===============================
R CMD BUILD
===============================
* checking for file ‘EMTscore/DESCRIPTION’ ... OK
* preparing ‘EMTscore’:
* 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 ‘EMTscore_0.99.3.tar.gz’
===============================
BiocCheckGitClone('EMTscore')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/44f56e4f8dcddf5bc1904bdf3a19fdf082d05d95/EMTscore
→ BiocVersion: 3.23
→ Package: EMTscore
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/44f56e4f8dcddf5bc1904bdf3a19fdf082d05d95/EMTscore.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/44f56e4f8dcddf5bc1904bdf3a19fdf082d05d95/EMTscore
→ 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 remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.49.12 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/4135/44f56e4f8dcddf5bc1904bdf3a19fdf082d05d95/EMTscore.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-06-10 02:02:56 UTC
* using option ‘--no-vignettes’
* checking for file ‘EMTscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EMTscore’ version ‘0.99.3’
* 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 ‘EMTscore’ can be installed ... OK
* checking installed package size ... INFO
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 7.2Mb
* 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 ... [18s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the package can be unloaded cleanly ... [17s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [17s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/19s] OK
* checking loading without being on the library search path ... [18s/18s] 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 ... [56s/56s] 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 ... [362s/459s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Execute_GSVA_parallel 118.852 2.564 76.045
add_EMT_score_multiple 35.206 13.960 45.750
Execute_ssGSEA_parallel 45.557 2.857 39.081
Execute_JASMINE_parallel 35.085 2.972 34.588
Execute_AUCell_parallel 14.058 2.189 23.740
Execute_JAS 1.998 0.552 16.940
Execute_GSVA 2.266 0.184 18.644
compute_Signature_score 1.009 0.411 12.958
Execute_ssGSEA 1.055 0.287 12.201
Execute_nnPCA_parallel 0.775 0.205 17.536
Execute_SCSE_parallel 0.668 0.291 16.637
Execute_AUCell 0.464 0.100 11.515
add_EMT_score_Bulk 0.417 0.135 12.191
Execute_M_dimension_plot 0.258 0.084 16.146
Execute_nnPCA 0.189 0.079 16.115
Execute_SCSE 0.181 0.080 11.875
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/19s]
[19s/19s] 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('EMTscore_0.99.3.tar.gz')
===============================
── Installing EMTscore ─────────────────────────────────────────────────────────
✔ Package installed successfully
── EMTscore session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0Mts3y/filef843b9a53d33/EMTscore
→ BiocVersion: 3.23
→ Package: EMTscore
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/44f56e4f8dcddf5bc1904bdf3a19fdf082d05d95/EMTscore.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /tmp/Rtmp0Mts3y/filef843b9a53d33/EMTscore
→ installDir: /tmp/Rtmp0Mts3y/filef843b65fb680
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EMTscore ───────────────────────────────────────────────
* 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...
→ ExperimentData
* 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 if 'Package:' field matches directory / tarball...
* 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 (23%).
* 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 EMTscore...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/AUCell.R (line 54, column 9)
• ...
• R/ssGSEA.R (line 28, column 10)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Pathway_score_correlation.R (line 69, column 21)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/EMTscore.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 12
functions greater than 50 lines.
The longest 5 functions are:
• plot_heatmap_function() (R/EMTscore_plot.R): 108 lines
• ...
• add_EMT_score() (R/Singlecell_EMTscore.R): 75 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• add_EMT_score.Rd
• ...
• plot_heatmap_function.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
Found in files:
• add_EMT_score.Rd
• plot_EMT_from_objects.Rd
• plot_heatmap_function.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; 263 lines (8%) are > 80 characters long.
First few lines:
• R/AUCell_multiple_genesets.R#L8 #' @param exprMatrix Numeric matrix or d
...
• ...
• vignettes/EMTscore.Rmd#L777 <h6 id="ref10"> Malta T, Sokolov A, Gent ...
i NOTE: Consider multiples of 4 spaces for line indents; 898 lines (29%) are
not.
First few lines:
• R/AUCell_multiple_genesets.R#L25 stringsAsFactors <- FALSE ...
• ...
• vignettes/EMTscore.Rmd#L731 } ...
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 'emtscore' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the EMTscore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.