===============================
R CMD BUILD
===============================
* checking for file SanityR/DESCRIPTION ... OK
* preparing SanityR:
* 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
Omitted LazyData from DESCRIPTION
* building SanityR_0.99.0.tar.gz
===============================
BiocCheckGitClone('SanityR')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR
BiocVersion: 3.22
Package: SanityR
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
SanityR.Rproj
* 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...
* Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
BiocCheck v1.45.7 results
1 ERRORS | 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR.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 SanityR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package SanityR version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directive that requires package methods:
exportMethods
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains methods.
* checking package dependencies ... ERROR
Namespace dependencies missing from DESCRIPTION Imports/Depends entries:
'BiocGenerics', 'BiocParallel', 'MatrixGenerics', 'S4Vectors',
'SummarizedExperiment', 'scuttle'
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR.Rcheck/00check.log
for details.
===============================
BiocCheck('SanityR_0.99.0.tar.gz')
===============================
Installing SanityR
Package installed successfully
SanityR session metadata
sourceDir: /tmp/RtmpHsZibh/file314016c60f1da/SanityR
BiocVersion: 3.22
Package: SanityR
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3835/SanityR_20250620162612/SanityR.BiocCheck
BiocCheckVersion: 1.45.7
sourceDir: /tmp/RtmpHsZibh/file314016c60f1da/SanityR
installDir: /tmp/RtmpHsZibh/file314017f566170
isTarBall: TRUE
platform: unix
Running BiocCheck on SanityR
* 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...
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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (50%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of SanityR...
* 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 is 1
function greater than 50 lines.
The longest 5 functions are:
.calculate_sanity_distance() (R/cell_distance.R): 62 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will 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; 80 lines (10%) are > 80 characters long.
First few lines:
R/cell_distance.R#L6 #' @param x A \linkS4class{SingleCellExp ...
...
vignettes/SanityR.Rmd#L178 `calculateSanityDistance` computes *all* ...
i NOTE: Consider multiples of 4 spaces for line indents; 36 lines (5%) are not.
First few lines:
R/cell_distance.R#L96 s ...
...
vignettes/SanityR.Rmd#L172 breaks = c(-1, ...
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 v1.45.7 results
0 ERRORS | 0 WARNINGS | i 6 NOTES
i See the SanityR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.