmt_entrez_path) at test-biological_integration.R:16:1
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]
Error: Test failures
Execution halted

Example timings

GWENA.Rcheck/GWENA-Ex.timings

name	user	system	elapsed
associate_phenotype	0.026	0.003	0.029