===============================
R CMD BUILD
===============================
* checking for file SpatialArtifacts/DESCRIPTION ... OK
* preparing SpatialArtifacts:
* checking DESCRIPTION meta-information ... 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
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:
SpatialArtifacts/data/spe_vignette.rda
* building SpatialArtifacts_0.99.0.tar.gz
===============================
BiocCheckGitClone('SpatialArtifacts')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/SpatialArtifacts_20260323171413/SpatialArtifacts
BiocVersion: 3.23
Package: SpatialArtifacts
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/SpatialArtifacts_20260323171413/SpatialArtifacts.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/SpatialArtifacts_20260323171413/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...
* 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
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/4172/SpatialArtifacts_20260323171413/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: 2026-03-23 17:15:26 UTC
* using option --no-vignettes
* checking for file SpatialArtifacts/DESCRIPTION ... OK
* this is package SpatialArtifacts version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'S4Vectors', 'dplyr', 'scuttle'
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/4172/SpatialArtifacts_20260323171413/SpatialArtifacts.Rcheck/00check.log
for details.
===============================
BiocCheck('SpatialArtifacts_0.99.0.tar.gz')
===============================
Installing SpatialArtifacts
Package installed successfully
SpatialArtifacts session metadata
sourceDir: /tmp/RtmpUqYzsj/file168ec53d402792/SpatialArtifacts
BiocVersion: 3.23
Package: SpatialArtifacts
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4172/SpatialArtifacts_20260323171413/SpatialArtifacts.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpUqYzsj/file168ec53d402792/SpatialArtifacts
installDir: /tmp/RtmpUqYzsj/file168ec57d1afb87
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...
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 (29%).
* 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:
hippocampus-edge-detection.qmd
* Checking whether vignette is built with 'R CMD build'...
ERROR: Vignette must be built by 'R CMD build'. Please see the `Vignette
Checks` section of the BiocCheck vignette.
* 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.qmd#L823 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.qmd#L817 - 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...
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 v1.47.20 results
2 ERRORS | 0 WARNINGS | i 13 NOTES
i See the SpatialArtifacts.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.