===============================
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_0.99.12.tar.gz
===============================
BiocCheckGitClone('ontoProc2')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/d1544e5b589538cac9234b08e3338d544144ed93/ontoProc2
BiocVersion: 3.23
Package: ontoProc2
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/d1544e5b589538cac9234b08e3338d544144ed93/ontoProc2.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/d1544e5b589538cac9234b08e3338d544144ed93/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/d1544e5b589538cac9234b08e3338d544144ed93/ontoProc2.Rcheck
* using R version 4.6.0 alpha (2026-03-30 r89742)
* 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: 2026-03-31 20:23:29 UTC
* using option --no-vignettes
* checking for file ontoProc2/DESCRIPTION ... OK
* this is package ontoProc2 version 0.99.12
* 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'.
cells_with_pmp: no visible global function definition for data
cells_with_pmp: no visible binding for global variable object
cells_with_pmp: no visible binding for global variable prtag
cells_with_pmp: no visible binding for global variable tag2cn
get_present_pmp: no visible global function definition for data
get_present_pmp: no visible binding for global variable object
get_present_pmp: no visible binding for global variable prtag
get_present_pmp: no visible binding for global variable prlab
get_present_pmp: no visible binding for global variable tag2cn
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 data download.file new object prlab prtag tag2cn
Consider adding
importFrom("methods", "as", "new")
importFrom("utils", "data", "download.file")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to data() loading into the global environment:
File ontoProc2/R/cells_with_pmp.R:
data("tag2cn", package = "ontoProc2")
File ontoProc2/R/get_present_pmp.R:
data("tag2cn", package = "ontoProc2")
See section Good practice in ?data.
* 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 ... [69s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
improveNodes 21.294 0.88 22.176
onto_plot2 21.832 0.24 22.073
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [2s/3s]
[3s/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 ... [5s/5s] OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4187/d1544e5b589538cac9234b08e3338d544144ed93/ontoProc2.Rcheck/00check.log
for details.
===============================
BiocCheck('ontoProc2_0.99.12.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
Installing ontoProc2
Package installed successfully
ontoProc2 session metadata
sourceDir: /tmp/RtmpomsyAZ/file11795f644684a2/ontoProc2
BiocVersion: 3.23
Package: ontoProc2
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/d1544e5b589538cac9234b08e3338d544144ed93/ontoProc2.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpomsyAZ/file11795f644684a2/ontoProc2
installDir: /tmp/RtmpomsyAZ/file11795f3540985f
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...
* 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 820, column 3)
...
print in R/zzz.R (line 4, column 14)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/celltoprotein.Rmd
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_.834() (R/SemsqlConn-S7.R): 97 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
cells_with_pmp.Rd
...
with_connection.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
Found in files:
cells_with_pmp.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; 35 lines (2%) are > 80 characters long.
First few lines:
R/cells_with_pmp.R#L29 ans <- dplyr::left_join(cl4pmp, mappr, ...
...
vignettes/uberonpeek.Rmd#L7 %\VignetteIndexEntry{uberonpeek -- a l ...
i NOTE: Consider multiples of 4 spaces for line indents; 377 lines (20%) are
not.
First few lines:
R/cells_with_pmp.R#L11 data("tag2cn", package = "ontoProc2") ...
...
vignettes/uberonpeek.Rmd#L105 |> 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 404 Not Found.
BiocCheck v1.47.20 results
1 ERRORS | 0 WARNINGS | i 9 NOTES
i See the ontoProc2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.