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R CMD BUILD
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* checking for file ‘enrichmet/DESCRIPTION’ ... OK
* preparing ‘enrichmet’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
Omitted ‘LazyData’ from DESCRIPTION
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘create_network_plot.R’
* building ‘enrichmet_0.99.14.tar.gz’
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BiocCheckGitClone('enrichmet')
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── Running Git clone checks on enrichmet ───────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3845/1b5366da5647f22dc9850b7d69a9e742a341df49/enrichmet.Rcheck’
* using R version 4.6.1 (2026-06-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-09-18 22:16:26 UTC
* using option ‘--no-vignettes’
* checking for file ‘enrichmet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichmet’ version ‘0.99.14’
* 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 ‘enrichmet’ 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 ... WARNING
Found the following files with non-ASCII characters:
R/enrichmet.R
R/helpers.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘curl’ ‘data.table’
Namespace in Imports field not imported from: ‘KEGGREST’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
fetch_kegg_chebi: no visible global function definition for
‘read.delim’
fetch_kegg_pathway_metabolites: no visible global function definition
for ‘read.delim’
fetch_kegg_pathway_metabolites: no visible global function definition
for ‘aggregate’
fetch_lion_lipid_ontology: no visible global function definition for
‘aggregate’
fetch_reactome_reactions: no visible global function definition for
‘read.delim’
Undefined global functions or variables:
aggregate read.delim
Consider adding
importFrom("stats", "aggregate")
importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 ... [7s/37s] ERROR
Running examples in ‘enrichmet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_centrality_plot
> ### Title: Create Centrality Plot
> ### Aliases: create_centrality_plot
>
> ### ** Examples
>
> # Always-runnable minimal example (no network)
> cen <- data.frame(
+ Metabolite = c("C00031", "C00022", "C00074"),
+ RBC_Metabolite = c(0.12, 0.08, 0.05),
+ stringsAsFactors = FALSE
+ )
> create_centrality_plot(cen, top_n = 3)
>
>
> PathwayVsMetabolites <- fetch_kegg_pathway_metabolites(organism = "hsa")
> kegg_lookup <- fetch_kegg_compound_lookup()
>
> metabolomics_path <- get_cached_file(
+ "https://zenodo.org/api/records/17819145/files/example_data.csv/content"
+ )
Warning: download failed
web resource path: ‘https://zenodo.org/api/records/17819145/files/example_data.csv/content’
local file path: ‘/home/pkgbuild/.cache/R/BiocFileCache/40578612820e4_content’
reason: HTTP 504 Gateway Timeout.
Warning: bfcadd() failed; resource removed
rid: BFC118
fpath: ‘https://zenodo.org/api/records/17819145/files/example_data.csv/content’
reason: download failed
Error: Failed to download resource: https://zenodo.org/api/records/17819145/files/example_data.csv/content
bfcadd() failed; see warnings()
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/36s]
[6s/36s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(enrichmet)
>
> test_check("enrichmet")
Saving _problems/test-enrichmet-30.R
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-enrichmet.R:27:1'): (code run outside of `test_that()`) ────────
Error in `file(file, "rt")`: cannot open the connection to 'https://zenodo.org/api/records/17819145/files/summary_stat.csv/content'
Backtrace:
▆
1. └─utils::read.csv(...) at test-enrichmet.R:27:1
2. └─utils::read.table(...)
3. └─base::file(file, "rt")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
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] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character ↔ (U+2194)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 3 ERRORs, 3 WARNINGs, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3845/1b5366da5647f22dc9850b7d69a9e742a341df49/enrichmet.Rcheck/00check.log’
for details.
===============================
BiocCheck('enrichmet_0.99.14.tar.gz')
===============================
── Installing enrichmet ────────────────────────────────────────────────────────
✔ Package installed successfully
── enrichmet session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvfWQl9/file4203935095f95/enrichmet
→ BiocVersion: 3.23
→ Package: enrichmet
→ PackageVersion: 0.99.14
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3845/1b5366da5647f22dc9850b7d69a9e742a341df49/enrichmet.BiocCheck
→ BiocCheckVersion: 1.49.31
→ sourceDir: /tmp/RtmpvfWQl9/file4203935095f95/enrichmet
→ installDir: /tmp/RtmpvfWQl9/file42039590346f5/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on enrichmet ──────────────────────────────────────────────
* 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 4.1.0 to 4.6.0
* 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (29%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking CITATION...
i (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()'.
* 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 enrichmet...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• fetch_background_data.R (line 247, column 9)
• fetch_background_data.R (line 304, column 9)
• fetch_background_data.R (line 672, column 9)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/helpers.R (line 154, column 5)
• ...
• cat() in R/helpers.R (line 161, column 9)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/fetch_background_data.R (line 845, column 13)
• R/fetch_background_data.R (line 890, column 17)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/fetch_background_data.R (line 892, column 21)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/helpers.R (line 42, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 25
functions greater than 50 lines.
The longest 5 functions are:
• enrichmet() (R/enrichmet.R): 413 lines
• ...
• fetch_lion_lipid_ontology() (R/fetch_background_data.R): 245 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• fetch_kegg_compound_lookup.Rd
• ...
• get_cached_file.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
• fetch_kegg_compound_lookup.Rd
• ...
• fetch_reactome_reactions.Rd
* 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; 356 lines (5%) are > 80 characters long.
First few lines:
• R/calculate_metabolite_centrality.R#L6 #' @param PathwayVsMetabolites A
data fr ...
• ...
• vignettes/Tutorial.Rmd#L365 3. Molenaar, M. R., Jeucken, A., Wassena ...
i NOTE: Consider multiples of 4 spaces for line indents; 524 lines (7%) are
not.
First few lines:
• R/calculate_metabolite_centrality.R#L40 !is.na(Metabolites ...
• ...
• vignettes/Tutorial.Rmd#L80 Section 3.3); or ...
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 'enrichmet' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.31 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the enrichmet.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.