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R CMD BUILD
===============================
* checking for file ‘scTypeEval/DESCRIPTION’ ... OK
* preparing ‘scTypeEval’:
* 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 ‘scTypeEval_0.99.23.tar.gz’
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BiocCheckGitClone('scTypeEval')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4102/39747a9c31d57fda1e53749872949f09892e824b/scTypeEval
→ BiocVersion: 3.23
→ Package: scTypeEval
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4102/39747a9c31d57fda1e53749872949f09892e824b/scTypeEval.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4102/39747a9c31d57fda1e53749872949f09892e824b/scTypeEval
→ 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 v1.47.18 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/4102/39747a9c31d57fda1e53749872949f09892e824b/scTypeEval.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘scTypeEval/DESCRIPTION’ ... OK
* this is package ‘scTypeEval’ version ‘0.99.23’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘scTypeEval’ 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [11s/11s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Run.GeneMarkers 5.509 0.343 5.853
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [94s/84s]
[94s/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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('scTypeEval_0.99.23.tar.gz')
===============================
── Installing scTypeEval ───────────────────────────────────────────────────────
✔ Package installed successfully
── scTypeEval session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVcDjHA/file1b566e40be418c/scTypeEval
→ BiocVersion: 3.23
→ Package: scTypeEval
→ PackageVersion: 0.99.23
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4102/39747a9c31d57fda1e53749872949f09892e824b/scTypeEval.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /tmp/RtmpVcDjHA/file1b566e40be418c/scTypeEval
→ installDir: /tmp/RtmpVcDjHA/file1b566e263c8c40
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scTypeEval ─────────────────────────────────────────────
* 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 4.3.0 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 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 (25%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scTypeEval...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/clustering_optimization.R (line 88, column 28)
• ...
• R/main.R (line 1245, column 17)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• GeneMarkers.R (line 26, column 49)
• ...
• ReciprocalClassification.R (line 239, column 36)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/main.R (line 73, column 15)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/add.DimReduction.Rd
i Found @ in man/Run.ProcessingData.Rd
i Found @ in vignettes/scTypeEval.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressWarnings() in R/Dissimilarity.R (line 16, column 4)
• suppressMessages() in R/Dissimilarity.R (line 17, column 7)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
The longest 5 functions are:
• get.optimal_clustering() (R/main.R): 178 lines
• ...
• _anonymous_.2006() (R/main.R): 97 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• get.optimal_clustering.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• get.optimal_clustering.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• get.optimal_clustering.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; 433 lines (7%) are > 80 characters long.
First few lines:
• R/clustering_optimization.R#L1 # auxiliary function to process all data ...
• ...
• R/utils.R#L184 if(!is.null(black.list) && verbose){m ...
i NOTE: Consider multiples of 4 spaces for line indents; 3039 lines (51%) are
not.
First few lines:
• R/assays_plots.R#L5 pl <- ggplot2::ggplot() + ...
• ...
• vignettes/scTypeEval.Rmd#L525 biology or annotation issues ...
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 v1.47.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 13 NOTES
i See the scTypeEval.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.