[ Started: 2023-01-19 01:49:01 CET ] [ wppi v1.6.0 for BioC-3.16 from https://github.com/AnaGalhoz37/wppi@main ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.34.2 ─ BiocVersion: 3.16 ─ Package: wppi ─ PackageVersion: 1.6.0 ─ sourceDir: /tmp/Rtmps4V9JD/file113c5061db2333/wppi ─ installDir: /tmp/Rtmps4V9JD/file113c50239b69da ─ BiocCheckDir: /home/omnipath/testing/bioc/wppi/bioc-3.16/2023-01-19_0148/wppi/wppi.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 4.1 to 4.2.0. * 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 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 pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of wppi... * Checking coding practice... * NOTE: Avoid 1:...; use seq_len() or seq_along() * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 21 functions greater than 50 lines. * Checking man page documentation... [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Contains 1 files. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.2-3.16/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-01-19 01:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-01-19 01:49:14] [TRACE] [OmnipathR] Cache locked: FALSE * Checking package NEWS... * Checking unit tests... * NOTE: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 37 lines (2%) 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 '?repositories' 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 name is in support site watched tags. ─ BiocCheck results ── 0 ERRORS | 0 WARNINGS | 7 NOTES See the wppi.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2023-01-19 01:49:16 CET ]