Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/tidyexposomics
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.3 LTS)/x86_64   WARNINGS     ERROR     skipped     OK  

nebbiolo2 Summary

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Package: tidyexposomics
Version: 0.99.4
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data tidyexposomics
BuildTime: 4 minutes 19.68 seconds
CheckCommand: BiocCheckGitClone('tidyexposomics') && /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3928/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3928/c2d7a15f9729026b85bbc95b0c992a6266fed96d/tidyexposomics.install-out.txt tidyexposomics_0.99.4.tar.gz && BiocCheck('tidyexposomics_0.99.4.tar.gz', `new-package`=TRUE)
CheckTime: 8 minutes 12.20 seconds
BuildBinCommand:
BuildBinTime:
PackageFileSize: 5077.98 KiB
BuildID:: tidyexposomics_20250918220520
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: tidyexposomics. Starting Build package. Starting Check package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 1.

nebbiolo2 BUILD SRC output

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 R CMD BUILD

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* 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


nebbiolo2 CHECK output

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 BiocCheckGitClone('tidyexposomics')

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 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')




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 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.





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 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.

nebbiolo2 BUILD BIN output

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