===============================
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_0.99.4.tar.gz
===============================
BiocCheckGitClone('tidyexposomics')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/c2d7a15f9729026b85bbc95b0c992a6266fed96d/tidyexposomics
BiocVersion: 3.22
Package: tidyexposomics
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/c2d7a15f9729026b85bbc95b0c992a6266fed96d/tidyexposomics.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/c2d7a15f9729026b85bbc95b0c992a6266fed96d/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/c2d7a15f9729026b85bbc95b0c992a6266fed96d/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 0.99.4
* 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 ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking whether startup messages can be suppressed ... [10s/10s] 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 ... [149s/149s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_enrichment 40.189 2.379 41.655
run_enrichment 33.437 2.367 33.631
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [83s/94s]
[83s/94s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
7. basilisk::obtainEnvironmentPath(env)
8. basilisk::lockExternalDir(exdir, exclusive = FALSE)
9. dir.expiry::lockDirectory(path, ...)
10. filelock::lock(plock, exclusive = FALSE)
Error ('test-run_multiomics_integration.R:17:9'): run_multiomics_integration works with 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-run_multiomics_integration.R:17:9
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 2 | WARN 32 | SKIP 0 | 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/c2d7a15f9729026b85bbc95b0c992a6266fed96d/tidyexposomics.Rcheck/00check.log
for details.
===============================
BiocCheck('tidyexposomics_0.99.4.tar.gz')
===============================
Installing tidyexposomics
Package installed successfully
tidyexposomics session metadata
sourceDir: /tmp/RtmpQTQVVi/file15e72c7111c/tidyexposomics
BiocVersion: 3.22
Package: tidyexposomics
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3928/c2d7a15f9729026b85bbc95b0c992a6266fed96d/tidyexposomics.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmpQTQVVi/file15e72c7111c/tidyexposomics
installDir: /tmp/RtmpQTQVVi/file15e72ca4d271
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...
i NOTE: Update R version dependency from 4.4.0 to 4.5.0
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
tidyexposomics.Rmd
* 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...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 366 lines (2%) 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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/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
1 ERRORS | 0 WARNINGS | i 5 NOTES
i See the tidyexposomics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.