[ Started: 2026-06-07 20:37:08 CEST ] [ CellNOptR v1.56.0 for BioC-3.22 from https://git.bioconductor.org/packages/CellNOptR@RELEASE_3_22 (2244640 2025-10-29 10:09:33) ] Loading required package: BiocCheck ── Installing CellNOptR ──────────────────────────────────────────────────────── ✔ Package installed successfully ── CellNOptR session metadata ────────────────────────────────────────────────── → sourceDir: /tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR → BiocVersion: 3.22 → Package: CellNOptR → PackageVersion: 1.56.0 → BiocCheckDir: /mnt/disk0/build/bioc-check/cellnoptr/bioc-3.22/2026-06-07_2036/CellNOptR/CellNOptR.BiocCheck → BiocCheckVersion: 1.46.3 → sourceDir: /tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR → installDir: /tmp/Rtmpu72aZv/file8d0922a9bd8c7 → isTarBall: TRUE → platform: unix ── Running BiocCheck on CellNOptR ────────────────────────────────────────────── * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R version dependency... ℹ NOTE: Update R version dependency from 4.0.0 to 4.5.0 * 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... Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR/man/createAndRunILP.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR/man/createILPBitstringAll.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR/man/cutModel.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR/man/invokeCPLEX.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpu72aZv/file8d0923ed46d2c/CellNOptR/man/writeFile.Rd' ℹ NOTE: Consider adding these automatically suggested biocViews: GraphAndNetwork 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... ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION * 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... ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant, consider adding the 'fnd' role to the list of authors. * Checking NAMESPACE... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ℹ NOTE: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/CellNOptR-vignette.Rmd * Checking package installation calls in R code... * Checking for library/require of CellNOptR... ! WARNING: Avoid the use of 'library' or 'require' in R code Found in files: • require() in R/readRules.R (line 75, column 60) • require() in R/readRules.R (line 139, column 60) * Checking coding practice... ℹ NOTE: Avoid sapply(); use vapply() Found in files: • R/CNOlist.R (line 38, column 31) • ... • R/readSBMLQual.R (line 45, column 32) ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • cleanupILP.R (line 34, column 21) • ... • writeSIF.R (line 30, column 30) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • print() in R/CNOdata.R (line 37, column 9) • ... • cat() in R/writeReport.R (line 262, column 9) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/buildBitString.R (line 29, column 22) • ... • R/writeSIF.R (line 21, column 9) ℹ NOTE: Avoid the use of 'paste' in condition signals Found in files: • R/checkSignals.R (line 32, column 14) • ... • R/writeSIF.R (line 34, column 17) ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions Found in files: • R/buildBitString.R (line 31, column 18) • ... • R/simulateTN.R (line 20, column 14) ℹ NOTE: Avoid system() ; use system2() Found in files: • system() in R/invokeCPLEX.R (line 39, column 5) • system() in R/invokeCPLEX.R (line 42, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ NOTE: Avoid '<<-' if possible (found 22 times) • <<- in R/readRules.R (line 166, column 35) • ... • <<- in R/readRules.R (line 353, column 40) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 56 functions greater than 50 lines. The longest 5 functions are: • plotModel() (R/plotModel.R): 392 lines • ... • makeCNOlist() (R/makeCNOlist.R): 334 lines * Checking man page documentation... ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages. • man/CNOlist-class.Rd ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/checkSignals.Rd • ... • man/writeSIF.Rd ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • CNOdata.Rd • ... • readSBMLQual.Rd ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man pages use at least one of these tags. Found in files: • CNOdata.Rd • ... • readSBMLQual.Rd ℹ NOTE: Use donttest instead of dontrun. Found in files: • CNOdata.Rd • ... • readSBMLQual.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; 707 lines (6%) are > 80 characters long. First few lines: • R/buildBitString.R#L31 stop("CellNOpt Error: argume ... • ... • vignettes/CellNOptR-vignette.Rmd#L754 Saez-Rodriguez, J.: Identifying Drug E ... ℹ NOTE: Consider 4 spaces instead of tabs; 1886 lines (15%) contain tabs. First few lines: • R/checkSignals.R#L58 stimuli <- colnames(CNOlist@stimuli) ... • ... • vignettes/CellNOptR-vignette.Rmd#L36 install.packages("remotes") ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 1153 lines (9%) are not. First few lines: • R/checkSignals.R#L58 stimuli <- colnames(CNOlist@stimuli) ... • ... • vignettes/CellNOptR-vignette.Rmd#L756 (2010). ... 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... 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org * Checking for bioc-devel mailing list subscription... ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... ℹ Maintainer is registered at support site. ℹ Package is in the Support Site Watched Tags. ── BiocCheck v1.46.3 results ─────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 23 NOTES ℹ See the CellNOptR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2026-06-07 20:37:48 CEST ]