===============================
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
* building cellNexus_0.99.7.tar.gz
===============================
BiocCheckGitClone('cellNexus')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus
BiocVersion: 3.23
Package: cellNexus
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus
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 v1.47.7 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/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus.Rcheck
* using R Under development (unstable) (2025-12-22 r89219)
* 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 cellNexus/DESCRIPTION ... OK
* checking extension type ... Package
* this is package cellNexus version 0.99.7
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] 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 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 ... [41s/41s] NOTE
assert_single_cell_metadata: no visible binding for global variable
dataset_id
assert_single_cell_metadata: no visible binding for global variable
cell_id
calculate_pseudobulk: no visible binding for global variable
sample_id
calculate_pseudobulk: no visible binding for global variable
cell_type_unified_ensemble
calculate_pseudobulk: no visible binding for global variable
aggregated_cells
calculate_pseudobulk: no visible global function definition for
across
calculate_pseudobulk: no visible global function definition for
everything
clean_and_report_NA_columns: no visible global function definition for
where
clean_and_report_NA_columns: no visible global function definition for
all_of
create_interface_app : server: no visible global function definition
for reactive
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
get_metacell: no visible binding for global variable atlas_id
get_pseudobulk: no visible binding for global variable atlas_id
get_single_cell_experiment: no visible binding for global variable
atlas_id
get_single_cell_experiment : <anonymous>: no visible binding for global
variable atlas_id
group_to_data_container: no visible global function definition for
contains
group_to_data_container: no visible global function definition for
matches
organize_inputs: no visible global function definition for is
sync_assay_files: no visible binding for global variable full_url
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:
across aggregated_cells all_of atlas_id cell_id
cell_type_unified_ensemble contains dataset_id everything
file_id_cellNexus_single_cell file_id_db full_url is matches
meta_filename reactive sample_id where
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [45s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculate_pseudobulk 6.785 0.981 7.766
get_pseudobulk 0.942 0.096 9.932
SAMPLE_DATABASE_URL 0.385 0.097 10.843
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running spelling.R [0s/0s]
Running testthat.R [47s/172s]
[47s/173s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3984/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus.Rcheck/00check.log
for details.
===============================
BiocCheck('cellNexus_0.99.7.tar.gz')
===============================
Installing cellNexus
Package installed successfully
cellNexus session metadata
sourceDir: /tmp/RtmpcSPZs2/file10d1a45817df4c/cellNexus
BiocVersion: 3.23
Package: cellNexus
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3984/d972cd9a3d6b02d43cbb0adeb1c1001da138769a/cellNexus.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/RtmpcSPZs2/file10d1a45817df4c/cellNexus
installDir: /tmp/RtmpcSPZs2/file10d1a49ca3328
isTarBall: TRUE
platform: unix
Running BiocCheck on cellNexus
* 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 4.5.0 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,
DataImport
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 (21%).
* 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:
cellNexus.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpcSPZs2/file10d1a45817df4c/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...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/interface_app.R (line 303, column 13)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/counts.R (line 444, column 12)
...
R/utils.R (line 240, column 9)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressMessages() in R/counts.R (line 680, column 92)
suppressWarnings() in R/utils.R (line 64, column 9)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
The longest 5 functions are:
create_interface_app() (R/interface_app.R): 210 lines
...
get_single_cell_experiment() (R/counts.R): 104 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
create_interface_app.Rd
import_one_sce.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
Found in files:
create_interface_app.Rd
import_one_sce.Rd
pbmc3k_sce.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
create_interface_app.Rd
import_one_sce.Rd
pbmc3k_sce.Rd
* 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; 296 lines (9%) are > 80 characters long.
First few lines:
R/counts_per_million.R#L21 sce <- SingleCellExperiment(list(cpm = ...
...
vignettes/cellNexus.Rmd#L544 The metacell (e.g `metacell_2`, `metacel ...
i NOTE: Consider multiples of 4 spaces for line indents; 718 lines (21%) are
not.
First few lines:
R/counts_per_million.R#L13 # Save SCE to the cache directory coun ...
...
vignettes/cellNexus.Rmd#L496 get_single_cell_experiment(cache_direc ...
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 v1.47.7 results
0 ERRORS | 0 WARNINGS | i 14 NOTES
i See the cellNexus.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.