===============================
R CMD BUILD
===============================
* checking for file ‘cellNexus/DESCRIPTION’ ... OK
* preparing ‘cellNexus’:
* 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 ‘cellNexus_0.99.23.tar.gz’
===============================
BiocCheckGitClone('cellNexus')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/cellNexus_20260526070843/cellNexus
→ BiocVersion: 3.23
→ Package: cellNexus
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/cellNexus_20260526070843/cellNexus.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/cellNexus_20260526070843/cellNexus
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3984/cellNexus_20260526070843/cellNexus/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.49.6 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/3984/cellNexus_20260526070843/cellNexus.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-26 11:10:35 UTC
* using option ‘--no-vignettes’
* checking for file ‘cellNexus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellNexus’ version ‘0.99.23’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘cellNexus’ 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [11s/11s] 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 ... [35s/35s] OK
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [46s/60s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
join_census_table 0.691 8.317 6.469
get_SingleCellExperiment 1.483 0.199 10.384
SAMPLE_DATABASE_URL 0.336 0.036 8.804
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [43s/83s]
[44s/84s] 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 ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('cellNexus_0.99.23.tar.gz')
===============================
── Installing cellNexus ────────────────────────────────────────────────────────
✔ Package installed successfully
── cellNexus session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9vNiaB/file1224ba4231a990/cellNexus
→ BiocVersion: 3.23
→ Package: cellNexus
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/cellNexus_20260526070843/cellNexus.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/Rtmp9vNiaB/file1224ba4231a990/cellNexus
→ installDir: /tmp/Rtmp9vNiaB/file1224ba1648258c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cellNexus ──────────────────────────────────────────────
* 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 4.5.0 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 if 'Package:' field matches directory / tarball...
* 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 (24%).
* 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...
! WARNING: Evaluate more vignette chunks.
i 18 out of 18 code chunks = 100% unevaluated
i
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cellNexus...
* 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 are 7
functions greater than 50 lines.
The longest 5 functions are:
• create_interface_app() (R/interface_app.R): 383 lines
• ...
• downsample_metadata() (R/dev.R): 80 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
* 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; 672 lines (15%) are > 80 characters long.
First few lines:
• R/counts.R#L52 #' @param data A data frame containing, ...
• ...
• vignettes/metadata-explore.Rmd#L223 #> [169] SummarizedExperiment_1.40.0
...
i NOTE: Consider multiples of 4 spaces for line indents; 986 lines (22%) are
not.
First few lines:
• R/counts_per_million.R#L15 # Avoid completely empty cells ...
• ...
• vignettes/metadata-explore.Rmd#L152 ) ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 4 NOTES
i See the cellNexus.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.