[ Started: 2024-11-20 13:17:30 CET ]
[ dorothea v1.7.4 for BioC-3.20 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ]

Loading required package: BiocCheck
── Installing dorothea ─────────────────────────────────────────────────────────
✔ Package installed successfully
── dorothea session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea
→ BiocVersion: 3.20
→ Package: dorothea
→ PackageVersion: 1.7.4
→ BiocCheckDir: /mnt/disk0/build/bioc-check/dorothea/bioc-3.20/2024-11-20_1315/dorothea/dorothea.BiocCheck
→ BiocCheckVersion: 1.42.0
→ sourceDir: /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea
→ installDir: /tmp/Rtmp4T9SLJ/file104a1163fbf2a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dorothea ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea//inst/extdata/for_vignette/seurat_object.RDS
• /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea/inst/extdata/for_vignette/seurat_object.RDS
• /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea/inst/extdata/for_vignette/seurat_object.RDS
! WARNING: Data files exceed the 5MB size limit.
Use 'ExperimentHub' or 'AnnotationHub' for the files:
• /tmp/Rtmp4T9SLJ/file104a1203b8244/dorothea/inst/extdata/for_vignette/seurat_object.RDS
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* 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...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/dorothea.Rmd
* Checking package installation calls in R code...
* Checking for library/require of dorothea...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/helpers.R (line 18, column 16)
• R/helpers.R (line 20, column 18)
• R/helpers.R (line 21, column 12)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
• .Deprecated() in R/viper_wrapper.R (line 128, column 3)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/dorothea_hs_pancancer.Rd
• ...
• man/entire_database.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; 12 lines (2%) are > 80 characters long.
First few lines:
• R/data.R#L27 #' A table reporting signed human TF-tar ...
• ...
• vignettes/dorothea.Rmd#L171 Similarly to DoRothEA, the majority of T ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 104 lines (19%) are
not.
First few lines:
• R/helpers.R#L18 regulon_list = split(df, df$tf) ...
• ...
• vignettes/dorothea.Rmd#L192 theme(legend.position = "none") ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.42.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | • 7 NOTES
ℹ See the dorothea.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2024-11-20 13:18:10 CET ]