===============================
BiocCheckGitClone('scECODA')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA
→ BiocVersion: 3.23
→ Package: scECODA
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA
→ 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...
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 v1.47.20 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/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA.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 14:16:54 UTC
* using option ‘--no-vignettes’
* checking for file ‘scECODA/DESCRIPTION’ ... OK
* this is package ‘scECODA’ version ‘0.99.4’
* 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 ‘scECODA’ 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [24s/24s] NOTE
ecoda: no visible global function definition for ‘slot<-’
ecoda_helper: no visible global function definition for ‘slot<-’
find_hvcs: no visible global function definition for ‘slot<-’
Undefined global functions or variables:
slot<-
Consider adding
importFrom("methods", "slot<-")
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 ... WARNING
Codoc mismatches from Rd file 'plot_pca.Rd':
plot_pca
Code: function(ecoda_object, slot = c("clr", "clr_hvc", "counts",
"counts_imp", "freq", "freq_imp", "asin_sqrt", "pb"),
label_col = NULL, scale. = FALSE, title = NULL,
title_show_n_features = TRUE, legend_title = "Group",
show_label_samples = FALSE, score_digits = 3,
cluster_score = TRUE, mod_score = TRUE, sil_score =
FALSE, anosim_score = TRUE, anosim_permutations = 99,
anosim_parallel = 1, ari_nclusts = NULL, knn_k = 3,
pointsize = 3, labelsize = 4, coord_equal = TRUE, axes
= c(1, 2), invisible = c("var", "quali"), geom =
"point", n_hv_feat_show = Inf, repel = TRUE)
Docs: function(ecoda_object, slot = c("clr", "clr_hvc", "counts",
"counts_imp", "freq", "freq_imp", "asin_sqrt", "pb"),
label_col = NULL, scale. = FALSE, title = NULL,
title_show_n_features = TRUE, legend_title = "Group",
show_label_samples = FALSE, score_digits = 3,
cluster_score = TRUE, mod_score = TRUE, sil_score =
FALSE, anosim_score = TRUE, anosim_permutations = 99,
anosim_parallel = detectCores(), ari_nclusts = NULL,
knn_k = 3, pointsize = 3, labelsize = 4, coord_equal =
TRUE, axes = c(1, 2), invisible = c("var", "quali"),
geom = "point", n_hv_feat_show = Inf, repel = TRUE)
Mismatches in argument default values:
Name: 'anosim_parallel' Code: 1 Docs: detectCores()
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/37s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calc_anosim 6.587 0.129 6.716
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[9s/9s] 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 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA.Rcheck/00check.log’
for details.
===============================
BiocCheck('scECODA_0.99.4.tar.gz')
===============================
── Installing scECODA ──────────────────────────────────────────────────────────
✔ Package installed successfully
── scECODA session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNYhZQJ/file728ce7c2ae64b/scECODA
→ BiocVersion: 3.23
→ Package: scECODA
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4104/0edd3f5bf353d482a1c42b54ba65f366fac3b14c/scECODA.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpNYhZQJ/file728ce7c2ae64b/scECODA
→ installDir: /tmp/RtmpNYhZQJ/file728ce4cc5a2d6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scECODA ────────────────────────────────────────────────
* 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:
WorkflowManagement
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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (14%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• scECODA.rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scECODA...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• plotting.r (line 548, column 15)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/scECODA.rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
The longest 5 functions are:
• plot_pca() (R/plotting.r): 125 lines
• ...
• ecoda() (R/main.r): 92 lines
* 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; 17 lines (1%) are > 80 characters long.
First few lines:
• R/main.r#L395 #' \item \strong{frac_min:} Replaces z ...
• ...
• vignettes/scECODA.rmd#L347 Interestingly, we see that cell type com ...
i NOTE: Consider multiples of 4 spaces for line indents; 175 lines (6%) are
not.
First few lines:
• R/main.r#L125 data_is_freq = FALSE, ...
• ...
• vignettes/scECODA.rmd#L456 #, n_hv_feat_show = 5 # optionally, sh ...
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 | ⚠ 0 WARNINGS | i 10 NOTES
i See the scECODA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.