[ Started: 2024-08-17 01:00:22 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/RtmpTg0zwk/fileca59b76563e0a/wppi
→ BiocVersion: 3.20
→ Package: wppi
→ PackageVersion: 1.6.0
→ BiocCheckDir: /mnt/disk0/build/bioc-check/wppi/bioc-3.20/2024-08-17_0059/wppi/wppi.BiocCheck
→ BiocCheckVersion: 1.41.12
→ sourceDir: /tmp/RtmpTg0zwk/fileca59b76563e0a/wppi
→ installDir: /tmp/RtmpTg0zwk/fileca59b117de090
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wppi ───────────────────────────────────────────────────
ℹ Checking for deprecated package usage...
✔ Checking for deprecated package usage... [10ms]

ℹ Checking for remote package usage...
✔ Checking for remote package usage... [12ms]

ℹ Checking for 'LazyData: true' usage...
✔ Checking for 'LazyData: true' usage... [6ms]

ℹ Checking version number...
✔ Checking version number... [6ms]

ℹ Checking for version number mismatch...
✔ Checking for version number mismatch... [6ms]

ℹ Checking version number validity...
✔ Checking version number validity... [6ms]

! W: y of x.y.z version should be odd in devel
ℹ Checking R version dependency...
✔ Checking R version dependency... [6ms]

ℹ N: Update R version dependency from 4.1 to 4.4.0.
ℹ Checking package size...
✔ Checking package size... [10ms]

ℹ Checking individual file sizes...
✔ Checking individual file sizes... [6ms]

ℹ Checking biocViews...
✔ Checking biocViews... [6ms]

ℹ Checking that biocViews are present...
✔ Checking that biocViews are present... [6ms]

ℹ Checking package type based on biocViews...
✔ Checking package type based on biocViews... [6ms]

→ Software
ℹ Checking for non-trivial biocViews...
✔ Checking for non-trivial biocViews... [10ms]

ℹ Checking that biocViews come from the same category...
✔ Checking that biocViews come from the same category... [7ms]

ℹ Checking biocViews validity...
✔ Checking biocViews validity... [6ms]

ℹ Checking for recommended biocViews...
✔ Checking for recommended biocViews... [6ms]

ℹ Checking build system compatibility...
✔ Checking build system compatibility... [6ms]

ℹ Checking for proper Description: field...
✔ Checking for proper Description: field... [6ms]

ℹ Checking if DESCRIPTION is well formatted...
✔ Checking if DESCRIPTION is well formatted... [6ms]

ℹ Checking for whitespace in DESCRIPTION field names...
✔ Checking for whitespace in DESCRIPTION field names... [6ms]

ℹ Checking that Package field matches directory/tarball name...
✔ Checking that Package field matches directory/tarball name... [6ms]

ℹ Checking for Version: field...
✔ Checking for Version: field... [6ms]

ℹ Checking License: for restrictive use...
✔ Checking License: for restrictive use... [6ms]

ℹ Checking for recommended DESCRIPTION fields...
✔ Checking for recommended DESCRIPTION fields... [6ms]

ℹ Checking for Bioconductor software dependencies...
✔ Checking for Bioconductor software dependencies... [6ms]

! W: 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.
ℹ Checking for pinned package versions in DESCRIPTION...
✔ Checking for pinned package versions in DESCRIPTION... [6ms]

ℹ Checking .Rbuildignore...
✔ Checking .Rbuildignore... [6ms]

ℹ Checking for stray BiocCheck output folders...
✔ Checking for stray BiocCheck output folders... [6ms]

ℹ Checking vignette directory...
✔ Checking vignette directory... [6ms]

ℹ Checking package installation calls in R code...
✔ Checking package installation calls in R code... [10ms]

ℹ Checking for library/require of wppi...
✔ Checking for library/require of wppi... [9ms]

ℹ Checking coding practice...
✔ Checking coding practice... [7ms]

ℹ N: Avoid 1:...; use seq_len() or seq_along()
ℹ Checking parsed R code in R directory, examples, vignettes...
✔ Checking parsed R code in R directory, examples, vignettes... [6ms]

ℹ Checking function lengths...
✔ Checking function lengths... [6ms]

ℹ N: The recommended function length is 50 lines or less. There are 2 functions
greater than 50 lines.
ℹ Checking man page documentation...
✔ Checking man page documentation... [6ms]

[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-17 01:00:36] [TRACE]   [OmnipathR] Cache locked: FALSE
ℹ Checking package NEWS...
✔ Checking package NEWS... [6ms]

ℹ Checking unit tests...
✔ Checking unit tests... [6ms]

ℹ N: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
ℹ Checking skip_on_bioc() in tests...
✔ Checking skip_on_bioc() in tests... [6ms]

ℹ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne…
✔ Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vigne…

ℹ N: Consider shorter lines; 2 lines (0%) are > 80 characters long.
ℹ N: Consider multiples of 4 spaces for line indents; 15 lines (1%) are not.
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.
ℹ Checking if package already exists in CRAN...
✔ Checking if package already exists in CRAN... [6ms]

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
ℹ Checking for bioc-devel mailing list subscription...
✔ Checking for bioc-devel mailing list subscription... [6ms]

ℹ N: 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
ℹ Checking for support site registration...
✔ Checking for support site registration... [6ms]

✖ E: Unable to find your email in the Support Site: HTTP 504 Gateway Timeout.
── BiocCheck v1.41.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | • 7 NOTES
ℹ See the wppi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2024-08-17 01:01:38 CEST ]