===============================
R CMD BUILD
===============================
* checking for file ‘spARI/DESCRIPTION’ ... OK
* preparing ‘spARI’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘spARI_0.99.1.tar.gz’
===============================
BiocCheckGitClone('spARI')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI
→ BiocVersion: 3.22
→ Package: spARI
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• data/.DS_Store
• ...
• vignettes/.DS_Store
* Checking individual file sizes...
* 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 v1.45.12 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/3874/spARI_20250804164347/spARI.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spARI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spARI’ 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 ‘spARI’ can be installed ... ERROR
Installation failed.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI.Rcheck/00check.log’
for details.
===============================
BiocCheck('spARI_0.99.1.tar.gz')
===============================
── Installing spARI ────────────────────────────────────────────────────────────
✔ Package installed successfully
── spARI session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpm9SOKm/file2a3554494996ed/spARI
→ BiocVersion: 3.22
→ Package: spARI
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3874/spARI_20250804164347/spARI.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/Rtmpm9SOKm/file2a3554494996ed/spARI
→ installDir: /tmp/Rtmpm9SOKm/file2a355449875568
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spARI ──────────────────────────────────────────────────
* 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 new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Spatial
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (33%).
* 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• spARI.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/spARI.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spARI...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/perm_test.R (line 115, column 25)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• perm_test.R (line 100, column 11)
• ...
• spARI.R (line 136, column 16)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/perm_test.R (line 79, column 5)
• cat() in R/perm_test.R (line 92, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/perm_test.R (line 41, column 11)
• ...
• R/spARI.R (line 183, column 18)
! WARNING: Remove set.seed usage (found 1 times)
• set.seed() in R/perm_test.R (line 114, column 5)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/spARI.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 2
functions greater than 50 lines.
The longest 5 functions are:
• spARI() (R/spARI.R): 140 lines
• perm_test() (R/perm_test.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/c1_labels.Rd
• ...
• man/true_labels.Rd
* Checking package NEWS...
! WARNING: news(package='spARI') failed with news file: spARI/NEWS.md. Refer to
https://contributions.bioconductor.org/news.html to be included in Bioconductor
release announcements.
* 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; 58 lines (9%) are > 80 characters long.
First few lines:
• R/perm_test.R#L1 #' The function perm_test is the main fu ...
• ...
• vignettes/spARI.Rmd#L219 Then we use the SpatialExperiment object ...
i NOTE: Consider multiples of 4 spaces for line indents; 154 lines (23%) are
not.
First few lines:
• R/perm_test.R#L42 f_func_input=NULL, ...
• ...
• vignettes/spARI.Rmd#L215 spatialCoords = coords_matrix ...
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 v1.45.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | i 16 NOTES
i See the spARI.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.