===============================
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_0.99.14.tar.gz
===============================
BiocCheckGitClone('ontoProc2')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/c8b64906b178c06b52470d2dc6057f03b452f376/ontoProc2
BiocVersion: 3.23
Package: ontoProc2
PackageVersion: 0.99.14
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/c8b64906b178c06b52470d2dc6057f03b452f376/ontoProc2.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/c8b64906b178c06b52470d2dc6057f03b452f376/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 v1.47.25 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/c8b64906b178c06b52470d2dc6057f03b452f376/ontoProc2.Rcheck
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-11 17:55:01 UTC
* using option --no-vignettes
* checking for file ontoProc2/DESCRIPTION ... OK
* this is package ontoProc2 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 ... 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 ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/6s] 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 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 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
Undefined global functions or variables:
object prlab prtag tag2cn
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 ... OK
* 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 ... [64s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
improveNodes 20.611 0.725 21.339
onto_plot2 20.575 0.230 20.807
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [2s/2s]
[2s/2s] 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/4s] OK
* DONE
Status: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4187/c8b64906b178c06b52470d2dc6057f03b452f376/ontoProc2.Rcheck/00check.log
for details.
===============================
BiocCheck('ontoProc2_0.99.14.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
Installing ontoProc2
Package installed successfully
ontoProc2 session metadata
sourceDir: /tmp/RtmpatUw4M/file2869e3ff6e0e2/ontoProc2
BiocVersion: 3.23
Package: ontoProc2
PackageVersion: 0.99.14
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/c8b64906b178c06b52470d2dc6057f03b452f376/ontoProc2.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /tmp/RtmpatUw4M/file2869e3ff6e0e2/ontoProc2
installDir: /tmp/RtmpatUw4M/file2869e42596dba
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 (25%).
* 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 867, column 3)
...
print in R/zzz.R (line 5, column 14)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/SemsqlConn-S7.R (line 632, column 14)
R/SemsqlConn-S7.R (line 637, column 14)
R/SemsqlConn-S7.R (line 642, 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_.881() (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; 46 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; 399 lines (21%) 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...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.25 results
0 ERRORS | 0 WARNINGS | i 10 NOTES
i See the ontoProc2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.