===============================
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
* looking to see if a ‘data/datalist’ file should be added
* building ‘ontoProc2_0.99.16.tar.gz’
===============================
BiocCheckGitClone('ontoProc2')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/ontoProc2
→ BiocVersion: 3.23
→ Package: ontoProc2
→ PackageVersion: 0.99.16
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/ontoProc2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/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 for remote package usage...
* 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 v1.49.4 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/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/ontoProc2.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-05-07 21:06:14 UTC
* using option ‘--no-vignettes’
* checking for file ‘ontoProc2/DESCRIPTION’ ... OK
* this is package ‘ontoProc2’ version ‘0.99.16’
* 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 ‘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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [7s/7s] NOTE
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 ... [69s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
onto_plot2 21.647 0.277 21.925
improve_nodes 21.237 0.548 21.787
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/ontoProc2.Rcheck/00check.log’
for details.
===============================
BiocCheck('ontoProc2_0.99.16.tar.gz')
===============================
── Installing ontoProc2 ────────────────────────────────────────────────────────
✔ Package installed successfully
── ontoProc2 session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpT7IcrE/file2544a361fd501f/ontoProc2
→ BiocVersion: 3.23
→ Package: ontoProc2
→ PackageVersion: 0.99.16
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4187/74bcf7ea282d6a13f434bec26bac570f5815b609/ontoProc2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpT7IcrE/file2544a361fd501f/ontoProc2
→ installDir: /tmp/RtmpT7IcrE/file2544a3224e9bb7
→ 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 if 'Package:' field matches directory / tarball...
* 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 879, column 3)
• ...
• print in R/SemsqlConn-S7.R (line 871, column 12)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/SemsqlConn-S7.R (line 649, column 14)
• R/SemsqlConn-S7.R (line 654, column 14)
• R/SemsqlConn-S7.R (line 659, 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_.891() (R/SemsqlConn-S7.R): 97 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/PREDICATES.Rd
• man/print.Rd
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; 64 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; 451 lines (14%) 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 v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 10 NOTES
i See the ontoProc2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.