===============================
R CMD BUILD
===============================
* checking for file ‘DenoIST/DESCRIPTION’ ... OK
* preparing ‘DenoIST’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘DenoIST/tests/testthat/denoist_results/denoist_results.rds’
‘DenoIST/tests/testthat/testdata/test_coords.rds’
‘DenoIST/tests/testthat/testdata/test_mat.rds’
‘DenoIST/tests/testthat/testdata/test_spe.rds’
‘DenoIST/tests/testthat/testdata/test_tx.rds’
‘DenoIST/vignettes/example_spe.rds’ ‘DenoIST/vignettes/result.rds’
‘DenoIST/vignettes/tx_sub.rds’
* building ‘DenoIST_0.99.0.tar.gz’
===============================
BiocCheckGitClone('DenoIST')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST
→ BiocVersion: 3.23
→ Package: DenoIST
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* 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 v1.47.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DenoIST/DESCRIPTION’ ... OK
* this is package ‘DenoIST’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DenoIST’ can be installed ... ERROR
Installation failed.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST.Rcheck/00check.log’
for details.
===============================
BiocCheck('DenoIST_0.99.0.tar.gz')
===============================
── Installing DenoIST ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DenoIST session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEp9GiW/file2bca565ab63a11/DenoIST
→ BiocVersion: 3.23
→ Package: DenoIST
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4038/DenoIST_20251226170251/DenoIST.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/RtmpEp9GiW/file2bca565ab63a11/DenoIST
→ installDir: /tmp/RtmpEp9GiW/file2bca562847b1d6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DenoIST ────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 3.5.0 to 4.6.0
* 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...
i Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• denoist_spe.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DenoIST...
* Checking coding practice...
* 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 3
functions greater than 50 lines.
The longest 5 functions are:
• local_offset_distance_with_background() (R/neighbour_offset.R): 127 lines
• solve_poisson_mixture() (R/pmm_model.R): 107 lines
• denoist() (R/denoist.R): 99 lines
* Checking man page documentation...
* 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; 51 lines (8%) are > 80 characters long.
First few lines:
• R/denoist.R#L19 #' @param tx_x Column name for the x coo ...
• ...
• vignettes/denoist_spe.Rmd#L138 adj <- plot_feature_scatter(coords = spa ...
i NOTE: Consider multiples of 4 spaces for line indents; 214 lines (35%) are
not.
First few lines:
• R/denoist.R#L59 # TODO:check input type ...
• ...
• vignettes/denoist_spe.Rmd#L132 return(p) ...
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...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the DenoIST.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.