===============================
R CMD BUILD
===============================
* checking for file ‘tidyexposomics/DESCRIPTION’ ... OK
* preparing ‘tidyexposomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory ‘tidyexposomics/inst/app/www’ is empty
* building ‘tidyexposomics_0.99.5.tar.gz’
===============================
BiocCheckGitClone('tidyexposomics')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics
→ BiocVersion: 3.22
→ Package: tidyexposomics
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• tidyexposomics.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidyexposomics/DESCRIPTION’ ... OK
* this is package ‘tidyexposomics’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘tidyexposomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [11s/11s] OK
* checking use of S3 registration ... 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 ... [40s/40s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [148s/149s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_enrichment 39.323 3.034 41.822
run_enrichment 33.759 2.160 33.895
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [86s/94s]
[87s/95s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test-run_multiomics_integration.R:3:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-extract_top_factor_features.R:18:9'): extract_top_factor_features works for MOFA ──
Error in `lock(plock, exclusive = FALSE)`: Cannot open lock file: No such file or directory
Backtrace:
▆
1. └─base::eval(...)
2. └─base::eval(...)
3. └─tidyexposomics::run_multiomics_integration(...) at test-extract_top_factor_features.R:18:9
4. └─tidyexposomics:::.run_mofa2(...)
5. └─MOFA2::run_mofa(mofa, outfile, use_basilisk = TRUE)
6. └─basilisk::basiliskStart(mofa_env)
7. └─basilisk::obtainEnvironmentPath(env)
8. └─basilisk::lockExternalDir(exdir, exclusive = FALSE)
9. └─dir.expiry::lockDirectory(path, ...)
10. └─filelock::lock(plock, exclusive = FALSE)
[ FAIL 1 | WARN 32 | SKIP 1 | PASS 197 ]
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 ... [5s/5s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidyexposomics_0.99.5.tar.gz')
===============================
── Installing tidyexposomics ───────────────────────────────────────────────────
✔ Package installed successfully
── tidyexposomics session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpl3rQXN/file26416124054cb4/tidyexposomics
→ BiocVersion: 3.22
→ Package: tidyexposomics
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/16aeeb297c324c42a40ece5750aa55df46110f18/tidyexposomics.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmpl3rQXN/file26416124054cb4/tidyexposomics
→ installDir: /tmp/Rtmpl3rQXN/file26416177cfacef
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tidyexposomics ─────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (24%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of tidyexposomics...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 69
functions greater than 50 lines.
The longest 5 functions are:
• .ont_annot_build_server() (R/server_ont_annot.R): 233 lines
• ...
• .plot_summary_enrichment() (R/plot_enrichment.R): 206 lines
* Checking man page documentation...
Registered S3 method overwritten by 'mixOmics':
method from
print.rgcca RGCCA
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
i NOTE: skip_on_bioc() found in testthat files:
test-run_multiomics_integration.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 392 lines (3%) are > 80 characters long.
First few lines:
• R/create_exposomicset.R#L3 #' Constructs a `MultiAssayExperiment` o ...
• ...
• vignettes/tidyexposomics.Rmd#L1421 Wild, C. P. (2005). Complementing the ge
...
i NOTE: Consider multiples of 4 spaces for line indents; 11 lines (0%) are not.
First few lines:
• R/interface_ont_annot.R#L11 h1,h4 { color:#1e0c1f; } ...
• ...
• R/run_sensitivity_analysis.R#L243 ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 4 NOTES
i See the tidyexposomics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.