[ Started: 2024-12-14 12:30:33 CET ] [ OmnipathR v3.15.1 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (4ffd9ec 2024-11-07 16:20:19) ] Loading required package: BiocCheck ── Installing OmnipathR ──────────────────────────────────────────────────────── ✔ Package installed successfully ── OmnipathR session metadata ────────────────────────────────────────────────── → sourceDir: /tmp/Rtmpx2BGJq/file1bde67255cb810/OmnipathR → BiocVersion: 3.20 → Package: OmnipathR → PackageVersion: 3.15.1 → BiocCheckDir: /mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2024-12-14_1222/OmnipathR/OmnipathR.BiocCheck → BiocCheckVersion: 1.42.0 → sourceDir: /tmp/Rtmpx2BGJq/file1bde67255cb810/OmnipathR → installDir: /tmp/Rtmpx2BGJq/file1bde6720b210dd → isTarBall: TRUE → platform: unix ── Running BiocCheck on OmnipathR ────────────────────────────────────────────── * 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... ! WARNING: y of x.y.z version should be even in release * Checking R version dependency... ℹ NOTE: Update R version dependency from 4.0 to 4.4.0. * 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: GenePrediction 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... ! WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of OmnipathR... * Checking coding practice... '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: • cat() in R/annotations.R (line 135, column 9) • ... • print() in R/uniprot.R (line 31, column 5) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/adecorate.R (line 38, column 23) • ... • R/homologene.R (line 250, column 17) ! WARNING: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes Found in files: • misc.R (line 1112, column 24) • misc.R (line 1119, column 28) ! WARNING: .Deprecated / .Defunct usage (found 27 times) • .Deprecated() in R/annotations.R (line 180, column 5) • ... • .Deprecated() in R/resources.R (line 97, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times) • suppressWarnings() in R/cache.R (line 66, column 5) • ... • suppressWarnings() in R/tfcensus.R (line 48, column 5) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 74 functions greater than 50 lines. The longest 5 functions are: • homology_translate() (R/homology.R): 220 lines • ... • filter_intercell_network() (R/intercell.R): 160 lines * Checking man page documentation... [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Contains 1 files. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpx2BGJq/file1bde6720b210dd/lib/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpx2BGJq/file1bde6720b210dd/lib/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpx2BGJq/file1bde6720b210dd/lib/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [TRACE] [OmnipathR] Reading JSON from `/tmp/Rtmpx2BGJq/file1bde6720b210dd/lib/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-14 12:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-14 12:31:20] [TRACE] [OmnipathR] Cache locked: FALSE ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • consensuspathdb_download.Rd • ... • unnest_evidences.Rd ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man pages use at least one of these tags. Found in files: • consensuspathdb_download.Rd • ... • unnest_evidences.Rd ℹ NOTE: Use donttest instead of dontrun. Found in files: • consensuspathdb_download.Rd • ... • unnest_evidences.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; 61 lines (0%) are > 80 characters long. First few lines: • R/annotations.R#L38 #' \url{https://archive.omnipathdb.org/o ... • ... • vignettes/omnipath_intro.Rmd#L765 `r BiocStyle::Biocpkg("OmnipathR")` prov ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 86 lines (0%) are not. First few lines: • R/chalmers_gem.R#L123 slice(metabolites, ... • ... • vignettes/drug_targets.Rmd#L158 print(all(drug_targets$in_OP)) ... 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 v1.42.0 results ─────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 4 WARNINGS | • 12 NOTES ℹ See the OmnipathR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2024-12-14 12:31:24 CET ]