===============================
R CMD BUILD
===============================
* checking for file ‘SpatialArtifacts/DESCRIPTION’ ... OK
* preparing ‘SpatialArtifacts’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘SpatialArtifacts_0.99.1.tar.gz’
===============================
BiocCheckGitClone('SpatialArtifacts')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts
→ BiocVersion: 3.23
→ Package: SpatialArtifacts
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts
→ 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...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 v1.47.20 results ──────────────────────────────────────────────────
✖ 1 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/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-26 17:49:13 UTC
* using option ‘--no-vignettes’
* checking for file ‘SpatialArtifacts/DESCRIPTION’ ... OK
* this is package ‘SpatialArtifacts’ version ‘0.99.1’
* 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 ‘SpatialArtifacts’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘ggplot2’ ‘patchwork’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [24s/24s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'detectEdgeArtifacts.Rd':
\examples lines wider than 100 characters:
spe_visium <- detectEdgeArtifacts(spe_vignette, platform = "visium", qc_metric = "sum", batch_var = "sample_id")
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/62s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
detectEdgeArtifacts 42.045 0.441 42.492
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts.Rcheck/00check.log’
for details.
===============================
BiocCheck('SpatialArtifacts_0.99.1.tar.gz')
===============================
── Installing SpatialArtifacts ─────────────────────────────────────────────────
✔ Package installed successfully
── SpatialArtifacts session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpRu3Y2w/file28e90cb451867/SpatialArtifacts
→ BiocVersion: 3.23
→ Package: SpatialArtifacts
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/17337cf2087dd4a5c6853eddcc8ca8ea7ea1ca61/SpatialArtifacts.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpRu3Y2w/file28e90cb451867/SpatialArtifacts
→ installDir: /tmp/RtmpRu3Y2w/file28e90c40563529
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialArtifacts ───────────────────────────────────────
* 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 (40%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
• hippocampus-edge-detection.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SpatialArtifacts...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/edge_helper_functions_visium.R (line 218, column 14)
• R/edge_helper_functions_visium.R (line 504, column 15)
• R/edge_helper_functions_visium.R (line 663, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• edge_helper_functions_visium.R (line 86, column 22)
• ...
• edge_helper_functions_VisiumHD.R (line 366, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/detectEdgeArtifacts.R (line 38, column 9)
* 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 8
functions greater than 50 lines.
The longest 5 functions are:
• detectEdgeArtifacts_VisiumHD() (R/detectEdgeDryspots_VisiumHD.R): 313 lines
• ...
• problemAreas() (R/edge_helper_functions_visium.R): 112 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
• detectEdgeArtifacts_VisiumHD.Rd
• detectEdgeArtifacts.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• detectEdgeArtifacts_VisiumHD.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 194 lines (7%) are > 80 characters long.
First few lines:
• R/classifyEdgeArtifacts.R#L4 #' and size (large vs. small). This func ...
• ...
• vignettes/hippocampus-edge-detection.Rmd#L806 Overall, **SpatialArtifacts**
provides a ...
i NOTE: Consider multiples of 4 spaces for line indents; 894 lines (32%) are
not.
First few lines:
• R/classifyEdgeArtifacts.R#L106 spe, ...
• ...
• vignettes/hippocampus-edge-detection.Rmd#L800 - Without scaling, artifacts
will be ...
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 v1.47.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the SpatialArtifacts.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.