===============================
R CMD BUILD
===============================
* checking for file ‘anndataR/DESCRIPTION’ ... OK
* preparing ‘anndataR’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* building ‘anndataR_0.99.4.tar.gz’
===============================
BiocCheckGitClone('anndataR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3907/a95ccf9a976ecc08f56ae50b5b918fba35f6ff10/anndataR
→ BiocVersion: 3.22
→ Package: anndataR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3907/a95ccf9a976ecc08f56ae50b5b918fba35f6ff10/anndataR.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3907/a95ccf9a976ecc08f56ae50b5b918fba35f6ff10/anndataR
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3907/a95ccf9a976ecc08f56ae50b5b918fba35f6ff10/anndataR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘anndataR/DESCRIPTION’ ... OK
* this is package ‘anndataR’ version ‘0.99.4’
* 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 ‘anndataR’ 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 ... OK
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking whether startup messages can be suppressed ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [70s/71s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
read_h5ad 31.534 0.793 32.338
as_AnnData 18.051 0.887 18.940
write_h5ad 7.285 0.017 7.302
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [10m/10m]
[10m/10m] OK
* 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 ... [5s/4s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('anndataR_0.99.4.tar.gz')
===============================
── Installing anndataR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── anndataR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCrRqT3/file1a17c53b1c91f3/anndataR
→ BiocVersion: 3.22
→ Package: anndataR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3907/a95ccf9a976ecc08f56ae50b5b918fba35f6ff10/anndataR.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpCrRqT3/file1a17c53b1c91f3/anndataR
→ installDir: /tmp/RtmpCrRqT3/file1a17c579d91813
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on anndataR ───────────────────────────────────────────────
* 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
• usage_python.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of anndataR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/AbstractAnnData.R (line 95, column 7)
• cat() in R/AbstractAnnData.R (line 114, column 11)
* 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 19
functions greater than 50 lines.
The longest 5 functions are:
• as_Seurat() (R/as_Seurat.R): 172 lines
• ...
• initialize() (R/ReticulateAnnData.R): 120 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• reticulate-helpers.Rd
* 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; 220 lines (3%) are > 80 characters long.
First few lines:
• R/AbstractAnnData-s3methods.R#L7 #' **Subsetting behaviour**: The `[` met ...
• ...
• vignettes/usage_singlecellexperiment.Rmd#L122 You can again customize the
conversion p ...
i NOTE: Consider multiples of 4 spaces for line indents; 2726 lines (32%) are
not.
First few lines:
• R/AbstractAnnData-s3methods.R#L82 x$shape() ...
• ...
• vignettes/usage_singlecellexperiment.Rmd#L135 uns_mapping = c("Bool",
"IntScalar") ...
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 v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 6 NOTES
i See the anndataR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.