[ Started: 2024-10-19 12:58:02 CEST ] [ OmnipathR v3.12.4 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (edb3c69 2024-10-02 12:46:04) ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.40.0 ─ BiocVersion: 3.19 ─ Package: OmnipathR ─ PackageVersion: 3.12.4 ─ sourceDir: /tmp/RtmpyD7LlR/file298b1d41ce1e03/OmnipathR ─ installDir: /tmp/RtmpyD7LlR/file298b1ddfb50b4 ─ BiocCheckDir: /mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-19_1251/OmnipathR/OmnipathR.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * 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... * 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... * NOTE: Consider adding these automatically suggested biocViews: GenePrediction Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... * 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 * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead * WARNING: .Deprecated / .Defunct usage (found 26 times) * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 63 functions greater than 50 lines. * Checking man page documentation... [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Contains 1 files. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpyD7LlR/file298b1ddfb50b4/lib/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpyD7LlR/file298b1ddfb50b4/lib/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpyD7LlR/file298b1ddfb50b4/lib/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpyD7LlR/file298b1ddfb50b4/lib/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-19 12:58:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-19 12:58:42] [TRACE] [OmnipathR] Cache locked: FALSE * NOTE: Consider adding runnable examples to man pages that document exported objects. * NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 15% of man pages use at least one of these tags. * NOTE: Use donttest{} instead of dontrun{}. * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 55 lines (0%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 55 lines (0%) are not. See https://contributions.bioconductor.org/r-code.html 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... * 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... Maintainer is registered at support site. Package is in the Support Site Watched Tags. ─ BiocCheck results ── 0 ERRORS | 2 WARNINGS | 12 NOTES See the OmnipathR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2024-10-19 12:58:45 CEST ]