===============================
R CMD BUILD
===============================
* checking for file ‘ontoProc2/DESCRIPTION’ ... OK
* preparing ‘ontoProc2’:
* 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
WARNING: directory ‘ontoProc2/.github’ is empty
WARNING: directory ‘ontoProc2/docs’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘ontoProc2_0.99.5.tar.gz’
===============================
BiocCheckGitClone('ontoProc2')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/ontoProc2_20260324153140/ontoProc2
→ BiocVersion: 3.23
→ Package: ontoProc2
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/ontoProc2_20260324153140/ontoProc2.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/ontoProc2_20260324153140/ontoProc2
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 v1.47.20 results ──────────────────────────────────────────────────
✖ 0 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/4187/ontoProc2_20260324153140/ontoProc2.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-24 15:36:32 UTC
* using option ‘--no-vignettes’
* checking for file ‘ontoProc2/DESCRIPTION’ ... OK
* this is package ‘ontoProc2’ version ‘0.99.5’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ontoProc2’ 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
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 ... [7s/7s] NOTE
File ‘ontoProc2/R/zzz.R’:
.onLoad calls:
cat("<SemsqlConn>", " prefix:", x@ontology_prefix, " | labeled terms:", format(n_labels, big.mark = ","), "\n")
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in '?.onAttach'.
make_graphNEL_from_ontology_plot: no visible global function definition
for ‘new’
make_graphNEL_from_ontology_plot: no visible global function definition
for ‘as’
retrieve_semsql_conn: no visible global function definition for
‘download.file’
Undefined global functions or variables:
as download.file new
Consider adding
importFrom("methods", "as", "new")
importFrom("utils", "download.file")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in Rd file 'SemsqlConn.Rd'
‘con’ ‘db_path’ ‘ontology_prefix’
Undocumented arguments in Rd file 'count_by_prefix.Rd'
‘...’
Undocumented arguments in Rd file 'count_descendants.Rd'
‘...’
Documented arguments not in \usage in Rd file 'count_descendants.Rd':
‘term_id’ ‘predicate’
Undocumented arguments in Rd file 'describe_table.Rd'
‘...’
Documented arguments not in \usage in Rd file 'describe_table.Rd':
‘table_name’
Undocumented arguments in Rd file 'disconnect.Rd'
‘...’
Documented arguments not in \usage in Rd file 'disconnect.Rd':
‘quiet’
Undocumented arguments in Rd file 'find_by_restriction.Rd'
‘...’
Documented arguments not in \usage in Rd file 'find_by_restriction.Rd':
‘property’ ‘filler’ ‘include_filler_descendants’
Undocumented arguments in Rd file 'find_intersection.Rd'
‘...’
Documented arguments not in \usage in Rd file 'find_intersection.Rd':
‘superclass_id’ ‘relation_property’ ‘related_to_id’
Undocumented arguments in Rd file 'get_ancestors.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_ancestors.Rd':
‘term_id’ ‘predicates’ ‘include_self’
Undocumented arguments in Rd file 'get_definition.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_definition.Rd':
‘term_id’
Undocumented arguments in Rd file 'get_descendants.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_descendants.Rd':
‘term_id’ ‘predicates’ ‘include_self’
Undocumented arguments in Rd file 'get_direct_edges.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_direct_edges.Rd':
‘term_id’ ‘direction’
Undocumented arguments in Rd file 'get_direct_subclasses.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_direct_subclasses.Rd':
‘term_id’
Undocumented arguments in Rd file 'get_direct_superclasses.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_direct_superclasses.Rd':
‘term_id’
Undocumented arguments in Rd file 'get_label.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_label.Rd':
‘term_id’
Undocumented arguments in Rd file 'get_prefix.Rd'
‘...’
Undocumented arguments in Rd file 'get_restrictions.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_restrictions.Rd':
‘term_id’
Undocumented arguments in Rd file 'get_synonyms.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_synonyms.Rd':
‘term_id’ ‘type’
Undocumented arguments in Rd file 'get_term_info.Rd'
‘...’
Documented arguments not in \usage in Rd file 'get_term_info.Rd':
‘term_id’
Undocumented arguments in Rd file 'is_connected.Rd'
‘...’
Undocumented arguments in Rd file 'list_tables.Rd'
‘...’
Undocumented arguments in Rd file 'reconnect.Rd'
‘...’
Undocumented arguments in Rd file 'report.Rd'
‘...’
Undocumented arguments in Rd file 'run_query.Rd'
‘...’
Documented arguments not in \usage in Rd file 'run_query.Rd':
‘sql’
Undocumented arguments in Rd file 'search_labels.Rd'
‘...’
Documented arguments not in \usage in Rd file 'search_labels.Rd':
‘pattern’ ‘limit’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [68s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
improveNodes 21.758 0.709 22.480
onto_plot2 21.261 0.413 21.675
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/3s] OK
* 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 ... [4s/3s] OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4187/ontoProc2_20260324153140/ontoProc2.Rcheck/00check.log’
for details.
===============================
BiocCheck('ontoProc2_0.99.5.tar.gz')
===============================
── Installing ontoProc2 ────────────────────────────────────────────────────────
✔ Package installed successfully
── ontoProc2 session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKzEuF5/file1754d82c339208/ontoProc2
→ BiocVersion: 3.23
→ Package: ontoProc2
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/ontoProc2_20260324153140/ontoProc2.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpKzEuF5/file1754d82c339208/ontoProc2
→ installDir: /tmp/RtmpKzEuF5/file1754d819a180ff
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ontoProc2 ──────────────────────────────────────────────
* 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 4.5.0 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...
i NOTE: Consider adding these automatically suggested biocViews: GO
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (27%).
* 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 ontoProc2...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/SemsqlConn-S7.R (line 796, column 3)
• ...
• print in R/zzz.R (line 4, column 12)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/graphNEL.R (line 52, column 14)
• ...
• R/zzz.R (line 3, column 9)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/ontoProc2.Rmd
i Found @ in vignettes/uberonpeek.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• _anonymous_.808() (R/SemsqlConn-S7.R): 77 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/print.Rd
• man/SemsqlConn.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• make_graphNEL_from_ontology_plot.Rd
• ...
• with_connection.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• make_graphNEL_from_ontology_plot.Rd
• semsql_to_oi.Rd
• with_connection.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• semsql_to_oi.Rd
• with_connection.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; 33 lines (2%) are > 80 characters long.
First few lines:
• R/data.R#L1 #' a named vector with values rdfs label ...
• ...
• vignettes/uberonpeek.Rmd#L7 %\VignetteIndexEntry{uberonpeek -- a l ...
i NOTE: Consider multiples of 4 spaces for line indents; 289 lines (19%) are
not.
First few lines:
• R/graphNEL.R#L53 nn = paste(sub(" ", "\n", ont$name[node ...
• ...
• vignettes/uberonpeek.Rmd#L100 |> dplyr::select(subject)) ] ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.20 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 11 NOTES
i See the ontoProc2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.