===============================
R CMD BUILD
===============================
* checking for file ‘xCell2/DESCRIPTION’ ... OK
* preparing ‘xCell2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘xCell2_0.99.7.tar.gz’
===============================
BiocCheckGitClone('xCell2')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.7
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xCell2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xCell2’ version ‘0.99.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘ontoProc’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2.Rcheck/00check.log’
for details.
===============================
BiocCheck('xCell2_0.99.7.tar.gz')
===============================
── Installing xCell2 ───────────────────────────────────────────────────────────
✔ Package installed successfully
── xCell2 session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpjb0WJA/file3a037a7d070e8b/xCell2
→ BiocVersion: 3.20
→ Package: xCell2
→ PackageVersion: 0.99.7
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3540/194ef43522832f8bbd911a30bd8c6698e82738b0/xCell2.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/Rtmpjb0WJA/file3a037a7d070e8b/xCell2
→ installDir: /tmp/Rtmpjb0WJA/file3a037a5bd30b91
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on xCell2 ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* 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...
i Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of xCell2...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/xCell2GetLineage.Rd
i Found @ in man/xCell2Train.Rd
i Found @ in vignettes/xCell2-vignette.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• CreateSignatures() (R/xCell2Train.R): 175 lines
• ...
• xCell2Train() (R/xCell2Train.R): 107 lines
* Checking man page documentation...
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
* 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; 192 lines (11%) are > 80 characters long.
First few lines:
• R/data.R#L8 #' @description A table that provides a ...
• ...
• vignettes/xCell2-vignette.Rmd#L324 - Aran, D. (2021). Extracting insights f
...
i NOTE: Consider multiples of 4 spaces for line indents; 490 lines (28%) are
not.
First few lines:
• R/xCell2Analysis.R#L30 xcell2object, ...
• ...
• vignettes/xCell2-vignette.Rmd#L272 xcell2object = DICE_demo.xCell2Ref ...
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...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
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 ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 5 NOTES
i See the xCell2.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.