===============================
R CMD BUILD
===============================
* checking for file ‘CSOA/DESCRIPTION’ ... OK
* preparing ‘CSOA’:
* 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 ‘CSOA_0.99.0.tar.gz’
===============================
BiocCheckGitClone('CSOA')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA
→ BiocVersion: 3.22
→ Package: CSOA
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA
→ 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 for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.45.8 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA.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 ‘CSOA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSOA’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 serialization versions ... OK
* checking whether package ‘CSOA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] 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 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 ... [37s/37s] NOTE
attachCellScores.SingleCellExperiment: no visible global function
definition for ‘colData<-’
basicHeatmap: no visible binding for global variable ‘.data’
byCorrectDF: no visible binding for global variable ‘pvalAdj’
connectedComponents: no visible binding for global variable ‘gene1’
connectedComponents: no visible binding for global variable ‘gene2’
distFreq: no visible binding for global variable ‘nEdges’
featureWes: no visible global function definition for ‘Idents<-’
filterOverlaps: no visible binding for global variable ‘rawAggRank’
findRankCutoff: no visible binding for global variable ‘n’
geneRadialPlot: no visible binding for global variable ‘x’
geneRadialPlot: no visible binding for global variable ‘y’
geneRadialPlot: no visible binding for global variable ‘r’
geneRadialPlot: no visible binding for global variable ‘nEdges’
geneRadialPlot: no visible binding for global variable ‘gene’
geneRadialPlot: no visible binding for global variable ‘group’
hullToPolygon: no visible binding for global variable ‘x’
networkPlot: no visible binding for global variable ‘weight’
networkPlot: no visible binding for global variable ‘name’
overlapCutoffPlot: no visible binding for global variable ‘x’
overlapCutoffPlot: no visible binding for global variable ‘y’
overlapCutoffPlot: no visible binding for global variable ‘xEnd’
overlapCutoffPlot: no visible binding for global variable ‘yEnd’
overlapCutoffPlot: no visible binding for global variable ‘n’
scoreModules : <anonymous>: no visible binding for global variable
‘component’
Undefined global functions or variables:
.data Idents<- colData<- component gene gene1 gene2 group n nEdges
name pvalAdj r rawAggRank weight x xEnd y yEnd
* 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 files in ‘vignettes’ ... OK
* checking examples ... [82s/82s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scoreOverlaps 6.613 0.059 6.673
featureWes 6.313 0.260 6.581
scoreCells 6.497 0.002 6.499
runCSOA 6.103 0.277 6.381
scoreModules 6.053 0.039 6.093
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [13s/13s]
[13s/13s] 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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA.Rcheck/00check.log’
for details.
===============================
BiocCheck('CSOA_0.99.0.tar.gz')
===============================
── Installing CSOA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── CSOA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAA5ySG/file67c0a37bb1c21/CSOA
→ BiocVersion: 3.22
→ Package: CSOA
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3871/CSOA_20250722164830/CSOA.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /tmp/RtmpAA5ySG/file67c0a37bb1c21/CSOA
→ installDir: /tmp/RtmpAA5ySG/file67c0a46ba4e47
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CSOA ───────────────────────────────────────────────────
* 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...
i Bioconductor dependencies found in Imports & Depends (8%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• V1-Getting-started-with-CSOA.Rmd
• V2-The-CSOA-algorithm.Rmd
• V3-Advanced-CSOA.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CSOA...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/visualization.R (line 31, column 5)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/extra_filter.R (line 89, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 84 lines (3%) are > 80 characters long.
First few lines:
• R/compute_cell_scores_tools.R#L10 #' @param normExp A min-max normalized e
...
• ...
• vignettes/V3-Advanced-CSOA.Rmd#L311 ```{r, message=FALSE, out.height='100%',
...
i NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
First few lines:
• vignettes/V1-Getting-started-with-CSOA.Rmd#L75 'CFB', 'GDF15', 'MUC1 ...
• ...
• vignettes/V3-Advanced-CSOA.Rmd#L258 'ALDH1A3', 'VTCN1', ' ...
i NOTE: Consider multiples of 4 spaces for line indents; 204 lines (6%) are
not.
First few lines:
• R/compute_cell_scores_tools.R#L35 ' and its minimum must be p ...
• ...
• vignettes/V3-Advanced-CSOA.Rmd#L338 extraCircles=2) ...
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 v1.45.8 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the CSOA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.