===============================
BiocCheckGitClone('EMTscore')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/EMTscore
→ BiocVersion: 3.23
→ Package: EMTscore
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/EMTscore.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/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...
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 v1.49.6 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/4135/EMTscore_20260518180336/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: 2026-05-18 18:12:58 UTC
* using option ‘--no-vignettes’
* checking for file ‘EMTscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EMTscore’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 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 ‘EMTscore’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Seurat::Assays’ by ‘SummarizedExperiment::Assays’ when loading ‘EMTscore’
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table:::=’ by ‘rlang:::=’ when loading ‘EMTscore’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/EMTscore.Rcheck/00install.out’ for details.
* 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
R/utils.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘GSEABase’
Namespaces in Imports field not imported from:
‘Cairo’ ‘ComplexHeatmap’ ‘RColorBrewer’ ‘circlize’ ‘ggalluvial’
‘ggtext’ ‘ggthemes’ ‘grid’ ‘gridExtra’ ‘mclust’ ‘paletteer’
‘pheatmap’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [49s/49s] NOTE
Execute_AUCell_parallel: no visible binding for global variable ‘k’
Execute_E_M_plot: no visible global function definition for ‘sd’
Execute_E_M_plot: no visible binding for global variable ‘mE’
Execute_E_M_plot: no visible binding for global variable ‘mM’
Execute_E_M_plot: no visible binding for global variable ‘sdM’
Execute_E_M_plot: no visible binding for global variable ‘sdE’
Execute_GSVA_parallel: no visible binding for global variable ‘k’
Execute_JASMINE_parallel: no visible binding for global variable ‘k’
Execute_M_dimension_plot: no visible global function definition for
‘sd’
Execute_M_dimension_plot: no visible binding for global variable ‘mM1’
Execute_M_dimension_plot: no visible binding for global variable ‘mM2’
Execute_M_dimension_plot: no visible binding for global variable ‘sdM2’
Execute_M_dimension_plot: no visible binding for global variable ‘sdM1’
Execute_SCSE_parallel: no visible binding for global variable ‘k’
Execute_nnPCA_parallel: no visible binding for global variable ‘k’
Execute_ssGSEA_parallel: no visible binding for global variable ‘k’
add_EMT_score_Bulk: no visible global function definition for
‘Execute_ssGSVA’
correlate_sample_scores: no visible global function definition for
‘complete.cases’
correlate_sample_scores: no visible global function definition for
‘cor.test’
plot_heatmap_function: no visible global function definition for
‘colorRamp2’
plot_heatmap_function: no visible global function definition for
‘rowAnnotation’
plot_heatmap_function: no visible global function definition for
‘HeatmapAnnotation’
plot_heatmap_function: no visible global function definition for
‘Heatmap’
predict_cluster_labels: no visible global function definition for
‘Mclust’
predict_cluster_labels: no visible global function definition for
‘kmeans’
Undefined global functions or variables:
Execute_ssGSVA Heatmap HeatmapAnnotation Mclust colorRamp2
complete.cases cor.test k kmeans mE mM mM1 mM2 rowAnnotation sd sdE
sdM sdM1 sdM2
Consider adding
importFrom("stats", "complete.cases", "cor.test", "kmeans", "sd")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'add_EMT_score.Rd':
\examples lines wider than 100 characters:
gmt_file <- system.file("extdata", "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.v2025.1.Hs.gmt", package = "EMTscore")
seurat_objs <- add_EMT_score(objects, gmt_file = gmt, emt_name = "EMT_score", method = "nnPCA",nnPCA_dim = 1)
Rd file 'add_EMT_score_Bulk.Rd':
\examples lines wider than 100 characters:
res <- add_EMT_score_Bulk(expr_mat = geneExp, gmt_file, emt_name = "EMT", method = "AUCell", dimension = 1)
res_list <- add_EMT_score_Bulk(expr_mat_list = exprs, gmt_file, emt_name = "EMT", method = "nnPCA", dimension = 1)
Rd file 'compute_Signature_score_SingleCell.Rd':
\examples lines wider than 100 characters:
result <- compute_Signature_score_SingleCell(files, signature_files, score_name = c("Stemness_Score", "Senescence_Score"))
Rd file 'predict_cluster_labels.Rd':
\examples lines wider than 100 characters:
labels_gmm <- predict_cluster_labels(nnPCA_Result_multiple, method = "GMM", n_clusters = 3, PC_name = c("Escore", "Mscore"))
labels_km <- predict_cluster_labels(nnPCA_Result_multiple, method = "Kmeans", n_clusters = 3,PC_name = c("Escore", "Mscore"))
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘GO’ ‘MSigDB_Hallmark’ ‘SCSE_Result_EMT’
‘Tan_et_al_cell_line_E_signature’ ‘Tan_et_al_cell_line_M_signature’
‘Tan_et_al_tumor_E_signature’ ‘Tan_et_al_tumor_M_signature’
‘data_for_plot’ ‘labels’ ‘nnPCA_Result_multiple’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [185s/198s] ERROR
Running examples in ‘EMTscore-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Execute_M_dimension_plot
> ### Title: Plot M dimension scores
> ### Aliases: Execute_M_dimension_plot
>
> ### ** Examples
>
> plot2 <- Execute_M_dimension_plot(
+ data_for_plot,
+ M1_colname = "M1_score",
+ M2_colname = "M2_score",
+ celltype_colname = "celltype_annotation",
+ colors = c("#F87189", "#CE9031", "#A48CF5", "#97A430", "#39A7D0", "#E57D5F",
+ "#84C7B9", "#E1AF64", "#C26CCF", "#B0BF43", "#57C3E8", "#F29D9E", "#92AAE6")
+ )
Error: object 'data_for_plot' not found
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Execute_GSVA_parallel 103.819 2.583 64.823
Execute_JASMINE_parallel 34.196 2.092 36.050
Execute_AUCell_parallel 13.045 2.070 24.557
Execute_GSVA 2.197 0.116 14.143
Execute_JAS 0.742 0.137 17.555
Execute_AUCell 0.420 0.112 17.393
* 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/EMTscore.Rcheck/00check.log’
for details.
===============================
BiocCheck('EMTscore_0.99.0.tar.gz')
===============================
── Installing EMTscore ─────────────────────────────────────────────────────────
✔ Package installed successfully
── EMTscore session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHvq955/file2c66f373599a1a/EMTscore
→ BiocVersion: 3.23
→ Package: EMTscore
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4135/EMTscore_20260518180336/EMTscore.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpHvq955/file2c66f373599a1a/EMTscore
→ installDir: /tmp/RtmpHvq955/file2c66f333845cda
→ 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 3.5.0 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...
i NOTE: Consider adding these automatically suggested biocViews: SingleCellData
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 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (16%).
* 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:
• EMTscore.Rmd
* 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 1:...; use seq_len() or seq_along()
Found in files:
• AUCell_multiple_genesets.R (line 68, column 39)
• ...
• utils.R (line 162, column 25)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/utils.R (line 189, column 3)
• print() in R/utils.R (line 192, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/AUCell.R (line 54, column 15)
• ...
• R/ssGSEA.R (line 28, column 10)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/generate_gmt_from_genelists.R (line 31, column 12)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Pathway_score_correlation.R (line 65, 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...
Warning: replacing previous import ‘Seurat::Assays’ by ‘SummarizedExperiment::Assays’ when loading ‘EMTscore’
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘EMTscore’
Warning: replacing previous import ‘data.table:::=’ by ‘rlang:::=’ when loading ‘EMTscore’
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• Arrange_plots.Rd
• plot_heatmap_function.Rd
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 277 lines (9%) are > 80 characters long.
First few lines:
• R/AUCell_multiple_genesets.R#L8 #' @param exprMatrix Numeric matrix or d
...
• ...
• vignettes/EMTscore.Rmd#L776 <h6 id="ref10"> Malta T, Sokolov A, Gent ...
i NOTE: Consider 4 spaces instead of tabs; 43 lines (1%) contain tabs.
First few lines:
• R/AUCell.R#L54 genes = unlist(read_gmt(Genesets)$gene) ...
• ...
• R/SCSE.R#L63 } ...
i NOTE: Consider multiples of 4 spaces for line indents; 873 lines (30%) are
not.
First few lines:
• R/AUCell_multiple_genesets.R#L25 stringsAsFactors <- FALSE ...
• ...
• vignettes/EMTscore.Rmd#L730 } ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 18 NOTES
i See the EMTscore.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.