[ Started: 2024-09-23 17:14:12 CEST ]
[ wppi v1.6.0 for BioC-3.20 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]

Loading required package: BiocCheck
── Installing wppi ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── wppi session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8fjG6w/file665bd51a7dfeb/wppi
→ BiocVersion: 3.20
→ Package: wppi
→ PackageVersion: 1.6.0
→ BiocCheckDir: /mnt/disk0/build/bioc-check/wppi/bioc-3.20/2024-09-23_1712/wppi/wppi.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmp8fjG6w/file665bd51a7dfeb/wppi
→ installDir: /tmp/Rtmp8fjG6w/file665bd172d9331
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wppi ───────────────────────────────────────────────────
* 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 odd in devel
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1 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...
* 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 wppi...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• WPPI_functions.R (line 296, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
• score_candidate_genes_from_PPI() (R/WPPI_app.R): 111 lines
• weighted_adj() (R/WPPI_functions.R): 94 lines
* Checking man page documentation...
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-23 17:14:25] [TRACE]   [OmnipathR] Cache locked: FALSE
* Checking package NEWS...
* Checking unit tests...
ℹ 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...
ℹ NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long.
First few lines:
• vignettes/wppi_workflow.Rmd#L41 it's possible to use custom databases. ...
• vignettes/wppi_workflow.Rmd#L222 plot(graph_op_1,vertex.label = ifelse(sc ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 15 lines (1%) are not.
First few lines:
• R/WPPI_functions.R#L297 i <- adj_i[w] ...
• ...
• R/WPPI_functions.R#L314 functional_annot(HPO_data, gen ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | • 7 NOTES
ℹ See the wppi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2024-09-23 17:14:27 CEST ]