===============================
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_0.99.12.tar.gz
===============================
BiocCheckGitClone('cellNexus')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/cellNexus
BiocVersion: 3.23
Package: cellNexus
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/cellNexus.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/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/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/cellNexus/.gitignore'
* 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 v1.47.20 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/3984/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/cellNexus.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: 2026-03-19 06:10:27 UTC
* using option --no-vignettes
* checking for file cellNexus/DESCRIPTION ... OK
* checking extension type ... Package
* this is package cellNexus version 0.99.12
* 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [14s/14s] 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 ... [42s/42s] NOTE
.fetch_experiments: no visible binding for global variable atlas_id
.fetch_experiments : <anonymous> : <anonymous>: no visible global
function definition for assay<-
.fetch_experiments : <anonymous> : <anonymous>: no visible global
function definition for assayNames
build_assay_file_list: no visible binding for global variable
full_url
create_interface_app : server: no visible global function definition
for isolate
delete_counts: no visible binding for global variable file_id_db
delete_counts: no visible binding for global variable meta_filename
get_metacell: no visible binding for global variable
file_id_cellNexus_single_cell
group_to_data_container: no visible global function definition for
select
group_to_data_container: no visible global function definition for
contains
group_to_data_container: no visible global function definition for
matches
group_to_data_container: no visible binding for global variable
sample_id
group_to_data_container: no visible binding for global variable
metacell_id
group_to_data_container: no visible global function definition for
left_join
group_to_data_container: no visible global function definition for
any_of
join_census_table: no visible global function definition for
left_join
join_metacell_table: no visible global function definition for
left_join
sync_metadata_assay_files: no visible binding for global variable
atlas_id
validate_data: no visible binding for global variable atlas_id
Undefined global functions or variables:
any_of assay<- assayNames atlas_id contains
file_id_cellNexus_single_cell file_id_db full_url isolate left_join
matches meta_filename metacell_id sample_id select
* 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 ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('cellNexus_0.99.12.tar.gz')
===============================
Installing cellNexus
Package installed successfully
cellNexus session metadata
sourceDir: /tmp/RtmpvS7eFc/file28f68741720f10/cellNexus
BiocVersion: 3.23
Package: cellNexus
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/ad1fdbc6b893161ee1d6591fa5a8cc65190905be/cellNexus.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpvS7eFc/file28f68741720f10/cellNexus
installDir: /tmp/RtmpvS7eFc/file28f68739cf1e74
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...
i NOTE: Consider adding these automatically suggested biocViews: SingleCell
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (28%).
* 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 25 out of 46 code chunks = 54% unevaluated
i
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
cellNexus.Rmd
gene-expression-explore.Rmd
metadata-explore.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/gene-expression-explore.Rmd
vignettes/metadata-explore.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpvS7eFc/file28f68741720f10/cellNexus/vignettes/cellNexus.Rmd
* 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...
i NOTE: Avoid '<<-' if possible (found 1 times)
<<- in R/utils.R (line 27, column 39)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressMessages() in R/counts.R (line 530, column 5)
suppressWarnings() in R/utils.R (line 77, column 5)
* 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:
create_interface_app() (R/interface_app.R): 367 lines
...
sync_remote_files() (R/utils.R): 58 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
join_census_table.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; 328 lines (8%) are > 80 characters long.
First few lines:
R/counts_per_million.R#L21 sce <- SingleCellExperiment(list(cpm = ...
...
vignettes/metadata-explore.Rmd#L104 | `file_id_cellNexus_pseudobulk` | Inter
...
i NOTE: Consider multiples of 4 spaces for line indents; 585 lines (15%) are
not.
First few lines:
R/counts_per_million.R#L15 ...
...
vignettes/metadata-explore.Rmd#L123 ) ...
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 v1.47.20 results
0 ERRORS | 1 WARNINGS | i 10 NOTES
i See the cellNexus.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.